EEMB

Department of Genetics Institute of Molecular and Cell Biology
University of Tartu
23 Riia Street
Tartu 51010
Estonia

E-mail: signe.viggor@ut.ee (Signe Viggor)
Phone +372 7 376 038

EEMB

History of our activity dates back to the center of the last century. Believe, we have a long history behind ....

EEMB

Our mission is to find the bacteria that helps to extend the life of a human for unlimited number of years.

EEMB

We do not have any adverticements at the moment. Sorry!

EEMB

All our products have competitive prices. Do not worry, you can buy most of them. Explain you wishes and we shall give you a good offer.

EEMB

(Estonian Electronic Microbial dataBase)
is an electronic database of Estonian National Collection of Microbes that currently hosts three collections of microorganisms:

  • CELMS (Collection of Environmental and Laboratory Microbial Strains) at Institute of Molecular and Cell Biology, University of Tartu
  • HUMB (Human Microbiota Biobank) at Department of Microbiology, University of Tartu
  • CREP (Collection of Reproductive Tract Microorganisms) at Competence Centre on Health Technologies  
   

EEMB contacts

  • reet.mandar [at] ut.ee (Reet Mändar)
  • hugo.mandar [at] ut.ee (Hugo Mändar)   

CELMS

CELMS is a collection of non-medical environmental and laboratory microbial strains situated at the Institute of Molecular and Cell Biology, University of Tartu. The collection was founded in 1995. Since year 2008 the collection is registered at WFCC-MIRCEN World Data Centre for Microorganisms (registry number 926).

 

CELMS is a member of ECCO (European Culture Collections’ Organisation). The collection is financed by the Estonian Ministry of Education and Research. Majority of strains have been isolated from polluted areas with strong oil shale mining and chemical industry impact. Since year 2008 bacterial isolates from different regions of the Baltic Sea have been added to the collection. Main tasks of the collection are extension of collection with new strains and type cultures, characterization of strains and distribution of microorganisms for purpose of research and education. Our main research activities are related to use molecular methods for characterization of microbial strains and diversity of functional genes.

CELMS Guidelines

Guidelines for management and use of the scientific Collection of Environmental and Laboratory Microbial Strains (CELMS) at the Institute of Molecular and Cell Biology, University of Tartu

 1. General

The Collection of Environmental and Laboratory Microbial Strains (with the acronym CELMS) is a non-medical scientific collection that contains microbes isolated from different contaminated soil and water samples, mostly from Estonia, including the Baltic Sea. The collection was established in order to collect and preserve microbes able to biodegrade various pollutants or producing useful compounds. Additionally, the collection holds microbial strains that are selected and/or constructed in laboratory conditions and bear certain characteristics.


The CELMS collection was founded in 1995. Since the year 2008 the collection is registered at WFCC-MIRCEN (World Federation of Culture Collections, World Data Centre for Microorganisms, registry number 926). CELMS is a member of ECCO (European Culture Collections Organisation). The collection is financed by the Estonian Ministry of Education and Research. CELMS is located at the Institute of Molecular and Cell Biology, University of Tartu (23 Riia Street, Tartu 51010). The guidelines for using the collection can be found here at this website, the public catalogue is available on the Estonian Electronic Microbial dataBase (EEMB) website (http://eemb.ut.ee/) in English and Estonian. 


2. Special regulations

The idea of the CELMS collection is to promote microbiological studies, especially in case of the strains having potential value in industry and biotechnological enterprises, including applications reducing environmental pollution. On the other hand, the aim of the CELMS collection is also to preserve the microbial strains as our public wealth. Coming from the fact that the CELMS collection deals with a genetic resource, it has to meet the demands of the Nagoya protocol. The Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization (ABS) to the Convention on Biological Diversity is a supplementary agreement to the Convention on Biological Diversity (CBD). It provides a transparent legal framework for the effective implementation of one of the three objectives of the CBD: the fair and equitable sharing of benefits arising out of the utilization of genetic resources. 


The CELMS collection is divided into two different catalogues:

1) The public collection with a catalogue available on the EEMB website: the microbial strains with thoroughly characterized features, data of which has been published. This collection is open for international ordering free of charge;

2) Non-public microbial collection that has restrictions for public use coming mostly from copyright issues (Budapest Treaty, World Intellectual Property Organization (WIPO)) and that will be included to the public collection after becoming free from restrictions (patents, copyright, publishing conditions etc).


Storing and maintaining of the first collection as well as managing the respective database and catalogue are responsibilities of the collection manager and the collection curator. The second collection has a general catalogue with restricted access (on a server of Tartu University (\\albert.domenis.ut.ee) with access of restriced range of persons). Storing of this collection is a responsibility of scientists working with these microbes on a daily basis, until these strains will be added to the public collection. Information about these strains is stored in the catalogue encoded and in accordance with the law.


The value of microbiologically and genetically uncharacterized strains could not be determined and hence these microbes are worthless for public use.


The CELMS collection is open for ordering and free use only for non-commercial acitivities. The potential commercial use must be regulated via the copyright contracts with the persons who isolated and characterized the strains in accordance with the rules approved in the University of Tartu and according to the laws of the Estonian Republic.


3. Structure and management of the collection

The collection is formed of collected, bought and donated as well as laboratory constructed/selected microbial strains and the respective information stored in the digital database.


When submitting new strains to the public collection of CELMS, a contract (Material Transfer Agreement, MTA) is signed between the person submitting the strains and the collection manager. This contract must contain information about the submitted strain(s): specific characteristics (ability to degrade or produce certain chemicals, resistance to drugs, presence of plasmids etc), general (isolation location/source, important features necessary for strain identification etc) and specific information (nucleotide sequence and GenBank deposition data) as well as information concerning published scientific data and restrictions coming from copyright issues etc. These contracts are signed and archived.


Management of the collection is done with the help of electronic database developed on the basis of dbForge Studio forMySQL Professional. In the nearest future, the CELMS database is planned to be integrated to the eBiodiversity web interface (http://elurikkus.ut.ee/).


The CELMS collection also coordinates and collects data about all other microbial strains stored and used in Estonia, mostly coming from the need to fulfill the requirements of the Nagoya protocol, coordinated by the FAO (Food and Agriculture Organization of the United Nations).


4. Storage and viability control of the samples

The storage items (microbial strains) are stored at -80 °C in multiple parallels in multiple freezers. Isolated strains are preserved inside sterile cryovials. The terms of preservation (temperature, running maintenance of the freezers) are controlled by the staff responsible for the collection. The freezers are equipped with fault detection and alarm transmitting systems. In case of danger to the storage rooms, actions are in compliance with the university security rules.


The collection is preserved in locked refrigerators. The collection is accessible only to the assigned personnel, in absence of those persons only to the assigned substitutes. No third party has access to the collection.


5. Use and availability of the collection

The strains preserved in the collection as well as all information about them are freely available for use for academic research (non-commercial purposes) within the institution.


The microbial strains are available for other institutions of the University of Tartu as well as other parts according to MTA (Material Transfer Agreement) for academic research (non-commercial purposes). For signing the contract, please contact the collection personnel. These contracts are archived.

CELMS Team

Ain Heinaru

Eeva Heinaru
Eve Naanuri
Signe Viggor
Merike Jõesaar

CELMS Contacts

Department of Genetics Institute of Molecular and Cell Biology
University of Tartu
23 Riia Street
Tartu 51010
Estonia

E-mail: signe.viggor@ut.ee (Signe Viggor)
Phone +372 7 376 038

CELMS Publikatsioonid / Publications

Celms_publications

Published articles in Journals
Nr Reference name Keywords File link
1 Heinaru et al., 2000 (FEMS Microbiology Ecology) Isolation of phenol and p-cresol degraders; catabolic types; occurrence of plasmid DNA; phenol monooxygenase, catechol 1,2-dioxygenase, catechol 2,3-dioxygenase, protocatechuate 3,4-dioxygenase, p-hydroxybenzoate hydroxylase enzyme activities; File
2 Heinaru et al., 2001 (FEMS Microbiology Ecology) Mechanisms regulating degradation of phenol, p-cresol and benzoate from their mixtures; Pseudomonas strains of different catabolic types; metabolic intermediates; diauxia File
3 Heinaru et al., 2005 (FEMS Microbiology Ecology) Microcosms; DGGE analysis; monitoring of population dynamics; decomposition of phenolic compounds and PAHs in microcosms File
4 Heinaru et al., 2009 (FEMS Microbiology Ecology) Pseudomonas fluorescens PC20; naphthalene and phenol plasmids; plasmid transfer; plasmid mobilization; IS elements; complete nucleotide sequence of pNAH20 File
5 Joesaar et al., 2010 (FEMS Microbiology Ecology) p-cresol methylhydroxylase; p-cresol degradation kinetics; sigma-54 dependent transcriptional regulation File
6 Juhanson et al., 2009 (FEMS Microbiology Ecology) Phytoremediation and bioaugmentation field experiments; survival of introduced strains; DGGE analysis; catabolic performance File
7 Jutkina et al., 2011 (Genes) IncP-9 plasmids; aromatic degraders of Baltic Sea File
8 Jutkina et al., 2013 (Plasmid) TOL plasmids; toluene catabolic genes; complete nucleotide sequence of pD2RT; growth kinetics of plasmid-bearing strains File
9 Merimaa et al., 2006 (Archives in Microbiology) Phenol hydroxylase; catechol 2,3-dioxygenase; phenol and p-cresol degraders; phylogenetic analysis File
10 Vedler et al., 2004 (Journal of Bacteriology) Herbicide 2,4-D; IncP-1 plasmids; complete nucleotide sequence of pEST4011; laboratory evolution File
11 Vedler et al., 2013 (Systematic and Applied Microbiology) Limnobacter spp; phenol-degrading bacteria of Baltic Sea; phenol hydroxylase; catechol 2,3-dioxygenase; phylogenetic analysis; total community DNA File
12 Viggor et al., 2008 (Biodegradation) Phenol hydrozylase; kinetic parameters; phenol-degrading pseudomonads File
13 Viggor et al., 2013 (Microbiological Research) Alkane biodegradation; microbioal communities; Baltic Sea; alkB clone library; microcosm experiments; DGGE analysis; phylogenetic trees File
14 Xu et al., 2011 (IJSEM) Pelagibacterium; novel member of the family Hyphomicrobiaceae; taxonomic characteristics File
15
Peebo et al., 2014 (Applied Microbiology and Biotechnology)
Acetate overflow; Acs; Continuous culture; Absolute proteomics; Acetylation
File
16 Kõiv et al., 2015 (Scientific Reports)

Changes in microbial community; potato tubers; pathogenesis File
17 Viggor et al., 2015 (Mar Pollut Bull) Alkane hydroxylase; Baltic Sea; alkB gene; n-alkane degrading bacterial strains File

18 Heinaru et al., 2016



Functional redundancy in phenol and toluene degradation in Pseudomonas stutzeri strains isolated from the Baltic Sea doi
19 Jõesaar et al., 2017 Strategy ofPseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate doi
20 Ilmjärv et al., 2017 Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria doi
21
Kõiv et al.,2020
Microbiome of root vegetables--a source of gluten-degrading bacteria
doi
22 Viggor et al.,2020
Microbial metabolic potential of phenol degradation in wastewater treatment plant of crude oil refinery: analysis of metagenomes and characterization of isolates
doi
23
Elken et al.,2020
Formation of new PHE plasmids in a phenol-polluted environment
doi
24
Nandy et al.,2021
Monitoring the growth, survival and phenol utilization of the fluorescent-tagged Pseudomonas oleovorans immobilized and free cells
doi


Magistritööd/Master's thesis

1. Kady Mäesalu, 2021, (supervisor) Anne Menert, Elektroonikaromude bioleostumise protsesside uurimine, Tartu Ülikool, Loodus- ja täppisteaduste valdkond, ökoloogia ja maateaduste instituut

2. Marge Puhm, 2020, (supervisor) Riho Teras, Ekstratsellulaarsete peptiidide mõju Pseudomonas putida biofilmile fis -i üleekspressiooni tingimustes, Tartu Ülikool.

3. Kristina Põšnograjeva, 2019, (supervisor) Tiina Alamäe; Katrin Viigand, Pärmide MAL klastrid ja valgud põhirõhuga Scheffersomyces stipitis'e -glükosidaasidel, Tartu Ülikool.

4. Aivar Meldre, 2019, (supervisor) Tiina Alamäe; Triinu Visnapuu; Katrin Viigand, Pärmi Blastobotrys adeninivorans -glükosidaasi AG2 iseloomustamine, Tartu Ülikool.

5. Liselle Luks, 2019, (supervisor) Anne Menert; Hans Priks; Triin Korb, Põlevkivi mikrobioloogiline töötlemine, Tartu Ülikool.

6. Angela Peeb, 2019, (supervisor) Jaak Truu; Kristjan Oopkaup, Naftareostuse mõju arktilise merejää mikroobikooslusele, Tartu Ülikool.

7. Ingrem Metsik, 2017, (supervisor) Maia Kivisaar; Tanel Ilmjärv, Hübriidse m-kresooli lagundamisraja efektiivsust suurendavad mutatsioonid bakteri Pseudomonas putida laboratoorses evolutsioonikatses, Tartu Ülikool.

8. Sirli Rosendahl, 2017, (supervisor) Hedvig Tamman; Rita Hõrak, Toksiin-antitoksiin süsteemide mõju Pseudomonas putida kohasusele ja stressitaluvusele, Tartu Ülikool.

9. Anneli Aasamets, 2016, (supervisor) Tiina Alamäe; Triinu Visnapuu, Levaani ja fruktooligosahhariidide süntees Pseudomonas syringae pv. tomato levaansukraasiga Lsc3, Tartu Ülikool.

10. Liisbeth Kose, 2016, (supervisor) Riho Teras, Pseudomonas putida GacS/A signaaliraja geenide transkriptsiooni regulatsioon, Tartu Ülikool.

11. Triin Korb, 2016, (supervisor) Anne Menert, Biodegradatiivse potentsiaaliga mikroobikooslused Eesti graptoliitargilliidist, Tartu Ülikool.

12. Maria Gromkova, 2015, (supervisor) Tiina Alamäe; Triinu Visnapuu; Karin Ernits, Pseudomonas syringae pv. tomato levansukraasi Lsc3 struktuuri ja funktsiooni seoste uurimine mutatsioonanalüüsiga, Tartu Ülikool.

13. Artemi Maljavin, 2015, (supervisor) Maia Kivisaar; Tatjana Jatsenko, "Mutageensuse" operoni osalus Pseudomonas putida rakkudes toimuvates mutatsiooniprotsessides, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

14. Maarja Grünbach, 2014, (supervisor) Eve Naanuri; Eeva Heinaru, Multikomponentsete monooksügenaaside mitmekesisus Läänemere tolueenilagundajates bakterites, Tartu Ülikool.

15. Merlin Soopere, 2014, (supervisor) Tiina Alamäe; Ene Talpsep, PCR-meetodi valideerimine Listeria monocytogenes'e tuvastamiseks toidu- ja hügieeniproovidest, Tartu Ülikool.

16. Mari Tagel, 2014, (supervisor) Maia Kivisaar, Uute mutatsioonisagedust mõjutavate geenide identifitseerimine bakteris Pseudomonas putida, Tartu Ülikool.

17. Kärt Ukkivi, 2013, (supervisor) Maia Kivisaar, Transkriptsiooni ja transkriptsiooniga seotud DNA reparatsiooni mõju mutatsiooniprotsessidele bakteris Pseudomonas putida, Tartu.

18. Ülvi Kana, 2013, (supervisor) Maia Kivisaar, NHEJ ensüümide osalus mutatsiooniprotsessides bakteris Pseudomonas putida, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

19. Tanel Ilmjärv, 2013, (supervisor) Maia Kivisaar; Heili Ilves, Pseudomonas putida mutatsiooniprotsesside sõltuvus kromosomaalsest lokalisatsioonist ja rakkudevahelisest kommunikatsioonist, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

20. Andres Ainelo, 2013, (supervisor) Rita Hõrak, Pseudomonas putida GraTA toksiin-antitoksiin süsteemi toimemehhanismide selgitamine, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

21. Hanna Ainelo, 2013, (supervisor) Riho Teras, Pseudomonas putida globaalse regulaatori Fis osalus biofilmi moodustumises, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

22. Kadi Tilk, 2013, (supervisor) Rita Hõrak, Pseudomonas putida ColRS süsteem on tsingi-, raua-, mangaani- ja kaadmiumiliiga tunnetav signaalirada, Tartu Ülikool.

23. Hedvig Tamman, 2012, (supervisor) Rita Hõrak, Pseudomonas putida kasvukiirust vähendav toksiin GraT supresseerib colR mutandi glükoossõltuvat lüüsi, Tartu Ülikool.

24. Karl Mumm, 2012, (supervisor) Rita Hõrak, Kas transkriptsioonifaktor ColR paikneb periplasmas?, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

25. Kertu Tiirik, 2012, (supervisor) Hiie Nõlvak; Jaak Truu, Antibiootikumiresistentsusgeenide tuvastamine Läänemere bakterplanktonist, Tartu Ülikool.

26. Sandra Käosaar, 2012, (supervisor) Tiina Alamäe, Mono- ja disahhariidid regulatsiooniprotsesside käivitajatena pärmil Hansenula polymorpha: uued meetodid, promootorid ja ekspressioonitüved, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

27. Jekaterina Jevtuševskaja, 2012, (supervisor) Andres Mäe; Liis Andresen, Plasmiidsete vektorsüsteemide konstrueerimine ja rakendamine Rsm süsteemi mõju uurimiseks taimepatogeenis Pectobacterium carotovorum alaml. carotovorum, Tartu Ülikool.

28. Karin Ernits, 2011, (supervisor) Tiina Alamäe; Triinu Visnapuu, Pseudomonas syringae pv. tomato levaansukraasi Lsc3 struktuuri modelleerimine ja mutantide iseloomustamine, Tartu Ülikool.

29. Ivo Krustok, 2011, (supervisor) Marika Truu; Jaak Truu, Horisontaal- ja vertikaalvooluliste filtrite mikroobikooslue dünaamika ja aktiivsus eksperimentaalses hallvee puhastussüsteemis, Tartu Ülikool.

30. Teele Ligi, 2011, (supervisor) Marika Truu; Jaak Truu, Denitrifikatsioonis osalev mikroobikooslus reostunud jõevett puhastavas läbivooluliste tehismärgalade kompleksis, Tartu Ülikool.

31. Mihkel Mäesaar, 2011, (supervisor) Jaak Truu; Jaanis Juhanson, Naftareostuse mõju Läänemere mikroobikooslusele, Tartu Ülikool.

32. Triinu Juurik, 2011, (supervisor) Maia Kivisaar; Kairi Tavita, Mutatsiooniprotsessid bakteri Pseudomonas putida kromosoomis, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

33. Andrio Lahesaare, 2011, (supervisor) Riho Teras; Heili Ilves, Globaalse regulaatorvalgu Fis-i seondumine Pseudomonas putida raua metabolismis ja biofilmi moodustamises osalevate geenide promootoraladele, Tartu Ülikool.

34. Anna Velts, 2010, (supervisor) Riho Teras, Pseudomonas putida Fis valgu kontsentratsioon erinevates kasvutingimustes, Tartu Ülikool.

35. Annika Teppo, 2010, (supervisor) Riho Teras, Pseudomonas putida kasvuhäirete põhjused glükoosi söötmes, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikooli

36. Tatjana Jatsenko, 2010, (supervisor) Maia Kivisaar; Kairi Tavita, Spetsialiseeritud DNA polümeraaside osalus mutatsiooniprotsessides Pseudomonas putida rakkudes, Tartu Ülikool.

37. Julia Sidorenko, 2010, (supervisor) Maia Kivisaar; Signe Saumaa, Study of the functions of DNA polymerase I in Pseudomonas putida, Tartu Ülikool.

38. Annika Vilem, 2010, (supervisor) Jaak Truu; Jaanis Juhanson, Lõhkeaineid lagundava bakterikonsortsiumi iseloomustamine molekulaarsete meetoditega, Tartu Ülikool.

39. Külliki Püvi, 2010, (supervisor) Rita Hõrak, Pseudomonas putida glükoosist sõltuvat autolüüsi mõjutavad geenid, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

40. Kai Jõers, 2010, (supervisor) Andres Mäe; Tanel Tenson, Chlamydia trachomatis prevalents ja populatsiooni geneetiline struktuur Eestis, Tartu Ülikool.

41. Olga Šapran, 2010, (supervisor) Rita Hõrak, Glükoosi metabolismigeenide osalus Pseudomonas putida colR mutandi glükoos-sõltuvas lüüsumises, Tartu Ülikool.

42. Andres Lõhmus, 2010, (supervisor) Tiina Alamäe, Hansenula polymorpha maltaasi geen reporterina bakterites: kasutamisvõimalused ja võrdlus GusA-reporteriga, Tartu Ülikool.

43. Julia Aprelkova, 2010, (supervisor) Indrek Suitso; Tiina Alamäe, Probiootilise bakteri Bacillus smithii TBMI12 spooride manustamise ohutuskatse sigade ning kanade näitel, Tartu Ülikool.

44. Liisa Lilje, 2009, (supervisor) Rita Hõrak; Marta Putrinš, ColRS signaaliraja ja TtgABC pumba roll Pseudomonas putida fenoolitolerantsuses, Tartu Ülikool.

45. Liisa Lilje, 2009, (supervisor) Rita Hõrak; Marta Putrinš, ColRS signaaliraja ja TtgABC pumba roll Pseudomonas putida fenoolitolerantsuses, Tartu Ülikool.

46. Jens-Konrad Preem, 2009, (supervisor) Jaak Truu, Trinukleotiidsed lihtsad kordusjärjestused Pseudomonas fluorescensi genoomis ja võimalused nende kasutamiseks perekond Pseudomonas liikide subtüpiseerimiseks, Tartu Ülikool.

47. Mario Mitt, 2009, (supervisor) Signe Viggor; Eve Naanuri, Alkaane lagundava bakterikonsortsiumi iseloomustamine Vilsandi rannikumeres, Tartu Ülikool.

48. Sander Kutti, 2009, (supervisor) Jaak Truu, Fosforit siduva filtermaterjali mikroobikooslus heitvee järelpuhastis, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

49. Hiie Nõlvak, 2008, (supervisor) Jaak Truu, Seiratava loodusliku tervenemise rakendusvõimaluste uurimine molekulaarsete meetoditega naftasaadustega saastunud ala pinnases, Tartu Ülikool.

50. Jekaterina Jutkina, 2008, (supervisor) Eeva Heinaru; Eve Naanuri, Pseudomonas fluorescens tüve PC20 plasmiidide järjestuse analüüs, Tartu Ülikool.

51. Kersti Tammus, 2008, (supervisor) Tiina Alamäe, Reportergeenide kasutamine pärmil Hansenula polymorpha: MAL-lookus ja selle promootorite regulatsioon, Tartu Ülikool.

52. Julia Jakovleva, 2008, (supervisor) Riho Teras, Tn4652 transpositsiooni sõltuvus DNA superspiralisatsioonist ja Fis-ist, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

53. Triinu Visnapuu, 2007, (supervisor) Tiina Alamäe, Levaansukraasi geenide ekspresseerimine Escherichia coli's ja valkude omaduste uurimine, Tartu Ülikool.

54. Karin Kask, 2007, (supervisor) Eerik Jõgi; Allan Nurk; Andres Mäe, Laktaadi tootmine Bacillus coagulans SIM-7 DSM 14043 vegetatiivsete rakkude ning spooridega, Tartu Ülikool.

55. Mari-Liis Ots, 2007, (supervisor) Allan Nurk; Andres Mäe; Oliver Meikar, Polühüdroksüalkanaadi süntees bakteris Pseudomonas mandelii Pc17, Tartu Ülikool.

56. Liis Andresen, 2007, (supervisor) Andres Mäe, Rcs signaaliülekande süsteemi roll taimepatogeeni Pectobacterium carotovorum alaml. carotovorum virulentsuses, Tartu Ülikoo.

57. Merit Aava, 2007, (supervisor) Eeva Heinaru, Multiplasmiidne süsteem naftaleeni ja fenooli lagundamiseks Pseudomonas fluorescens tüves PC20, Tartu Ülikool.

58. Lauri Koorits, 2007, (supervisor) Andres Tover; Maia Kivisaar, ImuB ja DnaE2 osalus Pseudomonas putida rakkudes toimuvates mutatsiooniprotsessides, Tartu Ülikool.

59. Mariliis Tark, 2006, (supervisor) Andres Tover; Maia Kivisaar, DNA reparatsioon Pseudomonas putida rakkudes, Tartu Ülikool.

60. Paula Ann Kivistik, 2006, (supervisor) Rita Hõrak; Maia Kivisaar, Pseudomonas putida kahekomponentse signaalsüsteemi ColRS märklaudgeenid, Tartu Ülikool.

61. Katrin Viigand, 2006, (supervisor) Tiina Alamäe, Hansenula polymorpha MAL-lookus, Tartu Ülikool.

62. Kairi Tavita, 2006, (supervisor) Maia Kivisaar; Andres Tover, Statsionaarse faasi sigma faktori RpoS osalus Pseudomonas putida nälgivas populatsioonis toimuvates adaptatsiooniprotsessides, Tartu Ülikool.

63. Liis Kärme, 2006, (supervisor) Jaak Truu, Biotervendusmeetodite kasutamine saasteainete biodegradatsiooni võimendamiseks poolkoksis, Tartu Ülikool.

64. Jaanis Juhanson, 2005, (supervisor) Jaak Truu, Fütoremediatsiooni ja bioaugmentatsiooni mõju poolkoksi mikroobikooslusele, Tartu Ülikool.

65. Hedi Laursoo, 2005, (supervisor) Andres Mäe, Taimepatogeenile Erwinia carotovora subsp. carotovora SCC3193 spetsiifilise mikrokiibi väljatöötamine, Tartu Ülikool.

66. Radi Tegova, 2004, (supervisor) Andres Tover; Maia Kivisaar, DNA polümeraas IV osalus Pseudomonas putida rakkudes toimuvates mutatsiooniprotsessides, Tartu Ülikool.

67. Marta Putrinš, 2004, (supervisor) Maia Kivisaar; Andres Tover, Rakkude füsioloogilisest seisundist tulenevad kontrollmehhanismid Pseudomonas putida fenooli degradatsiooni operoni pheBA transkriptsiooni regulatsioonil, Tartu Ülikool.

68. Pille Pärn, 2003, (supervisor) Tiina Alamäe, Hansenula polymorpha maltase, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

69. Signe Saumaa, 2002, (supervisor) Maia Kivisaar, DNA reparatsioonisüsteemide mõju mutatsioonispektri muutustele Pseudomonas putida kultuuri pikemaajalisel nälgimisel, Tartu Ülikool.

70. Ülle Saks, 2002, (supervisor) Andres Tover; Maia Kivisaar, Fenooli lagundamist määravate geenide transkriptsiooni regulatsioon bakteris Pseudomonas putida, Tartu Ülikool.

71. Heili Ilves, 2001, (supervisor) Maia Kivisaar; Rita Hõrak, Pseudomonas putida transposooni Tn4652 transpositsiooni regulatsioon, Tartu Ülikool.

72. Silja Laht, 2001, (supervisor) Tiina Alamäe, Pärmi Hansenula polymorpha glükokinaas: geeni kloneerimine ja valgu iseloomustamine, Tartu Ülikool.

73. Toomas Kramarenko, 2000, (supervisor) Tiina Alamäe, Heksoosi kinaaside roll suhkrute kataboliitses repressioonis pärmil Hansenula polymorpha, Tartu Ülikool.

74. Signe Viggor, 2000, (supervisor) Eeva Heinaru; Toomas Tenno, Alküül- ja hüdroksüfenoolide biodegradatsiooni uurimine erineva katabolismitüübiga bakteritüvedes, Tartu Ülikool.

75. Eve Naanuri, 1999, (supervisor) Ain Heinaru; Andres Mäe, Pseudomonas putida 2,4-diklorofenoksüatsetaadi lagundamist tagava plasmiidi pEST4011 tfdCB operoni ekspressioon ja regulatsioon LysR-tüüpi transkriptsiooni aktivaatori TfdR poolt, Tartu Ülikool.

Doktoritööd/Doctoral thesis

1. Kärt Ukkivi, 2020, (supervisor) Maia Kivisaar, Mutagenic effect of transcription and transcription-coupled repair factors in Pseudomonas putida, Tartu Ülikool.

2. Kadi Tilk, 2020, (supervisor) Rita Hõrak, Signals and responses of ColRS two-component system in Pseudomonas putida, Tartu Ülikool.

3. Hanna Ainelo, 2018, (supervisor) Riho Teras, Fis regulates Pseudomonas putida biofilm formation by controlling the expression of lapA, Tartu Ülikool.

4. Andrio Lahesaare, 2018, (supervisor) Riho Teras, The role of global regulator Fis in regulating the expression of lapF and the hydrophobicity of soil bacterium Pseudomonas, Tartu Ülikool.

5. Karin Ernits, 2019, (supervisor) Tiina Alamäe, Levansucrase Lsc3 and endo-levanase BT1760: characterization and application for the synthesis of novel prebiotics, Tartu Ülikool.

6. Katrin Viigand, 2018, (supervisor) Tiina Alamäe, Utilization of -glucosidic sugars by Ogataea (Hansenula) polymorpha, Tartu Ülikool.

7. Tatjana Jatsenko, 2018, (supervisor) Maia Kivisaar, Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads, Tartu Ülikool.

8. Andres Ainelo, 2018, (supervisor) Rita Hõrak; Jaanus Remme, Physiological effects of the Pseudomonas putida toxin GraT, Tartu Ülikool.

9. Hedvig Tamman, 2016, (supervisor) Rita Hõrak, The GraTA toxin-antitoxin system of Pseudomonas putida: regulation and role in stress tolerance, Tartu Ülikool.

10. Julia Sidorenko, 2015, (supervisor) Maia Kivisaar, Combating DNA damage and maintenance of genome integrity in pseudomonads, Tartu Ülikool.

11. Jekaterina Jutkina, 2014, (supervisor) Ain Heinaru; Eve Naanuri, The horizontal gene pool for aromatics degradation: bacterial catabolic plasmids of the Baltic Sea aquatic system, Tartu Ülikool.

12. Hiie Nõlvak, 2012, (supervisor) Ain Heinaru; Jaak Truu, Influence of qPCR workflow on target gene enumeration from environmental samples in the case of bioremediation potential estimation, Tartu Ülikool.

13. Liis Andresen, 2012, (supervisor) Andres Mäe, Regulation of virulence in plant-pathogenic pectobacteria, Tartu Ülikool.

14. Triinu Visnapuu, 2012, (supervisor) Tiina Alamäe, Levansucrases encoded in the genome of Pseudomonas syringae pv. tomato DC3000: heterologous expression, biochemical characterization, mutational analysis and spectrum of polymerization products, Tartu Ülikool.

15. Paula Ann Kivistik, 2011, (supervisor) Rita Hõrak; Maia Kivisaar, ColR-ColS signalling system and transposition of Tn4652 in the adaptation of Pseudomonas putida, Tartu Ülikool.

16. Merike Jõesaar, 2010, (supervisor) Ain Heinaru, Diversity of Key Catabolic Genes at Degradation of Phenol and P-cresol in Pseudomonads, Tartu Ülikool.

17. Signe Viggor, 2008, (supervisor) Ain Heinaru; Toomas Tenno, Impact of biochemical parameters of genetically diferent pseudomonads at the degradation of phenolic compounds, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond.

18. Eve Naanuri, 2005, (supervisor) Ain Heinaru, Structure of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011, Tartu Ülikool.

19. Jaak Truu, 2004, (supervisor) Ain Heinaru, Oil shale industry wastewater: impact on river microbial community and possibilities for bioremediation, Tartu Ülikool.

20. Jaanis Juhanson, 2010, (supervisor) Jaak Truu, Fütoremediatsiooni ja bioaugmentatsiooni mõju poolkoksi mikroobikooslusele, Tartu Ülikool.

21. Radi Tegova, 2009, (supervisor) Maia Kivisaar; Andres Tover, The role of specialized DNA polymerases in mutagenesis in Pseudomonas putida, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

22. Mariliis Tark, 2009, (supervisor) Maia Kivisaar, Mutagenic potential of DNA damage repair and tolerance mechanisms under starvation stress, Tartu Ülikool.

23. Marta Putrinš, 2008, (supervisor) Maia Kivisaar; Rita Hõrak, Pseudomonas putida vastused fenoolist tulenevatele metabolismi- ja stressisignaalidele, Tartu Ülikool.

24. Marika Truu, 2008, (supervisor) Mari Ivask; Jaak Truu, Impact of land use on microbial communities in Estonian soils, Tartu Ülikool.

25. Signe Saumaa, 2007, (supervisor) Maia Kivisaar, The role of DNA mismatch repair and oxidative DNA damage defense systems in avoidance of stationary phase mutations in Pseudomonas putida, Tartu Ülikool.

26. Heili Ilves, 2006, (supervisor) Rita Hõrak; Maia Kivisaar, Stress-induced transposition of Tn4652 in Pseudomonas putida, Tartu Ülikool.

27. Andres Tover, 2005, (supervisor) Maia Kivisaar, Regulation of transcription of the phenol degradation pheBA operon in Pseudomonas putida, Tartu Ülikool.

28. Riho Teras, 2005, (supervisor) Maia Kivisaar, Regulation of transcription from the fusion promoters generated by transposition of Tn4652 into the upstream region of pheBA operon in Pseudomonas putida, Tartu Ülikool.

29. Helen Udras, 2005, (supervisor) Tiina Alamäe, Hexose kinases and glucose transport in the yeast Hansenula polymorpha, Tartu Ülikool.

30. Rita Hõrak, 2002, (supervisor) Maia Kivisaar, Regulation of transposition of transposon Tn4652 in Pseudomonas putida, Tartu Ülikool.

31. Reet Marits, 2001, (supervisor) Andres Mäe, Role of two-component regulator system PehR-PehS and extracellular protease PrtW in virulence of Erwinia carotovora subsp. carotovora, Tartu Ülikool.

Patentne leiutis/Patents

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Sirli Sipp Kulli, Ain Heinaru, Tiit Maidre; Prioriteedi number: US2020157577; Prioriteedi kuupäev: 16.02.2016.

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Sirli Sipp Kulli, Ain Heinaru, Tiit Maidre; Prioriteedi number: EP3416759A1; Prioriteedi kuupäev: 16.02.2016.

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Ain Heinaru, Sirli Sipp Kulli, Tiit Maidre; Prioriteedi number: AU20170219431 20170216 ; Prioriteedi kuupäev: 16.02.2016.

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Ain Heinaru, Sirli Sipp Kulli, Tiit Maidre; Prioriteedi number: WO/2017/140324 ; Prioriteedi kuupäev: 16.02.2016.

Meetod graptoliitargilliidi metallorgaanilise aine lõhustamiseks mikroobikoosluse abil; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Sirli Sipp Kulli, Ain Heinaru, Tiit Maidre; Prioriteedi number: P201600003; Prioriteedi kuupäev: 16.02.2016.

CELMS

CELMS on Tartu ܬikooli Molekulaar- ja Rakubioloogia Instituudi juures asuv mittemeditsiinilise p䲩toluga looduslike ja laboratoorsete mikroobitüvede kollektsioon. See kollektsioon on asutatud 1995. aastal. Alates 2008. aastast on kollektsioon registreeritud WFCC-MIRCEN (World Data Centre for Microorganisms) juures (registreerimise number 926).


CELMS on ECCO (European Culture Collections' Organisation) liige. Kollektsiooni finantseeritakse Haridus- ja Teadusministeeriumi poolt. Kogus esindatud mikroobid on kogutud peamiselt Eesti erinevate saastunud piirkondade vee- ja pinnaseproovidest. Viimastel aastatel on kogusse lisandunud ka erinevate L䤮emere piirkondade mikrobioota proove. Kogu koostamisel on olnud põhirõhk biodegradatiivsete ja kasulikke ühendeid tootvate mikroobide kogumisel ja põhjalikul iseloomustamisel.

CELMS Eeskirjad

Tartu Ülikooli Molekulaar- ja rakubioloogia instituudis asuva keskkonna- ja laboratoorsete mikroobitüvede teaduskollektsiooni korralduse ja kasutamise eeskiri
1. Üldsätted
Keskkonna- ja laboratoorsete mikroobitüvede teaduskollektsioonis, akronüümiga CELMS (Collection of Environmental and Laboratory Microbial Strains), sisalduvad mikroobitüved on isoleeritud peamiselt Eesti erinevate saastunud piirkondade vee- ja pinnaseproovidest ning erinevate Läänemere piirkondade mikrobioota proovidest. Kogus esindatud mikroobid on kogutud põhirõhuga biodegradatiivsete ja kasulikke ühendeid tootvate mikroobide kogumisele. Kogusse on lisatud ka laboratoorselt selekteeritud ja/või konstrueeritud kindlate iseloomulike omadustega mikroobitüved. Kollektsioon CELMS on asutatud 1995. aastal.  Alates 2008. aastast on kollektsioon registreeritud WFCC-MIRCEN (World Federation of Culture Collections, World Data Centre for Microorganisms) juures (registreerimise number 926). CELMS on ECCO (European Culture Collections' Organisation) liige. Kollektsiooni finantseeritakse Haridus- ja Teadusministeeriumi poolt. Kollektsioon asub Tartu Ülikooli Molekulaar- ja rakubioloogia instituudis (Tartu 51010, Riia 23, Eesti). Kogu kasutamine toimub vastavalt eeskirjadele, mille leiate siit veebilehelt. Kollektsiooni kataloog on avalikult kättesaadav EEMB (Eesti Elektroonilise Mikroobide andmeBaasi) veebilehel http://eemb.ut.ee/ nii eesti kui inglise keeles.
2. Erisätted
Keskkonna- ja laboratoorsete mikroobitüvede teaduskollektsioon CELMS on loodud eesmärgiga soodustada mikrobioloogilist teadustööd, eelkõige seoses võimalustega kasutada mikroobitüvesid mikrobioloogiatööstuses ning biotehnoloogilises ettevõtluses, ka keskkonnabiotehnoloogilised rakendused keskkonnareostuse alandamiseks, teisalt aga säilitada mikroobitüvesid rahvusliku rikkusena. Kuivõrd siin on tegemist geneetilise ressursiga tegeleva mikroobide rahvuskollektsiooniga, siis järgib teaduskollektsioon Nagoya protokollist tulenevaid nõudeid. Nagoya protokoll reguleerib juurdepääsu geneetilistele ressurssidele ja nende kasutamist. 
Kollektsioon on käsitletav kahes erinevas kataloogide formaadis: 
1) Kindlate eriomadustega mikroobitüved, mis on põhjalikult geneetiliselt ja mikrobioloogiliselt iseloomustatud, mille teadustööga saadud tulemused on publitseeritud ja info millede kohta on kättesaadav EEMB kodulehel ning mis on rahvusvaheliselt avatud avalikuks kasutuseks (tüvede tellimine, tasuta saatmine vastavalt reeglistikule);
2) Mikroobitüved, mis on kollektsiooni osaks, kuid mille avalik kasutus omab eripiiranguid lähtuvalt eelkõige autoriõigustest (Budapest Treaty, World Intellectual Property Organization (WIPO)) ning mis lülitatakse avalikku kataloogi pärast piirangutest vabanemist (patendinõuded, autoriõigused, publitseerimistingimused jms).
Esimesena nimetatud kollektsiooni säilitamise ning andmebaasi ja kataloogi nõuetekohase haldamise ja kasutamise eest vastutavad kollektsiooni haldur ja kollektsiooni kuraator. Teisena märgitud mikroobitüvede kohta on koostatud mikroobitüvede üldkataloog, mis säilitatakse TÜ serveris kasutajaõigusega kaitstud kettal (\\albert.domenis.ut.ee). Vastavad mikroobitüved on mikroobikollektsiooni CELMS osaks, kuid nende säilitamise eest vastutavad vastavate mikroobitüvedega töötavad uurijad kuni nende kandmiseni avalikku mikroobitüvede kataloogi. Vastavat bioloogilist materjali säilitatakse infobaasis (kataloogis) kodeeritult, kooskõlas seadusaktidega. 
Ülalesitatud süsteem on tingitud ka asjaolust, et mikrobioloogiliselt ja geneetiliselt iseloomustamata ja eriomaduste selgitamiseta pole mikroobitüvede väärtus määratletav ja nad on väärtusetud avalikuks kasutuseks. 
CELMS on mikroobitüvede tellimiseks ja vabaks kasutuseks avatud mittekommertsiaalseks tegevuseks. Soov kollektsiooni mikroobitüvesid kasutada ärilistel eesmärkidel reguleeritakse läbi mikroobitüvede isoleerijate ja iseloomustajate autoriõiguste Tartu Ülikoolis kinnitatud reeglistiku alusel, lähtudes EV vastavatest seadusaktidest.  
3. Kollektsiooni komplekteerimine ja struktuur
Kollektsiooni moodustavad teadustöö käigus kogutud, ostetud või annetatud mikroobitüved ja laboratoorselt selekteeritud/konstrueeritud mutantsed mikroobitüved ning digitaalsesse andmebaasi talletatud informatsioon.
CELMS kollektsiooni uute säilikute lisandumisel avalikku kataloogi sõlmitakse mikroobitüve isoleerija/iseloomustaja ja kollektsiooni halduri vahel materjalide üleandmise leping (Material Transfer Agreement, MTA), milles on märgitud  üleantava mikroobitüve spetsiifilised eriomadused (nt võime lagundada teatud kemikaali,
ravimiresistentsus, plasmiidide olemasolu jms) ning üld- (isoleerimise koht, liigiline kuuluvus 16SrRNA geeni järjestused jms, liigilise kuuluvuse näitajad) ja eriinformatsioon (nukleotiidijärjestused ja nende deponeerimine andmebaasidesse), samuti andmed mikroobitüve avalike publikatsioonide kohta või hõivatus patentidega. Lepingud allkirjastatakse ja arhiveeritakse.
Kollektsiooni haldamiseks on kasutusel tarkvara dbForge Studio for MySQL. Edasiselt nähakse ette kollektsiooni andmebaasi internetipõhine ühildamine Eesti e-Elurikkuse (http://elurikkus.ut.ee/ andmebaasiga Eesti teaduse teekaardi aktiivsusena. See on vajalik selleks, et kollektsiooni andmebaas säilitatakse digitaalselt mitme koopiana, mis asuvad erinevates arvutites ja serverites. 
CELMS kollektsioon koordineerib ja koondab andmed ka kõigi teiste Eestis säilitatavate ja kasutatavate mirkoobitüvede kohta, eelkõige lähtuvalt
Ülemaailmse Põllumajandusorganisatsiooni (FAO) koordineeritavale Nagoya protokollist tulenevate geneetiliste ressursside  kui rahvusliku rikkuse säilitamise nõuete täitmisest.
Kuivõrd CELMS kollektsioon ei sisalda inim- ja loompatogeenseid mikroobitüvesid, siis pole eesmärgiks iga säilik varustada unikaalse ID-koodiga,  mis koosneks kollektsiooni akronüümi ja numbri kombinatsiooni. Kollektsioon asub TÜ Molekulaar- ja rakubioloogia instituudis (Riia 23-114, Tartu 51010). 
4. Säilikute hoidmine ja säilivuse kontroll 
Säilikuid (mikroobitüvesid) hoitakse -80°C juures mitmes korduses, mis on paigutatud erinevatesse külmikutesse. Isoleeritud tüvesid säilitatakse spetsiaalsetes säilitusviaalides.  Säilitustingimusi (külmikute temperatuuri ja külmikute jooksva hoolduse teostamist) jälgivad kollektsiooni eest vastutavad töötajad. Külmikud on varustatud külmikute häire edastusseadmega. Häire korral saadab seade vastava sõnumi eelnevalt kindlaks
määratud isikute mobiiltelefonile. Hoidlaruumide häireolukordadest teavitamine ning tegutsemise kord häireolukordades on kooskõlastatud  ülikooli turvateenistusega.
Kollektsiooni säilitatakse suletud külmikutes. Juurdepääs kollektsioonile on ainult selleks volitatud isikul (halduril), tema puudumisel (puhkus, lähetus jms) määratakse asendaja. Kolmandatel iskutel on juurdepääs ja säilituskohustus kollektsiooni nn kinnisele osale, mikroobitüvedele, millede omadusi uuritakse ning mis pole veel üle antud CELMS kollektsiooni avalikku kataloogi.
5. Säilikute kasutamine ja väljalaenutamine
Kollektsioonis säilitatavad mikroobitüved ning kogu informatsioon nende kohta on instituudisiseselt vabalt kättesaadav (teaduslikeks uuringuteks). Teistele Tartu Ülikooli instituutidele, samuti muudele osapooltele teaduslikeks uuringuteks (mittekommertsiaalseks tegevuseks) väljalaenutamise aluseks on materjalide üleandmise leping (Material Transfer Agreement, MTA). Lepingu allkirjastamiseks palun pöörduda kollektsiooni meeskonna poole. Need lepingud arhiveeritakse.

CELMS Kollektiiv

Ain Heinaru
Eeva Heinaru
Signe Viggor
Merike Jõesaar
Eve Naanuri

CELMS Kontaktid

Geneetika õppetool
Molekulaar- ja Rakubioloogia Instituut
Riia 23
Tartu 51010

E-mail: signe.viggor@ut.ee (Signe Viggor)
Phone +372 7 376 038

CELMS Publikatsioonid / Publications

Celms_publications

Published articles in Journals
Nr Reference name Keywords File link
1 Heinaru et al., 2000 (FEMS Microbiology Ecology) Isolation of phenol and p-cresol degraders; catabolic types; occurrence of plasmid DNA; phenol monooxygenase, catechol 1,2-dioxygenase, catechol 2,3-dioxygenase, protocatechuate 3,4-dioxygenase, p-hydroxybenzoate hydroxylase enzyme activities; File
2 Heinaru et al., 2001 (FEMS Microbiology Ecology) Mechanisms regulating degradation of phenol, p-cresol and benzoate from their mixtures; Pseudomonas strains of different catabolic types; metabolic intermediates; diauxia File
3 Heinaru et al., 2005 (FEMS Microbiology Ecology) Microcosms; DGGE analysis; monitoring of population dynamics; decomposition of phenolic compounds and PAHs in microcosms File
4 Heinaru et al., 2009 (FEMS Microbiology Ecology) Pseudomonas fluorescens PC20; naphthalene and phenol plasmids; plasmid transfer; plasmid mobilization; IS elements; complete nucleotide sequence of pNAH20 File
5 Joesaar et al., 2010 (FEMS Microbiology Ecology) p-cresol methylhydroxylase; p-cresol degradation kinetics; sigma-54 dependent transcriptional regulation File
6 Juhanson et al., 2009 (FEMS Microbiology Ecology) Phytoremediation and bioaugmentation field experiments; survival of introduced strains; DGGE analysis; catabolic performance File
7 Jutkina et al., 2011 (Genes) IncP-9 plasmids; aromatic degraders of Baltic Sea File
8 Jutkina et al., 2013 (Plasmid) TOL plasmids; toluene catabolic genes; complete nucleotide sequence of pD2RT; growth kinetics of plasmid-bearing strains File
9 Merimaa et al., 2006 (Archives in Microbiology) Phenol hydroxylase; catechol 2,3-dioxygenase; phenol and p-cresol degraders; phylogenetic analysis File
10 Vedler et al., 2004 (Journal of Bacteriology) Herbicide 2,4-D; IncP-1 plasmids; complete nucleotide sequence of pEST4011; laboratory evolution File
11 Vedler et al., 2013 (Systematic and Applied Microbiology) Limnobacter spp; phenol-degrading bacteria of Baltic Sea; phenol hydroxylase; catechol 2,3-dioxygenase; phylogenetic analysis; total community DNA File
12 Viggor et al., 2008 (Biodegradation) Phenol hydrozylase; kinetic parameters; phenol-degrading pseudomonads File
13 Viggor et al., 2013 (Microbiological Research) Alkane biodegradation; microbioal communities; Baltic Sea; alkB clone library; microcosm experiments; DGGE analysis; phylogenetic trees File
14 Xu et al., 2011 (IJSEM) Pelagibacterium; novel member of the family Hyphomicrobiaceae; taxonomic characteristics File
15
Peebo et al., 2014 (Applied Microbiology and Biotechnology)
Acetate overflow; Acs; Continuous culture; Absolute proteomics; Acetylation
File
16 Kõiv et al., 2015 (Scientific Reports)

Changes in microbial community; potato tubers; pathogenesis File
17 Viggor et al., 2015 (Mar Pollut Bull) Alkane hydroxylase; Baltic Sea; alkB gene; n-alkane degrading bacterial strains File

18 Heinaru et al., 2016



Functional redundancy in phenol and toluene degradation in Pseudomonas stutzeri strains isolated from the Baltic Sea doi
19 Jõesaar et al., 2017 Strategy ofPseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate doi
20 Ilmjärv et al., 2017 Contribution of increased mutagenesis to the evolution of pollutants-degrading indigenous bacteria doi
21
Kõiv et al.,2020
Microbiome of root vegetables--a source of gluten-degrading bacteria
doi
22 Viggor et al.,2020
Microbial metabolic potential of phenol degradation in wastewater treatment plant of crude oil refinery: analysis of metagenomes and characterization of isolates
doi
23
Elken et al.,2020
Formation of new PHE plasmids in a phenol-polluted environment
doi
24
Nandy et al.,2021
Monitoring the growth, survival and phenol utilization of the fluorescent-tagged Pseudomonas oleovorans immobilized and free cells
doi


Magistritööd/Master's thesis

1. Kady Mäesalu, 2021, (supervisor) Anne Menert, Elektroonikaromude bioleostumise protsesside uurimine, Tartu Ülikool, Loodus- ja täppisteaduste valdkond, ökoloogia ja maateaduste instituut

2. Marge Puhm, 2020, (supervisor) Riho Teras, Ekstratsellulaarsete peptiidide mõju Pseudomonas putida biofilmile fis -i üleekspressiooni tingimustes, Tartu Ülikool.

3. Kristina Põšnograjeva, 2019, (supervisor) Tiina Alamäe; Katrin Viigand, Pärmide MAL klastrid ja valgud põhirõhuga Scheffersomyces stipitis'e -glükosidaasidel, Tartu Ülikool.

4. Aivar Meldre, 2019, (supervisor) Tiina Alamäe; Triinu Visnapuu; Katrin Viigand, Pärmi Blastobotrys adeninivorans -glükosidaasi AG2 iseloomustamine, Tartu Ülikool.

5. Liselle Luks, 2019, (supervisor) Anne Menert; Hans Priks; Triin Korb, Põlevkivi mikrobioloogiline töötlemine, Tartu Ülikool.

6. Angela Peeb, 2019, (supervisor) Jaak Truu; Kristjan Oopkaup, Naftareostuse mõju arktilise merejää mikroobikooslusele, Tartu Ülikool.

7. Ingrem Metsik, 2017, (supervisor) Maia Kivisaar; Tanel Ilmjärv, Hübriidse m-kresooli lagundamisraja efektiivsust suurendavad mutatsioonid bakteri Pseudomonas putida laboratoorses evolutsioonikatses, Tartu Ülikool.

8. Sirli Rosendahl, 2017, (supervisor) Hedvig Tamman; Rita Hõrak, Toksiin-antitoksiin süsteemide mõju Pseudomonas putida kohasusele ja stressitaluvusele, Tartu Ülikool.

9. Anneli Aasamets, 2016, (supervisor) Tiina Alamäe; Triinu Visnapuu, Levaani ja fruktooligosahhariidide süntees Pseudomonas syringae pv. tomato levaansukraasiga Lsc3, Tartu Ülikool.

10. Liisbeth Kose, 2016, (supervisor) Riho Teras, Pseudomonas putida GacS/A signaaliraja geenide transkriptsiooni regulatsioon, Tartu Ülikool.

11. Triin Korb, 2016, (supervisor) Anne Menert, Biodegradatiivse potentsiaaliga mikroobikooslused Eesti graptoliitargilliidist, Tartu Ülikool.

12. Maria Gromkova, 2015, (supervisor) Tiina Alamäe; Triinu Visnapuu; Karin Ernits, Pseudomonas syringae pv. tomato levansukraasi Lsc3 struktuuri ja funktsiooni seoste uurimine mutatsioonanalüüsiga, Tartu Ülikool.

13. Artemi Maljavin, 2015, (supervisor) Maia Kivisaar; Tatjana Jatsenko, "Mutageensuse" operoni osalus Pseudomonas putida rakkudes toimuvates mutatsiooniprotsessides, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

14. Maarja Grünbach, 2014, (supervisor) Eve Naanuri; Eeva Heinaru, Multikomponentsete monooksügenaaside mitmekesisus Läänemere tolueenilagundajates bakterites, Tartu Ülikool.

15. Merlin Soopere, 2014, (supervisor) Tiina Alamäe; Ene Talpsep, PCR-meetodi valideerimine Listeria monocytogenes'e tuvastamiseks toidu- ja hügieeniproovidest, Tartu Ülikool.

16. Mari Tagel, 2014, (supervisor) Maia Kivisaar, Uute mutatsioonisagedust mõjutavate geenide identifitseerimine bakteris Pseudomonas putida, Tartu Ülikool.

17. Kärt Ukkivi, 2013, (supervisor) Maia Kivisaar, Transkriptsiooni ja transkriptsiooniga seotud DNA reparatsiooni mõju mutatsiooniprotsessidele bakteris Pseudomonas putida, Tartu.

18. Ülvi Kana, 2013, (supervisor) Maia Kivisaar, NHEJ ensüümide osalus mutatsiooniprotsessides bakteris Pseudomonas putida, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

19. Tanel Ilmjärv, 2013, (supervisor) Maia Kivisaar; Heili Ilves, Pseudomonas putida mutatsiooniprotsesside sõltuvus kromosomaalsest lokalisatsioonist ja rakkudevahelisest kommunikatsioonist, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

20. Andres Ainelo, 2013, (supervisor) Rita Hõrak, Pseudomonas putida GraTA toksiin-antitoksiin süsteemi toimemehhanismide selgitamine, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

21. Hanna Ainelo, 2013, (supervisor) Riho Teras, Pseudomonas putida globaalse regulaatori Fis osalus biofilmi moodustumises, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

22. Kadi Tilk, 2013, (supervisor) Rita Hõrak, Pseudomonas putida ColRS süsteem on tsingi-, raua-, mangaani- ja kaadmiumiliiga tunnetav signaalirada, Tartu Ülikool.

23. Hedvig Tamman, 2012, (supervisor) Rita Hõrak, Pseudomonas putida kasvukiirust vähendav toksiin GraT supresseerib colR mutandi glükoossõltuvat lüüsi, Tartu Ülikool.

24. Karl Mumm, 2012, (supervisor) Rita Hõrak, Kas transkriptsioonifaktor ColR paikneb periplasmas?, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

25. Kertu Tiirik, 2012, (supervisor) Hiie Nõlvak; Jaak Truu, Antibiootikumiresistentsusgeenide tuvastamine Läänemere bakterplanktonist, Tartu Ülikool.

26. Sandra Käosaar, 2012, (supervisor) Tiina Alamäe, Mono- ja disahhariidid regulatsiooniprotsesside käivitajatena pärmil Hansenula polymorpha: uued meetodid, promootorid ja ekspressioonitüved, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

27. Jekaterina Jevtuševskaja, 2012, (supervisor) Andres Mäe; Liis Andresen, Plasmiidsete vektorsüsteemide konstrueerimine ja rakendamine Rsm süsteemi mõju uurimiseks taimepatogeenis Pectobacterium carotovorum alaml. carotovorum, Tartu Ülikool.

28. Karin Ernits, 2011, (supervisor) Tiina Alamäe; Triinu Visnapuu, Pseudomonas syringae pv. tomato levaansukraasi Lsc3 struktuuri modelleerimine ja mutantide iseloomustamine, Tartu Ülikool.

29. Ivo Krustok, 2011, (supervisor) Marika Truu; Jaak Truu, Horisontaal- ja vertikaalvooluliste filtrite mikroobikooslue dünaamika ja aktiivsus eksperimentaalses hallvee puhastussüsteemis, Tartu Ülikool.

30. Teele Ligi, 2011, (supervisor) Marika Truu; Jaak Truu, Denitrifikatsioonis osalev mikroobikooslus reostunud jõevett puhastavas läbivooluliste tehismärgalade kompleksis, Tartu Ülikool.

31. Mihkel Mäesaar, 2011, (supervisor) Jaak Truu; Jaanis Juhanson, Naftareostuse mõju Läänemere mikroobikooslusele, Tartu Ülikool.

32. Triinu Juurik, 2011, (supervisor) Maia Kivisaar; Kairi Tavita, Mutatsiooniprotsessid bakteri Pseudomonas putida kromosoomis, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

33. Andrio Lahesaare, 2011, (supervisor) Riho Teras; Heili Ilves, Globaalse regulaatorvalgu Fis-i seondumine Pseudomonas putida raua metabolismis ja biofilmi moodustamises osalevate geenide promootoraladele, Tartu Ülikool.

34. Anna Velts, 2010, (supervisor) Riho Teras, Pseudomonas putida Fis valgu kontsentratsioon erinevates kasvutingimustes, Tartu Ülikool.

35. Annika Teppo, 2010, (supervisor) Riho Teras, Pseudomonas putida kasvuhäirete põhjused glükoosi söötmes, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikooli

36. Tatjana Jatsenko, 2010, (supervisor) Maia Kivisaar; Kairi Tavita, Spetsialiseeritud DNA polümeraaside osalus mutatsiooniprotsessides Pseudomonas putida rakkudes, Tartu Ülikool.

37. Julia Sidorenko, 2010, (supervisor) Maia Kivisaar; Signe Saumaa, Study of the functions of DNA polymerase I in Pseudomonas putida, Tartu Ülikool.

38. Annika Vilem, 2010, (supervisor) Jaak Truu; Jaanis Juhanson, Lõhkeaineid lagundava bakterikonsortsiumi iseloomustamine molekulaarsete meetoditega, Tartu Ülikool.

39. Külliki Püvi, 2010, (supervisor) Rita Hõrak, Pseudomonas putida glükoosist sõltuvat autolüüsi mõjutavad geenid, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

40. Kai Jõers, 2010, (supervisor) Andres Mäe; Tanel Tenson, Chlamydia trachomatis prevalents ja populatsiooni geneetiline struktuur Eestis, Tartu Ülikool.

41. Olga Šapran, 2010, (supervisor) Rita Hõrak, Glükoosi metabolismigeenide osalus Pseudomonas putida colR mutandi glükoos-sõltuvas lüüsumises, Tartu Ülikool.

42. Andres Lõhmus, 2010, (supervisor) Tiina Alamäe, Hansenula polymorpha maltaasi geen reporterina bakterites: kasutamisvõimalused ja võrdlus GusA-reporteriga, Tartu Ülikool.

43. Julia Aprelkova, 2010, (supervisor) Indrek Suitso; Tiina Alamäe, Probiootilise bakteri Bacillus smithii TBMI12 spooride manustamise ohutuskatse sigade ning kanade näitel, Tartu Ülikool.

44. Liisa Lilje, 2009, (supervisor) Rita Hõrak; Marta Putrinš, ColRS signaaliraja ja TtgABC pumba roll Pseudomonas putida fenoolitolerantsuses, Tartu Ülikool.

45. Liisa Lilje, 2009, (supervisor) Rita Hõrak; Marta Putrinš, ColRS signaaliraja ja TtgABC pumba roll Pseudomonas putida fenoolitolerantsuses, Tartu Ülikool.

46. Jens-Konrad Preem, 2009, (supervisor) Jaak Truu, Trinukleotiidsed lihtsad kordusjärjestused Pseudomonas fluorescensi genoomis ja võimalused nende kasutamiseks perekond Pseudomonas liikide subtüpiseerimiseks, Tartu Ülikool.

47. Mario Mitt, 2009, (supervisor) Signe Viggor; Eve Naanuri, Alkaane lagundava bakterikonsortsiumi iseloomustamine Vilsandi rannikumeres, Tartu Ülikool.

48. Sander Kutti, 2009, (supervisor) Jaak Truu, Fosforit siduva filtermaterjali mikroobikooslus heitvee järelpuhastis, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

49. Hiie Nõlvak, 2008, (supervisor) Jaak Truu, Seiratava loodusliku tervenemise rakendusvõimaluste uurimine molekulaarsete meetoditega naftasaadustega saastunud ala pinnases, Tartu Ülikool.

50. Jekaterina Jutkina, 2008, (supervisor) Eeva Heinaru; Eve Naanuri, Pseudomonas fluorescens tüve PC20 plasmiidide järjestuse analüüs, Tartu Ülikool.

51. Kersti Tammus, 2008, (supervisor) Tiina Alamäe, Reportergeenide kasutamine pärmil Hansenula polymorpha: MAL-lookus ja selle promootorite regulatsioon, Tartu Ülikool.

52. Julia Jakovleva, 2008, (supervisor) Riho Teras, Tn4652 transpositsiooni sõltuvus DNA superspiralisatsioonist ja Fis-ist, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

53. Triinu Visnapuu, 2007, (supervisor) Tiina Alamäe, Levaansukraasi geenide ekspresseerimine Escherichia coli's ja valkude omaduste uurimine, Tartu Ülikool.

54. Karin Kask, 2007, (supervisor) Eerik Jõgi; Allan Nurk; Andres Mäe, Laktaadi tootmine Bacillus coagulans SIM-7 DSM 14043 vegetatiivsete rakkude ning spooridega, Tartu Ülikool.

55. Mari-Liis Ots, 2007, (supervisor) Allan Nurk; Andres Mäe; Oliver Meikar, Polühüdroksüalkanaadi süntees bakteris Pseudomonas mandelii Pc17, Tartu Ülikool.

56. Liis Andresen, 2007, (supervisor) Andres Mäe, Rcs signaaliülekande süsteemi roll taimepatogeeni Pectobacterium carotovorum alaml. carotovorum virulentsuses, Tartu Ülikoo.

57. Merit Aava, 2007, (supervisor) Eeva Heinaru, Multiplasmiidne süsteem naftaleeni ja fenooli lagundamiseks Pseudomonas fluorescens tüves PC20, Tartu Ülikool.

58. Lauri Koorits, 2007, (supervisor) Andres Tover; Maia Kivisaar, ImuB ja DnaE2 osalus Pseudomonas putida rakkudes toimuvates mutatsiooniprotsessides, Tartu Ülikool.

59. Mariliis Tark, 2006, (supervisor) Andres Tover; Maia Kivisaar, DNA reparatsioon Pseudomonas putida rakkudes, Tartu Ülikool.

60. Paula Ann Kivistik, 2006, (supervisor) Rita Hõrak; Maia Kivisaar, Pseudomonas putida kahekomponentse signaalsüsteemi ColRS märklaudgeenid, Tartu Ülikool.

61. Katrin Viigand, 2006, (supervisor) Tiina Alamäe, Hansenula polymorpha MAL-lookus, Tartu Ülikool.

62. Kairi Tavita, 2006, (supervisor) Maia Kivisaar; Andres Tover, Statsionaarse faasi sigma faktori RpoS osalus Pseudomonas putida nälgivas populatsioonis toimuvates adaptatsiooniprotsessides, Tartu Ülikool.

63. Liis Kärme, 2006, (supervisor) Jaak Truu, Biotervendusmeetodite kasutamine saasteainete biodegradatsiooni võimendamiseks poolkoksis, Tartu Ülikool.

64. Jaanis Juhanson, 2005, (supervisor) Jaak Truu, Fütoremediatsiooni ja bioaugmentatsiooni mõju poolkoksi mikroobikooslusele, Tartu Ülikool.

65. Hedi Laursoo, 2005, (supervisor) Andres Mäe, Taimepatogeenile Erwinia carotovora subsp. carotovora SCC3193 spetsiifilise mikrokiibi väljatöötamine, Tartu Ülikool.

66. Radi Tegova, 2004, (supervisor) Andres Tover; Maia Kivisaar, DNA polümeraas IV osalus Pseudomonas putida rakkudes toimuvates mutatsiooniprotsessides, Tartu Ülikool.

67. Marta Putrinš, 2004, (supervisor) Maia Kivisaar; Andres Tover, Rakkude füsioloogilisest seisundist tulenevad kontrollmehhanismid Pseudomonas putida fenooli degradatsiooni operoni pheBA transkriptsiooni regulatsioonil, Tartu Ülikool.

68. Pille Pärn, 2003, (supervisor) Tiina Alamäe, Hansenula polymorpha maltase, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

69. Signe Saumaa, 2002, (supervisor) Maia Kivisaar, DNA reparatsioonisüsteemide mõju mutatsioonispektri muutustele Pseudomonas putida kultuuri pikemaajalisel nälgimisel, Tartu Ülikool.

70. Ülle Saks, 2002, (supervisor) Andres Tover; Maia Kivisaar, Fenooli lagundamist määravate geenide transkriptsiooni regulatsioon bakteris Pseudomonas putida, Tartu Ülikool.

71. Heili Ilves, 2001, (supervisor) Maia Kivisaar; Rita Hõrak, Pseudomonas putida transposooni Tn4652 transpositsiooni regulatsioon, Tartu Ülikool.

72. Silja Laht, 2001, (supervisor) Tiina Alamäe, Pärmi Hansenula polymorpha glükokinaas: geeni kloneerimine ja valgu iseloomustamine, Tartu Ülikool.

73. Toomas Kramarenko, 2000, (supervisor) Tiina Alamäe, Heksoosi kinaaside roll suhkrute kataboliitses repressioonis pärmil Hansenula polymorpha, Tartu Ülikool.

74. Signe Viggor, 2000, (supervisor) Eeva Heinaru; Toomas Tenno, Alküül- ja hüdroksüfenoolide biodegradatsiooni uurimine erineva katabolismitüübiga bakteritüvedes, Tartu Ülikool.

75. Eve Naanuri, 1999, (supervisor) Ain Heinaru; Andres Mäe, Pseudomonas putida 2,4-diklorofenoksüatsetaadi lagundamist tagava plasmiidi pEST4011 tfdCB operoni ekspressioon ja regulatsioon LysR-tüüpi transkriptsiooni aktivaatori TfdR poolt, Tartu Ülikool.

Doktoritööd/Doctoral thesis

1. Kärt Ukkivi, 2020, (supervisor) Maia Kivisaar, Mutagenic effect of transcription and transcription-coupled repair factors in Pseudomonas putida, Tartu Ülikool.

2. Kadi Tilk, 2020, (supervisor) Rita Hõrak, Signals and responses of ColRS two-component system in Pseudomonas putida, Tartu Ülikool.

3. Hanna Ainelo, 2018, (supervisor) Riho Teras, Fis regulates Pseudomonas putida biofilm formation by controlling the expression of lapA, Tartu Ülikool.

4. Andrio Lahesaare, 2018, (supervisor) Riho Teras, The role of global regulator Fis in regulating the expression of lapF and the hydrophobicity of soil bacterium Pseudomonas, Tartu Ülikool.

5. Karin Ernits, 2019, (supervisor) Tiina Alamäe, Levansucrase Lsc3 and endo-levanase BT1760: characterization and application for the synthesis of novel prebiotics, Tartu Ülikool.

6. Katrin Viigand, 2018, (supervisor) Tiina Alamäe, Utilization of -glucosidic sugars by Ogataea (Hansenula) polymorpha, Tartu Ülikool.

7. Tatjana Jatsenko, 2018, (supervisor) Maia Kivisaar, Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads, Tartu Ülikool.

8. Andres Ainelo, 2018, (supervisor) Rita Hõrak; Jaanus Remme, Physiological effects of the Pseudomonas putida toxin GraT, Tartu Ülikool.

9. Hedvig Tamman, 2016, (supervisor) Rita Hõrak, The GraTA toxin-antitoxin system of Pseudomonas putida: regulation and role in stress tolerance, Tartu Ülikool.

10. Julia Sidorenko, 2015, (supervisor) Maia Kivisaar, Combating DNA damage and maintenance of genome integrity in pseudomonads, Tartu Ülikool.

11. Jekaterina Jutkina, 2014, (supervisor) Ain Heinaru; Eve Naanuri, The horizontal gene pool for aromatics degradation: bacterial catabolic plasmids of the Baltic Sea aquatic system, Tartu Ülikool.

12. Hiie Nõlvak, 2012, (supervisor) Ain Heinaru; Jaak Truu, Influence of qPCR workflow on target gene enumeration from environmental samples in the case of bioremediation potential estimation, Tartu Ülikool.

13. Liis Andresen, 2012, (supervisor) Andres Mäe, Regulation of virulence in plant-pathogenic pectobacteria, Tartu Ülikool.

14. Triinu Visnapuu, 2012, (supervisor) Tiina Alamäe, Levansucrases encoded in the genome of Pseudomonas syringae pv. tomato DC3000: heterologous expression, biochemical characterization, mutational analysis and spectrum of polymerization products, Tartu Ülikool.

15. Paula Ann Kivistik, 2011, (supervisor) Rita Hõrak; Maia Kivisaar, ColR-ColS signalling system and transposition of Tn4652 in the adaptation of Pseudomonas putida, Tartu Ülikool.

16. Merike Jõesaar, 2010, (supervisor) Ain Heinaru, Diversity of Key Catabolic Genes at Degradation of Phenol and P-cresol in Pseudomonads, Tartu Ülikool.

17. Signe Viggor, 2008, (supervisor) Ain Heinaru; Toomas Tenno, Impact of biochemical parameters of genetically diferent pseudomonads at the degradation of phenolic compounds, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond.

18. Eve Naanuri, 2005, (supervisor) Ain Heinaru, Structure of the 2,4-dichlorophenoxyacetic acid-degradative plasmid pEST4011, Tartu Ülikool.

19. Jaak Truu, 2004, (supervisor) Ain Heinaru, Oil shale industry wastewater: impact on river microbial community and possibilities for bioremediation, Tartu Ülikool.

20. Jaanis Juhanson, 2010, (supervisor) Jaak Truu, Fütoremediatsiooni ja bioaugmentatsiooni mõju poolkoksi mikroobikooslusele, Tartu Ülikool.

21. Radi Tegova, 2009, (supervisor) Maia Kivisaar; Andres Tover, The role of specialized DNA polymerases in mutagenesis in Pseudomonas putida, Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool.

22. Mariliis Tark, 2009, (supervisor) Maia Kivisaar, Mutagenic potential of DNA damage repair and tolerance mechanisms under starvation stress, Tartu Ülikool.

23. Marta Putrinš, 2008, (supervisor) Maia Kivisaar; Rita Hõrak, Pseudomonas putida vastused fenoolist tulenevatele metabolismi- ja stressisignaalidele, Tartu Ülikool.

24. Marika Truu, 2008, (supervisor) Mari Ivask; Jaak Truu, Impact of land use on microbial communities in Estonian soils, Tartu Ülikool.

25. Signe Saumaa, 2007, (supervisor) Maia Kivisaar, The role of DNA mismatch repair and oxidative DNA damage defense systems in avoidance of stationary phase mutations in Pseudomonas putida, Tartu Ülikool.

26. Heili Ilves, 2006, (supervisor) Rita Hõrak; Maia Kivisaar, Stress-induced transposition of Tn4652 in Pseudomonas putida, Tartu Ülikool.

27. Andres Tover, 2005, (supervisor) Maia Kivisaar, Regulation of transcription of the phenol degradation pheBA operon in Pseudomonas putida, Tartu Ülikool.

28. Riho Teras, 2005, (supervisor) Maia Kivisaar, Regulation of transcription from the fusion promoters generated by transposition of Tn4652 into the upstream region of pheBA operon in Pseudomonas putida, Tartu Ülikool.

29. Helen Udras, 2005, (supervisor) Tiina Alamäe, Hexose kinases and glucose transport in the yeast Hansenula polymorpha, Tartu Ülikool.

30. Rita Hõrak, 2002, (supervisor) Maia Kivisaar, Regulation of transposition of transposon Tn4652 in Pseudomonas putida, Tartu Ülikool.

31. Reet Marits, 2001, (supervisor) Andres Mäe, Role of two-component regulator system PehR-PehS and extracellular protease PrtW in virulence of Erwinia carotovora subsp. carotovora, Tartu Ülikool.

Patentne leiutis/Patents

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Sirli Sipp Kulli, Ain Heinaru, Tiit Maidre; Prioriteedi number: US2020157577; Prioriteedi kuupäev: 16.02.2016.

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Sirli Sipp Kulli, Ain Heinaru, Tiit Maidre; Prioriteedi number: EP3416759A1; Prioriteedi kuupäev: 16.02.2016.

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Ain Heinaru, Sirli Sipp Kulli, Tiit Maidre; Prioriteedi number: AU20170219431 20170216 ; Prioriteedi kuupäev: 16.02.2016.

Method for decomposition of the metallorganic matter of graptolite-argillite by microbial consortium; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Ain Heinaru, Sirli Sipp Kulli, Tiit Maidre; Prioriteedi number: WO/2017/140324 ; Prioriteedi kuupäev: 16.02.2016.

Meetod graptoliitargilliidi metallorgaanilise aine lõhustamiseks mikroobikoosluse abil; Omanikud: BiotaTec OÜ; Autorid: Anne Menert, Maia Kivisaar, Sirli Sipp Kulli, Ain Heinaru, Tiit Maidre; Prioriteedi number: P201600003; Prioriteedi kuupäev: 16.02.2016.

HUMB

EEMB_humb_introduction_2021 About the Biobank


    Human Microbiota Biobank (HUMB) is located in the Department of Microbiology, Institute of Biomedicine and Transitional Medicine. The biobank contains more than 20,000 microbial strains of human origin and more than 3,000 microbiota samples. The collection has joined two international networks (WDCM, ECCO).Main goal of the collection is to support and promote research and development in the field of microbiota. An important area of work is the screening of the properties of beneficial bacteria of human body, leading to the development of novel probiotics. Another important area of work involves the causative agents of opportunistic infections, their spectrum of drug susceptibility and virulence factors.
The biobank was started in 1994, when the first microbiota samples and lactobacilli strains were obtained in frame of the Estonian-Swedish allergy study. In the following years, the biobank has been supplemented with thousands of microbiota samples and microbial strains through numerous research projects. Particularly valuable are the beneficial bacteria derived from the human microbiota - lactobacilli and bifidobacteria, but the collection also contains a large number of opportunistic bacteria. Hundreds of specimens are added to collection each year, originating from intestinal tract, oral cavity, respiratory tract, genital tract and skin. The collection also preserves several patented probiotic lactobacilli, as well as standard cultures purchased from other collections for quality control and comparative testing.
The information system of the collection is based on the MySQL platform. The PHPRunner software package (XLineSoft) has been used to create the database user interface, and the dbForge Studio for MySQL (Devart) software package has been used to build the database architecture, create and test procedures and functions. A modern cPanel environment is used to organize database security, platform and content updates, and archiving. Data is managed via a web browser. The basic data of the catalog is visible to the average user, the entire structure of the catalog is visible and editable by registered users. Work on the development of the database and website is organized in cooperation with the Institute of Physics of the University of Tartu.


Research and development

The biobank is constantly engaged in research - determining the properties of microbial strains, isolating and analyzing DNA, analyzing microbial communities, updating and organizing the database. An important part of the collection's work is the screening of the properties of beneficial bacteria (including lactobacilli and bifidobacteria) from the gastrointestinal tract, genital tract and oral cavity, one of the results of which is the development of novel probiotics. There has been a huge growth in the world in the development of functional foods and probiotic products for health promotion and prophylaxis of certain diseases. The research and development needed for this requires laboratory and clinical trials regulated by EU rules, which must confirm the efficacy and safety of the selected bacterial strains. Lactobacillus fermentum ME-3 (DSM 14241) is patented by the University of Tartu and is used in several products developed in cooperation with companies: 'Hellus' brand of dairy products (Tere AS), cheese 'Andre Salute' (Andre Juustufarm OÜ), probiotic yoghurt ice cream (Balbiino AS), probiotic Madagascar chocolate (Chocolala OÜ), it is also marketed as a Reg'Activ food supplement (OÜ NoraVita).

Another important field of the collection's work is to elucidate the sources of the causative agents of opportunistic infections, their drug susceptibility and virulence factors. This will allow to map their spread and to update the treatment guidelines. These works are based on a sub-collection of opportunistic bacteria associated with clinical infections, that have been collected in collaboration with various clinics and foreign partners. Using and / or supplementing the HUMB collection, national treatment guidelines have been developed, numerous doctoral and master's theses have been defended, and more than 400 scientific publications have been completed.
Biobank is open for scientific cooperation.

Please contact us to receive additional information about the strains:

tiiu.roop [at] ut.ee
eet.mandar [at] ut.ee

HUMB Guidelines

Guidelines for management and use of the scientific collection

Guidelines for management and use

of the scientific collection

Human Microbiota Biobank

at Department of Microbiology, University of Tartu

1. General

Human Microbiota Biobank (HUMB) is a scientific collection that contains microbe strains of human origin (including microbiota bacteria and opportunistic pathogens), samples of human microbiota and the extracted DNA samples. The biobank was established to support and promote research work on collecting, processing and preserving the information about the human microbes and their communities, as well as development of probiotics.

The collection is guided by the suggestions of the international organisations of the corresponding fields (ECCO : European Culture Collections’ Organizations, WFCC : World Federation of Culture Collections, CABRI : Common Access to Biological Resources and Information, OECD : Best Practice Guidelines for Biological Resource Centre), suggestions of Nagoya Protocol and legislations of University of Tartu.

The collection is registered at WDCM (World Data Centre for Microorganisms) as WFCC Estonian Human Microbiota Biobank (collection no. WDCM 977, acronym HUMB).

Information about the collection is accessible on the Estonian Electronic Microbial dataBase (EEMB) website in English (http://eemb.ut.ee/eng) and Estonian (http://eemb.ut.ee/)

On the basis of the collection, research work is done and formal education is given. The collection is openly available for the scientists working at Department of Microbiology, University of Tartu, as well as other scientists who need it for research or teaching purposes according to agreement of collection managers. The catalogue of the collection is openly accessible on the collection website.

2. Structure and management of biobank

The collection is formed of collected, bought and donated microbe strains and microbiota samples as well as information stored in the digital database.

The purpose of collecting and preserving the collection is to ensure its accessibility for research work, probiotic development and teaching purposes.

When submitting new strains to the collection, a contract is signed with the person submitting the strains. This contract must contain information about the amount of strains submitted, the project during which the materials were collected, financial source, workers involved and the region from which the material was collected. These contracts are signed and archived.

Management of the collection is done with the help of electronic database developed on the basis of dbForge Studio for MySQL Professional. The database includes several information about the preserved material, including the data about preservation (form, date, location, next check-up), heritage (nation, material, donator), identification (methods, results), determined properties, clinical and animal trials, publications (patents, papers, dissertations).

The collection database is stored digitally in a couple of copies that are located in different computers. Printouts of the database are done periodically.

Updates of the collection (information about new material or new information for existing material) are uploaded into the digital database steadily. The updates are managed by the collection administrator who collects necessary information from other staff, researchers and students.

Each preserved item has an unique ID-code which consists on the collection acronym and a number combination.

It is mandatory to document the geographical region of origin, the date of submitting the strain and the person who submitted the strain to the collection (EU Regulation No 511/2014).

It is mandatory to document the material, clinical information about the donor, geographical region, date of submission to the collection and the person adding the material for all microbiota preservatives.

The head and administrator of the collection are responsible for proper usage of the collection and database.

The collection is located at the Department of Microbiology, University of Tartu (Ravila 19, Tartu 50411, Estonia).

3. Storage and viability control of the samples

The preservatives (microbe strains, microbiota samples, extracted DNAs) are stored at -80°C in multiple parallels in multiple freezers. Isolated strains are preserved inside sterile cryovials in SKIM-milk medium or in special chemically treated cryosolutions in cryovials. Part of the strains are lyophilised and stored at +4°C.

Viability check of the strains is performed in 3-5 years depending on the species.

The terms of preservation (temperature, running maintenance of the freezers) are controlled by the staff responsible for the collection.

The collection is preserved in locked refrigerators. The collection is accessible only to the assigned person, in absence of those persons only to an assigned substitute. No third party has access to the collection.

Freezers are equipped with fault detection systems. In case of a malfunction, a message automatically is sent to the person assigned to the collection.

In case of danger to the storage rooms, actions are in compliance with the university security rules.

Samples are handled and utilized according to the “Regulations for handling infectious material” legislation (in force since 31.10.2013 nr. 119, RTL 2003, 115, 1831).

Biological materials are assigned a code and preserved according to the regulations of the Council of the European Union (Recommendation Rec(2006)4 of the Committee of Ministers of member states on research on biological materials of human origin).

 

4. Use and availability of biobank

The strains and other materials preserved in the collection as well as the information about them are accessible for academic research (noncommercial purposes) within the institution.

The microbe strains are available for other institutions of University of Tartu as well as other parts according to MTA (material transfer agreement) for academic research (noncommercial purposes). These contracts are archived. This cooperation results in shared publications, dissertations and patents.

Use of strains for commercial purposes by third parties are regulated in agreements concluded between University of Tartu and the user.

The collection catalogue is publicly accessible: http://eemb.ut.ee/.

Please contact us to receive additional information about the strains:

tiiu.roop [at] ut.ee

reet.mandar [at] ut.ee

HUMB Team

Team

Reet Mändar Ph.D. 

Marika Mikelsaar Ph.D. 

Irja Lutsar Ph.D. 

Epp Sepp Ph.D. 

Paul Naaber Ph.D. 

Siiri Kõljalg Ph.D. 

Epp Songisepp Ph.D. 

Jelena Štšepetova Ph.D.  

Krista Lõivukene Ph.D. 

Silver Türk Ph.D. 

Paul Korrovits Ph.D. 

Piret Kõll Ph.D. 

Tõnis Karki Ph.D. 

Tatjana Brilene Ph.D. 

Kai Truusalu Ph. D. 

Pirje Hütt Ph. D.  

Ülle Parm Ph. D. 

Tiiu Rööp M.Sc. 

Imbi Smidt M.Sc.  

Merle Rätsep M.Sc. 

Piia Müürsepp M.Sc. 

Veiko Vengerfeldt M.Sc. 

Mariheleen Rostok 

Dagmar Hoidmets

HUMB Contacts

Human Microbiota Biobank

Department of Microbiology

University of Tartu

Ravila 19

Tartu 50411

Estonia

 

 

E-mail:

tiiu.roop [at] ut.ee

reet.mandar [at] ut.ee



Please contact us to receive additional information about the strains.

We can perform also several additional tests for the strains.

HUMB Publikatsioonid / Publications

eemb_references_2023




PATENTS

 

M. Mikelsaar, M. Zilmer, T. Kullisaar, H. Annuk, E. Songisepp. International Patent application: no. PCT/EE02/00006 28.06.2002. The strain of microorganism Lactobacillus fermentum ME-3 as novel antimicrobial and antioxidant probiotic. Avaldatud Published 09.01.03. WO 030022131.

 

M. Mikelsaar, M. Zilmer, T. Kullisaar, H. Annuk, E. Songisepp. P200100356 29.06.2001: Mikroorganismi tüvi Lactobacillus fermentum ME-3 kui uudne antimikroobne ja antioksüdantne probiootikum.

 

Mikelsaar, M., Zilmer, M., Kullisaar, M., Annuk, H., Songisepp, E. Mikroorganismi tüvi Lactobacillus fermentum ME-3 kui antimikroobne ja antioksüdantne probiootikum. Patendi taotleja Tartu Ülikool. EV Patendiamet, patent nr. 12/P200100356, 19.12.2005

 

Songisepp, E.; Mikelsaar, M.; Rätsep, M.; Zilmer, M.; Zilmer , K.; Üksti, J.; Kõljalg, S. Isoleeritud mikroorganismi tüvi Lactobacillus plantarum Tensia DSM 21380 kui antimikroobne ja antihüpertensiivne probiotik, toiduprodukt ja Komposition mis sisaldab vastavat mikroorganismi ja selle mikroorganismi kasutus antihüpertensiivse ravimi valmistamiseks ja meetod patogeenide ja mitte-starter laktobatsillide allasurumiseks toiduproduktis. Espacenet 2009, WO2009138091. Strain and patent owner: Bio-Competence Centre of Healthy Dairy Products.

 

Mikelsaar, M.; Songisepp, E.; Smidt, I.; Stsepetova J., Hütt, P.; Zilmer, M.; Truusalu, K.; Kilk, K. PCT/EE2009/000006 Isolated Lactobacillus plantarum strain Inducia DSM 21379 as probiotic that enhances natural immunity and food products and medicinal preparations comprising it. Espacenet 2009, WO2009138092. Strain and patent owner: Bio-Competence Centre of Healthy Dairy Products.2015

 

 

Ph.D. DISSERTATIONS

 

Stanislav Tjagur, 2023, (sup) Margus Punab, Reet Mändar. Mycoplasma genitalium and other sexually transmitted infections causing urethritis - their prevalence, impact on male fertility parameters and prostate health.

Risto Vaikjärv, 2022, (sup) Reet Mändar, Siiri Kõljalg, Jelena Štšepetova, Priit Kasenõmm. Etiopathogenesis and diagnostics of peritonsillar abscess.

Tiina Drell, 2019, (sup) Epp Sepp; Madis Metsis. The Effect of Maternal Microbial Communities and Preterm Birth on the Development of Infant Gut Microbiota.

Veiko Vengerfeldt, 2018, (sup) Reet Mändar; Tiiu Kullisaar; Mare Saag. Apical periodontitis: prevalence and etiopathogenetic aspects.

Piia Jõgi, 2018, (sup) Irja Lutsar; Marje Oona. Epidemiological and clinical characteristics of pertussis in Estonia.

Piret Mitt, 2016, (sup) Matti Maimets; Paul Naaber. Healthcare-associated infections in Estonia - epidemiology and surveillance of bloodstream and surgical site infections.

Soeorg, H. Coagulase-negative staphylococci in gut of preterm neonates and in breast milk of their mothers. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2017.

 

Ausmees, K. Reproductive function in middle-aged males: Associations with prostate, lifestyle and coulpe infertility status. Disserationes Medicinae  Universitatis Tartuensis. Tartu, 2014.

 

Truusalu K. Probiotic lactobacilli in experimental persistent Salmonella infection. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2013.

 

Hütt P. Functional properties, persistence, safety and efficacy of potential probiotic lactobacilli. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2012.

 

Parm Ü. Early mucosal colonisation and its role in prediction of invasive infection in neonates at risk of early onset sepsis. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2012

 

Štšepetova J. The characterisation of intestinal lactic acid bacteria using bacteriological, biochemical and molecular approaches. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2011.

 

Metsvaht T. Optimal antibacterial therapy of neonates at risk of early onset sepsis. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2010.

 

Türk S. Etiopathogenetic aspects of chronic prostatitis: role of mycoplasmas, coryneform bacteria and oxidative stress. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2009.

 

Korrovits P. Asymptomatic inflammatory prostatitis: prevalence, etiological factors, diagnostic tools. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2008.

 

Andreson H. Diversity of Helicobacter pylori genotypes in Estonian patients with chronic inflammatory gastric disease. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2006.

 

Kõll P. Oral lactoflora in chronic periodontitis and periodontal health. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2006.

 

Kasenõmm P. Indicators for tonsillectomy in adults with recurrent tonsillitis clinical, microbiological and pathomorphological investigations. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2005.

 

Songisepp E. Evaluation of technological and functional properties of the new probiotic Lactobacillus fermentum ME-3. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2005

 

Lõivukene, K. Helicobacter pylori in gastric microbial ecology and its antimicrobial susceptibility pattern. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2003.

 

Krüüner, A. Drug-resistant Mycobacterium tuberculosis in Estonia. Karolinska Institutet, Stockholm, Sweden, 2003.

 

Annuk, H. Selection of medicinal plants and intestinal lactobacilli as antimicrobial components for functional foods. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2002.

 

Krüüner, A. Mycobacterium tuberculosis spread and drug resistance in Estonia. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 2001.

 

Kõljalg S. Acinetobacter - an important nosocomial pathogen. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 1999.

 

Sepp E. Formation of intestinal microbial ecosystem in children. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 1998.

 

Naaber P. Clostridium difficile infection and intestinal microbial ecology. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 1997.

 

Mändar R. Vaginal microflora during pregnancy and its transmission to newborn. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 1996.

 

Karki T. Quantitative composition of the human lactoflora and method for its examination. Dissertationes Medicinae Universitatis Tartuensis. Tartu, 1996.

 

 

MSc DISSERTATIONS



Greete Maasi, 2020, (sup) Reet Mändar, Jelena Štšepetova, Merike Jõesaar. Mutans-streptokokkide virulentsusfaktorid.

Siim Isküll, 2018, (sup) Kairi Koort; Paul Naaber. Antibiootikumidele resistentsete Klebsiella pneumoniae genotüübi ja fenotüübi võrdlus.

Katri Pärna, 2015, (sup) Epp Sepp; Siiri Kõljalg; Eve Elken. Integronid Läänemere piirkonna bioloogilistest materjalidest isoleeritud enterobakterites.

Anastasia Bilozor, 2013, (sup) Paul Naaber; Marina Ivanova; Lilian Järvekülg. Application of molecular and phenotypic methods for detection of resistance to carbapenems in Enterobacteriaceae strains isolated in the Baltic region.

Kristiine Pai. Balti regioonis kliinilistest materjalidest isoleeritud Escherichia coli tüvede laiendatud toimega beeta-laktamaaside produktsiooni fenotüübiline ja genotüübiline iseloomustus. Tartu, 2014. Juhendajad: Epp Sepp, Siiri Kõljalg, Andres Mäe.

 

Natalja Šebunova. Erinevate vanuserühmade tervete inimeste soolestiku mikroobikoosluse molekulaarne kvantitatiivne analüüs. Tartu, 2014. Juhendajad: Jelena Štšepetova, Eeva Heinaru.

 

Jana Lillo. Inimese kliinilistest materjalidest ja normaalsest soole mikrofloorast isoleeritud Escherichia coli tüvede virulentsusfaktorid. Tartu, 2013. Juhendajad: Epp Sepp, Siiri Kõljalg, Riho Teras.

 

Ave Ahelik. Oksüdatiivne stress viljatutel paaridel. Tartu, 2013. Juhendajad: Reet Mändar, Tiiu Kullisaar, Sulev Ingerpuu.

 

Eleri Lapp. Kehavälise viljastamise ebaedu põhjused: suguteede põletikud, tervislik seisund ja tervisekäitumine mõlemal partneril. Tartu, 2013. Juhendaja: Reet Mändar.

 

Riinu Kiiker. Ureaplasmad ja laktobatsillid viljatute paaride suguteede mikrobiootas ning seksuaalvahekorra mõju tupe mikroobikooslusele. Tartu, 2013. Juhendajad: Reet Mändar, Jaanis Juhanson.

 

Helen Oopkaup. Piimhappebakterite poolt toodetud bio- ja polüamiinide geeniklastrite biosünteesi molekulaarne analüüs. Tartu, 2013. Juhendajad: Jelena Štšepetova, Eeva Heinaru, Epp Songisepp.

 

Jana Lillo. Inimese kliinilistest materjalidest ja normaalsest soole mikrofloorast isoleeritud Escherichia coli tüvede virulentsusfaktorid. Tartu, 2013. Juhendajad: Epp Sepp, Siiri Kõljalg, Riho Teras.

 

Ave Ahelik. Oksüdatiivne stress viljatutel paaridel. Tartu, 2013. Juhendajad: Reet Mändar, Tiiu Kullisaar, Sulev Ingerpuu.

 

Eleri Lapp. Kehavälise viljastamise ebaedu põhjused: suguteede põletikud, tervislik seisund ja tervisekäitumine mõlemal partneril. Tartu, 2013. Juhendaja: Reet Mändar.

 

Riinu Kiiker. Ureaplasmad ja laktobatsillid viljatute paaride suguteede mikrobiootas ning seksuaalvahekorra mõju tupe mikroobikooslusele. Tartu, 2013. Juhendajad: Reet Mändar, Jaanis Juhanson.

 

Helen Oopkaup. Piimhappebakterite poolt toodetud bio- ja polüamiinide geeniklastrite biosünteesi molekulaarne analüüs. Tartu, 2013. Juhendajad: Jelena Štšepetova, Eeva Heinaru, Epp Songisepp.

 

Borovkova N. Influence of sexual intercourse on vaginal microbiota in infertile couples. Dissertation of Master's Degree. Tartu Ülikool, 2010.

 

Rätsep M. Antimicrobial properties of Lactobacillus plantarum strains and their application possibilities in dairy industry. Dissertation of Master's Degree. Tartu Ülikool, 2009.

 

Drell, T. Development of intestinal microbiota in pre- and fullterm infants. Dissertation of Master's Degree. Tartu Ülikool, 2009.

 

Songisepp, Epp. Lactobacillar starters with special biomarkers: biotechnological management and influence on the lactoflora of products and host. Dissertation of Master's Degree. Tartu, 2002.

 

Andreson, Helena. Molecular virulence markers of Helicobacter pylori strains spread in South Estonia. Dissertation of Master's Degree. Tartu, 2002.

 

Lõivukene K. Antibiotic susceptibility of Helicobacter pylori strains and it's relations with vacA and cagA genotype in patients with gastritis and peptic ulcer. Dissertation of Master's Degree. Tartu, 2000.

 

Smidt I. In vitro and in vivo interaction of intestinal indigenous lactobacilli and opportunistic pathogens Clostridium difficile and Escherichia coli. Dissertation of Master's Degree. Tartu, 1999

 

 

MONOGRAPHIES

 

Naaber, P., Mikelsaar, M. Interactions between lactobacilli and antibiotic-associated diarrhea. In: Advances in Applied Microbiology. Eds. A.I. Laskin, J.W. Bennett, G.M. Gadd. Volume 54. Elsevier Inc., 2004, 231-260.

 

Mikelsaar, M., Mändar, R., Sepp, E., Annuk, H. Human lactic acid microflora and its role in the welfare of the host. In: Lactic Acid Bacteria. Eds. S. Salminen, A. von Wright, A. Ouwehand. Marcel Dekker Inc., 2004, 453-506.

 

Mikelsaar, M., Mändar, R., Sepp, E.. Lactic acid microflora in the human microbial ecosystem and its development. In: Lactic Acid Bacteria, Marcel Dekker, Inc., New York, USA, 1998, 279-342. ISBN 0-8247-0133-X

 

Türk S, Kullisaar T, Korrovits P, Ausmees K, Punab M, Mändar R. (2011). Some etiopathogenetic aspects of chronic prostatitis: mycoplasmas, coryneform bacteria and oxidative stress. Charleston, CreateSpace, 98 p.

 

Korrovits P, Punab M, Mändar R. (2011). Asymptomatic inflammatory prostatitis. Charleston, CreateSpace, 68 p.

 

 

PAPERS IN INTERNATIONAL JOURNALS


2025

Mändar R, Mändar H, Rööp T; Mikelsaar M. Collection of human bacteria at University of Tartu, Estonia. Microbiology Resource Announcements, 2025 Dec 23:e0075825.

Sadam H,  Maruste R, Rähni A, Toots M, Piirsalu M, Pihlas L, Ausman H, Pihlak A, Laasfeld T, Rull K, Salumets A, Antson A, Tillmann V, Aleksejeva A, Rööp T, Štšepetova J, Sepp E, Mändar R, Palm K. Maternal antibodies shape infant immune response development in an epitope-specific manner. EBioMedicine.

Mikelsaar M, Songisepp E, Mändar, R. Teaduspõhiselt probiootikumidest: kas innovatiivsus on jõudnud probiootikumide rakendamiseni? Eesti Arst, 2025, 104 (3), 145-157.

Molina, NM, Canha-Gouveia A, Leones-Banos I, Sola-Leyva A, Vargas E, Ruiz-Duran S, Tenorio C, Clavero-Gilabert A, Mändar R, Altmäe S. The complementary seminovaginal microbiome in health and disease. Reproductive BioMedicine Online, 2025, 50 (5), ARTN 104707.

Mändar R, Smidt I, Rööp T, Hoidmets D, Kilk K, Zilmer M, Ausmees K, Salumets A. Development of probiotics for male reproductive tract health: in vitro experiments and clinical trial on healthy volunteers. Andrologia. 2025(1):000428.  

Peterson C, Tagoma A, Alnek K, Bärenson A, Vorobjova T, Talja I, Janson H, Kirss A, Kõljalg S, Sinkkonen A, Roslund MI, Uibo R, HEDIMED Investigator group. Antibodies against Clostridium butyricum in the children of mothers at risk for gestational diabetes. Immunol Med. 2025.

Štšepetova J, Šebunova N, Voor T, Soeorg H, Rätsep M, Mändar R, Mikelsaar M, Sepp E. Quantitative differences in the human intestinal microbiota through the stages of life: infants, children, adults and the elderly. Microbiol Res. 2025;16(3):60.  

Vorobjova T, Tagoma A, Peterson C, Talja I, Bärenson A, Alnek K, Janson H, Metsküla K, Kirss A, Sepp E, Rööp T, Kõljalg S, Uibo R; HEDIMED Investigator group. The level of I-FABP and IgA/IgG to beta-lactoglobulin in mothers at risk for gestational diabetes and in their children: association with antibodies to Bifidobacterium adolescentis and Bifidobacterium breve. Front Immunol. 2025.


2024

Kalamees R, Soeorg H, Ilmoja ML, Margus K, Lutsar I, Metsvaht T. Prospective validation of a model-informed precision dosing tool for vancomycin treatment in neonates. Antimicrob Agents Chemother. 2024. 

Koshovyi O, Komisarenko M, Osolodchenko T, Komissarenko A, Mändar R, Kõljalg S, et al. Eucalypt extracts prepared by a no-waste method and their 3D-printed dosage forms show antimicrobial and anti-inflammatory activity. Plants. 2024;13(6):2–20.

Mändar R, Saar M, Vaikjärv R, Parm Ü, Kasenõmm P, Kõljalg S, et al. Unveiling the etiology of peritonsillar abscess using next generation sequencing. CMI Commun. 2024;1(Suppl):765. 

Nguyen ATC, Nguyen NTL, Tran TTQ, Nguyen TT, Hoang TTA, Tran LM, Tran KT, Phan TDC, Nguyen XT, Le TM, Le AV, Salumets A, Mändar R. Prevalence and associated factors of bacterial vaginosis among pregnant women in Hue, Vietnam. J Infect Dev Ctries. 2024;18(6):925–931.

Tenson T, Telling K, Mitt P, Sepp E, Naaber P, Lass J, et al. Antibiotic resistance spread and resistance control options. Estonian experience. ImedRxiv 2024.04.02.24304316;

2023

Saar M, Vaikjärv R, Parm Ü, Kasenõmm P, Kõljalg S, Sepp E, Jaagura M, Salumets A, Štšepetova J, Mändar R. Unveiling the etiology of peritonsillar abscess using next generation sequencing. Ann Clin Microbiol Antimicrob. 2023 Nov 8;22(1):98.


Koort K, Sõsa K, Türk S, Lapp E, Talving E, Karits P, Rosenstein K, Jaagura M, Sekavin A, Sõritsa D, Haldre K, Karro H, Korrovits P, Salumets A, Mändar R. Lactobacillus crispatus-dominated vaginal microbiome and Acinetobacter-dominated seminal microbiome support beneficial ART outcome. Acta Obstet Gynecol Scand. 2023 Jul;102(7):921-934.


Mändar R, Sõerunurk G, Štšepetova J, Smidt I, Rööp T, Kõljalg S, Saare M, Ausmees K, Le DD, Jaagura M, Piiskop S, Tamm H, Salumets A. Impact of Lactobacillus crispatus-containing oral and vaginal probiotics on vaginal health: a randomised double-blind placebo controlled clinical trial. Benef Microbes. 2023 Apr 18;14(2):143-152.

 

Anh Thi Chau Nguyen, Na Thi Le Nguyen, Trang Thi Quynh Tran , Tuyen Thi Nguyen, Thu Thi Anh Hoang, Linh Manh Tran, Tuan Tran Khoi, Do Quoc Phan Thanh, Xuan Thanh Nguyen, Minh Tam Le, Van An Le, Andres Salumets, Reet Mändar. (2023). Prevalence and associated factors of bacterial vaginosis among pregnant women in Hue, Vietnam. The Journal of Infection in Developing Countries, x.

 

Lõivukene, K.; Kermes, K.; Sepp, E.; Naaber, P.; Mändar, R.; Kõljalg, S. (2023). Trends in the prevalence and antibiotic susceptibility of anaerobic Gram-negative bacteria causing clinical infections in Estonia. Sri Lankan Journal of Infectious Diseases, 13 (1), 29.

 

Parm Ü, Tiit-Vesingi A, Soeorg H, Štšepetova J, Truusalu K, Vorobjov S, Lutsar I, Metsvaht T. Effect of early directed implementation of family-integrated care measures on colonisation with Enterobacteriaceae in preterm neonates in NICU. BMJ Paediatr Open. 2023 May;7(1):e001712.

 

Štšepetova J, Rätsep M, Gerulis O, Jõesaar A, Mikelsaar M, Songisepp E. Impact of Lactiplantibacillus plantarum Inducia on metabolic and antioxidative response in cholesterol and BMI variable indices: randomised, double-blind, placebo-controlled trials. Benef Microbes. 2023 Mar 14;14(1):1-15. 

2022

Sepp E, Smidt I, Rööp T, Štšepetova J, Kõljalg S, Mikelsaar M, Soidla I, Ainsaar M, Kolk H, Vallas M, Jaagura M, Mändar R. Comparative analysis of gut microbiota in centenarians and young people: impact of eating habits and childhood living environment. Front Cell Infect Microbiol. 2022;12:851404.

Soeorg H, Noortoots A, Karu M, Saks K, Lass J, Lutsar I, Kõrgvee LT. Estimation of cefepime, piperacillin, and tazobactam clearance with iohexol-based glomerular filtration rate in paediatric patients. Eur J Clin Pharmacol. 2022;78(6):989–1001.

Soeorg H, Padari H, Kipper K, Ilmoja ML, Lutsar I, Metsvaht T. Pharmacokinetics of gentamicin components C1, C1a, and C2/C2a/C2b and subsequent decline in glomerular filtration rate in neonates. AAPS J. 2022;24(4):77.

Songisepp E, Štšepetova J, Rätsep M, Kuus L, Piir A, Kilk K, Mikelsaar M. Polyfunctional metabolic properties of the human strain Lactiplantibacillus plantarum Inducia (DSM 21379): experimental and clinical approaches. J Funct Foods. 2022;92:105064.

Šebunova N, Štšepetova J, Kullisaar T, Suija K, Rätsep A, Junkin I, Soeorg H, Lember M, Sillakivi T, Mändar R. Changes in adipokine levels and metabolic profiles following bariatric surgery. BMC Endocr Disord. 2022;22(1):33.

Štšepetova J, Simre K, Tagoma A, Uibo O, Peet A, SSiljander H, Tillmann V, Knip M, Mändar R, Uibo R. Maternal breast milk microbiota and immune markers in relation to subsequent development of celiac disease in offspring. Sci Rep. 2022;12(1):6607.

Maasi G, Štšepetova J, Jõesaar M, Olak J, Mändar R. Different Patterns of Virulence Genes in Streptococcus mutans and Streptococcus sobrinus Originating from Estonian Toddlers—Mothers Cohort. Microbiology Research. 2022; 13(4):928-936.

Nguyen ATC, Le Nguyen NT, Hoang TTA, Nguyen TT, Tran TTQ, Tran DNT, Nguyen ATK, Tran LM, Nguyen DHC, Le TM, Ho BD, Rööp T, Kõljalg S, Štšepetova J, Van Le A, Salumets A, Mändar R. Aerobic vaginitis in the third trimester and its impact on pregnancy outcomes. BMC Pregnancy Childbirth. 2022 May 24;22(1):432.

Štšepetova J, M. Rätsep, O. Gerulis, A. Jõesaar, M. Mikelsaar, E. Songisepp. Impact of Lactiplantibacillus plantarum Inducia on metabolic and antioxidative response in cholesterol and BMI variable indices: randomised, double-blind, placebo-controlled trials. Beneficial Microbes, ISSN 1876-2883 print, ISSN 1876-2891. 

 

Cook A, Sharland M, Yau Y, Group P, Bielicki J; PediBSI Group (Kõljalg S). Improving empiric antibiotic prescribing in pediatric bloodstream infections: a potential application of weighted-incidence syndromic combination antibiograms (WISCA). Expert Rev Anti Infect Ther. 2022 Mar;20(3):445-456.

 

2021


Tjagur S, Mändar R, Poolamets O, Pomm K, Punab M. Mycoplasma genitalium Provokes Seminal Inflammation among Infertile Males. Int J Mol Sci. 2021 Dec 15;22(24):13467. PMID: 34948264; PMCID: PMC8707260.

Šebunova N, Štšepetova J, Kullisaar T, Suija K, Rätsep A, Junkin I, Soeorg H, Lember M, Sillakivi T, Mändar R. Changes in adipokine levels and metabolic profiles following bariatric surgery. BMC Endocr Disord. Feb 3;22(1):33. PMID: 35114975; PMCID: PMC8812034.

Kõljalg, S.; Vaikjärv, R.; Smidt, I.; Rööp, T.; Chakrabarti, A.; Kasenõmm, P.; Mändar, R. (2021). Effect of erythritol and xylitol on Streptococcus pyogenes causing peritonsillar abscesses. Scientific Reports, 11 (1):15855.

Mikelsaar, Marika; Mändar, Reet. (2021). Commentary: Gut Microbiome and Space Travelers' Health: State of the Art and Possible Pro/Prebiotic Strategies for Long-Term Space Missions. Frontiers in Physiology, Mar 23;12:651977.

2020


Tjagur, Stanislav; Mändar, Reet; Punab, Margus (2020). Profile of sexually transmitted infections causing urethritis and a related inflammatory reaction in urine among heterosexual males: A flow-cytometry study. PLoS ONE, 15 (12), e0242227.

Mikelsaar, Marika; Jelena Štšepetova , Raik-Hiio Mikelsaar, Kai Truusalu, Imbi Smidt, Pirje Hütt, Merle Rätsep, Epp Songisepp (2020). Polyamines of human strain Lactobacillus plantarum Inducia induce modulation of innate immune markers. Journal of Functional Foods, 72, 19.

Telling K, Brauer A, Laht M, Kalmus P, Toompere K, Kisand V, Maimets M, Remm M, Tenson T, Lutsar I. Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia. Microorganisms. 2020 Jul 27;8(8):1130.

Kõljalg, Siiri; Smidt, Imbi; Chakrabarti, Anirikh; Bosscher, Douwina; Mändar, Reet (2020). Exploration of singular and synergistic effect of xylitol and erythritol on causative agents of dental caries. Scientific Reports, 10 (1), 6297.

Štšepetova , J.; Baranova, J.; Simm, J.; Parm, Ü.; Rööp, T.; Sokmann, S.; Korrovits, P.; Jaagura, M.; Rosenstein, K.; Salumets, A.; Mändar, R. (2020). The complex microbiome from native semen to embryo culture environment in human in vitro fertilization procedure. Reproductive Biology and Endocrinology, 18 (1), 113.

Mändar, Reet; Korrovits, Paul; Rahu, Kaja; Rahu, Mati; Sibul, Eeva Liisa; Mehik, Aare.; Punab, Margus. (2020). Dramatically deteriorated quality of life in men with prostatitis like symptoms. Andrology, 8 (1), 101109.


2019


Sepp E, Andreson R, Balode A, Bilozor A, Brauer A, Egorova S, Huik K, Ivanova M, Kaftyreva L, Kõljalg S, Kõressaar T, Makarova M, Miciuleviciene J, Pai K, Remm M, Rööp T, Naaber P. Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe. Front Microbiol. 2019 Nov 22;10:2465. 

Altmäe, Signe; Franasiak, Jason; Mändar, Reet. (2019). The seminal microbiome in health and disease. Nature Reviews Urology, 16 (12), 702721.

Minh Tam Le, Thi Le Na Nguyen, Duong Dinh Le, Tram Viet Quynh Ngo, Anh Thi Chau Nguyen, Bach Hoang Nguyen, Huy Vu Quoc Nguyen, Thanh Ngoc Cao, Andres Salumets, Reet Mändar. (2019). Does genital tract infection relate to tubal diseases in Vietnamese infertile women? The Journal of Infection in Developing Countries, 13 (10), 906913.

Bilozor, Anastasia; Balode, Arta; Chakhunashvili, Giorgi; Chumachenko, Tetyana; Egorova, Svetlana; Ivanova, Marina; Kaftyreva, Liidia; Kõljalg, Siiri; Kõressaar, Triinu; Lysenko, Olga; Miciuleviciene, Jolanta; Mändar, Reet; Lis, Danuta O.; Wesolowska, Monika Pomorska; Ratnik, Kaspar; Remm, Maido; Rudzko, Jelena; Rööp, Tiiu; Saule, Mara; Sepp, Epp ... Naaber, Paul (2019). Application of Molecular Methods for Carbapenemase Detection. Frontiers in Microbiology, 10, ARTN 1755.

Vaikjärv, Risto; Mändar, Reet; Kasenõmm, Priit (2019). Peritonsillar abscess is frequently accompanied by sepsis symptoms. European Archives of Oto-Rhino-Laryngology, 276 (6), 17211725.

Štšepetova , Jelena; Truu, Jaak; Runnel, Riina; Nõmmela, Rita; Saag, Mare; Olak, Jana; Nõlvak, Hiie; Preem, Jens-Konrad; Oopkaup, Kristjan; Krjutškov, Kaarel; Honkala, Eino; Honkala, Sisko; Mäkinen, Kauko; Mäkinen, Pirkko-Liisa; Vahlberg, Tero; Vermeiren, Joan; Bosscher, Douwina; de Cock, Peter; Mändar, Reet (2019). Impact of polyols on Oral microbiome of Estonian schoolchildren. BMC Oral Health, 19, ARTN 60.

Rostok, Mariheleen; Hütt, Pirje; Rööp, Tiiu; Smidt, Imbi; Štšepetova, Jelena; Salumets, Andres; Mändar, Reet. (2019). Potential vaginal probiotics: safety, tolerability and preliminary effectiveness. Beneficial Microbes, 10 (4), 385393.

Soeorg, Hiie; Metsvaht, Hanna Kadri; Keränen, Evamaria Elisabet; Eelmäe, Imbi; Merila, Mirjam; Ilmoja, Mari-Liis; Metsvaht, Tuuli; Lutsar, Irja. (2019). Genetic Relatedness of Staphylococcus haemolyticus in Gut and Skin of Preterm Neonates and Breast Milk of Their Mothers. The Pediatric Infectious Disease Journal Mar;38(3):308-313.

2018


Sepp, Epp; Smidt, Imbi; Stsepetova, Jelena; Roop, Tiiu; Hutt, Pirje; Ratsep, Merle; Mikelsaar, Marika (2018). The effect of Lactobacillus fermentum ME-3 on the intestinal microbiota and urine polyamines content: A double-blind placebo-controlled pilot trial. Journal of Functional Foods, 48, 430438.

Telling, Kaidi; Laht, Mailis; Brauer, Age; Remm, Maido; Kisand, Veljo; Maimets, Matti; Tenson, Tanel; Lutsar, Irja (2018). Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals. BMC Infectious Diseases, 18 (1), ARTN 513.

Sepp, Epp; Smidt, Imbi; Štšepetova , Jelena; Rööp, Tiiu; Hütt, Pirje; Rätsep, Merle; Mikelsaar, Marika (2018). The effect of Lactobacillus fermentum ME-3 on the intestinal microbiota and urine polyamines content: A double-blind placebo-controlled pilot trial. Journal of Functional Foods, 48, 430438.

Parm, Ülle; Štšepetova , Jelena; Eelmäe, Imbi; Merila, Mirjam; Ilmoja, Mari-Liis; Metsvaht, Tuuli; Lutsar, Irja; Soeorg, Hiie (2018). Genetic relatedness of Gram-negative bacteria colonizing gut and skin of neonates and mother's own milk. Journal of Perinatology, 38, 15031511.

Soeorg, Hiie; Treumuth, Sirli; Metsvaht, Hanna Kadri; Eelmäe, Imbi; Merila, Mirjam; Ilmoja, Mari-Liis; Lutsar, Irja; Metsvaht, Tuuli. (2018). Higher intake of coagulase-negative staphylococci from maternal milk promotes gut colonization with mecA-negative Staphylococcus epidermidis in preterm neonates. Journal of Perinatology Oct;38(10):1344-1352.

Ausmees K, Ehrlich-Peets K, Vallas M, Veskioja A, Rammul K, Rehema A, Zilmer M, Songisepp E, Kullisaar T. (2018). Fermented whey-based product improves the quality of life of males with moderate lower urinary tract symptoms: A randomized double-blind study. PLoS ONE Feb 23;13(2):e0191640.


Mändar, Reet; Türk, Silver; Korrovits, Paul; Ausmees, Kristo; Punab, Margus. (2018). Impact of sexual debut on culturable human seminal microbiota. Andrology, 6 (3), 510512.

Bichele, R.; Kärner, J.; Truusalu, K.; Smidt, I.; Mändar, R.; Conti, HR.; Gaffen, SL.; Peterson, P.; Laan, M.; Kisand, K. (2018). IL-22 neutralizing autoantibodies impair fungal clearance in murine oropharyngeal candidiasis model. European Journal of Immunology, 48(3), 464470.

Šebunova, Natalja; Štšepetova , Jelena; Sillakivi, Toomas; Mändar, Reet (2018). The prevalence of Helicobacter pylori in Estonian bariatric surgery patients. International Journal of Molecular Sciences, 19 (2), 110.

2017

 

Vengerfeldt, Veiko; Mändar, Reet; Nguyen, Minh Son; Saukas, Silvia; Saag, Mare. (2017). Apical periodontitis in southern Estonian population: prevalence and associations with quality of root canal fillings and coronal restorations. BMC Oral Health, 17 (1), 147.

Vengerfeldt, Veiko; Mändar, Reet; Saag, Mare; Piir, Anneli; Kullisaar, Tiiu (2017). Oxidative stress in patients with endodontic pathologies. Journal of Pain Research, 10, 20312040.

Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido (2017). StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ, 5, ARTN e3353e3353.

Soeorg H, Metsvaht T, Eelmäe I, Metsvaht HK, Treumuth S, Merila M, Ilmoja ML, Lutsar I. Coagulase-Negative Staphylococci in Human Milk From Mothers of Preterm Compared With Term Neonates. J Hum Lact. 2017 May;33(2):329-340.

 

Ahonen, M.; Kahru, A.; Ivask, A.; Kasemets, K.; Kõljalg,S.; Mantecca, P.; Vinkovi Vrek, I.; Keinänen-Toivola, M.; Crijns, F. (2017). Proactive Approach for Safe Use of Antimicrobial Coatings in Healthcare Settings: Opinion of the COST Action Network AMiCI. International Journal of Environmental Research and Public Health, 14 (4), 366.

Drell, Tiina; Štšepetova, Jelena; Simm, Jaak; Rull, Kristiina; Aleksejeva, Aira; Antson, Anne; Tillmann, Vallo; Metsis, Madis; Sepp, Epp; Salumets, Andres; Mändar, Reet. (2017). The Influence of Different Maternal Microbial Communities on the Development of Infant Gut and Oral Microbiota. Scientific Reports, 7, 9940.

 

Mändar, Reet; Punab, Margus; Korrovits, Paul; Türk, Silver; Ausmees, Kristo; Lapp, Eleri; Preem, Jens-Konrad; Oopkaup, Kristjan; Salumets, Andres; Truu, Jaak. (2017). Seminal microbiome in men with and without prostatitis. International Journal of Urology, 24(3): 211-216.

 

Korrovits, Paul; Poolamets, Olev; Mändar, Reet; Punab, Margus (2017). Inflammatory reaction found in prostate-specific material - method standardization and proposed optimal cut-off points. Andrology, 5(5): 958-963.

 

Kõljalg, Siiri; Mändar, Rando; Sõber, Tiina; Rööp, Tiiu; Mändar, Reet. (2017). High level bacterial contamination of secondary school students' mobile phones. Germs, 7, 73?77.10.18683/germs.2017.1111.

 

Rätsep M.; Kõljalg S.; Sepp E.; Smidt I.; Truusalu K.; Songisepp E.; Stsepetova J.; Naaber P.; Mikelsaar R.H.; Mikelsaar M. (2017). A combination of the probiotic and prebiotic product can prevent the germination of Clostridium difficile spores and infection. Anaerobe, 47, 94?103.

 

Tjagur, Stanislav; Mändar, Reet; Punab, Margus. (2017). Prevalence of Mycoplasma genitalium and other sexually transmitted infections causing urethritis among high-risk heterosexual male patients in Estonia. Infectious Diseases, x.10.1080/23744235.2017.1366044.

 

Soeorg, Hiie; Metsvaht, Tuuli; Eelmäe, Imbi; Metsvaht, Hanna Kadri; Treumuth, Sirli; Merila, Mirjam; Ilmoja, Mari-Liis; Lutsar, Irja (2017). Coagulase-Negative Staphylococci in Human Milk From Mothers of Preterm Compared With Term Neonates. Journal of human lactation : official journal of International Lactation Consultant Association, 33 (2), 329?340.

 

Soeorg H, Huik K, Parm Ü, Ilmoja ML, Metsvaht T, Lutsar I (2017). Molecular epidemiology of Staphylococcus epidermidis in neonatal intensive care units. APMIS, 125, 63?73.

 

Soeorg, Hiie; Metsvaht, Tuuli; Eelmäe, Imbi; Merila, Mirjam; Treumuth, Sirli; Huik, Kristi; Jürna-Ellam, Marika; Ilmoja, Mari-Liis; Lutsar, Irja (2017). The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci. Pediatric Research, 82 (5), 759?767.

 

Štšepetova , Jelena; Taelma, Heleri; Smidt, Imbi; Hütt,Pirje; Lapp, Eleri; Aotäht, E; Mändar, Reet (2017). Assessment of phenotypic and genotypic antibiotic susceptibility of vaginal Lactobacillus sp. Journal of Applied Microbiology, 123, 524?534.

 

2016

 

Padari, Helgi; Oselin, Kersti; Tasa, Tõnis; Metsvaht, Tuuli; Lõivukene, Krista; Lutsar, Irja (2016). Coagulase negative staphylococcal sepsis in neonates: do we need to adapt vancomycin dose or target? BMC Pediatrics, 16 (1), 206?206.

 

Vaikjärv, Risto; Kasenõmm, Priit; Jaanimäe, Liis; Kivisild, Ave; Rööp, Tiiu; Sepp, Epp; Mändar, Reet. (2016). Microbiology of peritonsillar abscess in the South Estonian population. Microbial Ecology in Health and Disease, 27, 27787.

 

Mändar, Karsten; Sõber, Tiina; Kõljalg, Siiri; Rööp, Tiiu; Mändar, Reet; Sepp, Epp. (2016). Microbiological contamination of the euro currency in Estonia. Infectious Diseases, 48 (10), 772?774, 10.1080/23744235.2016.1201725.

 

2015

 

Mikelsaar, Marika; Sepp, Epp; Štšepetova , Jelena; Hütt, Pirje; Zilmer, Kersti; Kullisaar, Tiiu; Zilamer, Mihkel. (2015). Regulation of plasma lipid profile by lactobacillus fermentum (probiotic strain ME-3 DSM14241) in a randomised controlled trial of clinically healthy adults. BMC Nutrition, 1 (27), 1?13, s40795-015-0020-z.

 

Smidt, Imbi; Kiiker, Riinu; Oopkaup, Helen; Lapp, Eleri; Rööp, Tiiu; Truusalu, Kai; Štšepetova, Jelena; Truu, Jaak; Mändar, Reet. (2015). Comparison of detection methods for vaginal lactobacilli . Beneficial Microbes, 2015 Apr 13:1-5

 

Mändar, Reet; Punab, Margus; Borovkova, Natalja; Lapp, Eleri; Kiiker, Riinu; Korrovits, Paul; Metspalu, Andres; Krjutškov, Kaarel; Nõlvak, Hiie; Preem, Jens-Konrad; Oopkaup, Kristjan; Salumets, Andres; Truu, Jaak. (2015). Complementary seminovaginal microbiome in couples. Research in Microbiology, 166(5), 440-7

 

Korrovits, Paul; Lapp, Eleri; Mändar, Reet. (2015). Couple-related factors of ART outcome. Clinical & Experimental Obstetrics & Gynecology, 166(5), 440-7.

 

Drell, Tiina; Larionova, Anneli; Voor, Tiia; Simm, Jaak; Julge, Kaja; Heilman, Kaire; Tillmann, Vallo; Štšepetova, Jelena; Sepp, Epp (2015). Differences in Gut Microbiota Between Atopic and Healthy Children. Current Microbiology, 71(2), 177 - 183.

 

Parm, Ülle; Metsvaht, Tuuli; Ilmoja, Mari-Liis; Lutsar, Irja (2015). Gut colonization by aerobic microorganisms is associated with route and type of nutrition in premature neonates. Nutrition Research, 35(6), 496 - 503.

 

Hütt, Pirje; Songisepp, Epp; Rätsep, Merle; Mahlapuu, Riina; Kilk, Kilk; Mikelsaar, Marika. (2015). Impact of probiotic L. plantarum TENSIA in different dairy products on anthropometric and blood biochemical indices of healthy adults. Beneficial Microbes, 2015; 6(3):233-43. 

 

Putrinš, Marta; Kogermann, Karin; Lukk, Eliisa; Lippus, Markus; Varik, Vallo; Tenson, Tanel (2015). Phenotypic heterogeneity enables uropathogenic Escherichia coli to evade killing by antibiotics and serum complement . Infection and immunity, 83(3), 1056 - 1067. 

 

 

2014

 

Rätsep, Merle; Naaber, Paul; Kõljalg, Siiri; Shkut, Elena; Sepp, Epp (2014). Effect of Lactobacillus Strain on Clinical Isoletes of Clostridium difficile in vitro. Journal of Probiotics and Health, 2, 1?5, 2329-8901.1000119

 

Kõljalg S, Telling K, Huik K, Murruste M, Saarevet V, Pauskar M, Lutsar I. First report of Wohlfahrtiimonas chitiniclastica from soft tissue and bone infection at an unusually high northern latitude. Folia Microbiol (Praha). 2014 Oct 11. [Epub ahead of print]

 

Drell T, Lutsar I, Stšepetova J, Parm U, Metsvaht T, Ilmoja ML, Simm J, Sepp E. The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing. Gut Microbes. 2014 May-Jun;5(3):304-12.

 

Kõljalg, Siiri; Truusalu, Kai; Štšepetova, Jelena; Pai, Kristiine; Vainumäe, Inga; Sepp, Epp; Mikelsaar, Marika (2014). The Escherihia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary tract infections. APMIS, 122(5), 452 - 458.

 

Lillo J, Pai K, Balode A, Makarova M, Huik K, Kõljalg S, Ivanova M, Kaftyreva L, Miciuleviciene J, Naaber P, Parv K, Pavelkovich A, Rööp T, Toompere K, Suzhaeva L, Sepp E. Differences in Extended-Spectrum Beta-Lactamase Producing Escherichia coli Virulence Factor Genes in the Baltic Sea Region. Biomed Res Int. 2014;2014:427254.

 

Lutsar I, Chazallon C, Carducci FI, Trafojer U, Abdelkader B, de Cabre VM, Esposito S, Giaquinto C, Heath PT, Ilmoja ML, Katragkou A, Lascoux C, Metsvaht T, Mitsiakos G, Netzer E, Pugni L, Roilides E, Saidi Y, Sarafidis K, Sharland M, Usonis V, Aboulker JP; NeoMero Consortium. Current management of late onset neonatal bacterial sepsis in five European countries. Eur J Pediatr. 2014 Aug;173(8):997-1004.

 

Lutsar I, Telling K, Metsvaht T. Treatment option for sepsis in children in the era of antibiotic resistance. Expert Rev Anti Infect Ther. 2014 Oct;12(10):1237-52.

 

Mitt, P.; Metsvaht, T.; Adamson, V.; Telling, K..; Naaber, P.; Lutsar, I.; Maimets , M. (2014). Five-year prospective surveillance of nosocomial bloodstream infections in an Estonian paediatric intensive care unit. Journal of Hospital Infection, 86(2), 95 - 99.

 

Pavelkovich, Anastasia; Balode, Arta; Edquist, Petra; Egorova, Svetlana; Ivanova, Marina; Kaftyreva, Lidia; Konovalenko, Irina; Kõljalg, Siiri; Lillo, Jana; Lipskaya, Lidia; Miciuleviciene, Jolanta; Pai, Kristiine; Parv, Kristel; Pärna, Katri; Rööp, Tiiu; Sepp, Epp; Štšepetova, Jelena; Naaber, Paul (2014). Detection of Carbapenemase-Producing Enterobacteriaceae in the Baltic Countries and St. Petersburg Area. BioMed Research International, 2014, Article 548960

 

Sepp E, Kolk H, Lõivukene K, Mikelsaar M. Higher blood glucose level associated with body mass index and gut microbiota in elderly people. Microb Ecol Health Dis. 2014 Jun 3;25.

 

Talja I, Kubo AL, Veijola R, Knip M, Simell O, Ilonen J, Vähä-Mäkilä M, Sepp E, Mikelsaar M, Utt M, Uibo R. Antibodies to Lactobacilli and Bifidobacteria in young children with different propensity to develop islet autoimmunity. J Immunol Res. 2014;2014:325938.

 

Türk S, Mazzoli S, Stšepetova J, Kuznetsova J, Mändar R. Coryneform bacteria in human semen: inter-assay variability in species composition detection and biofilm production ability. Microb Ecol Health Dis. 2014 Feb 14;25.

 

Vengerfeldt V, Spilka K, Saag M, Preem JK, Oopkaup K, Truu J, Mändar R. Highly Diverse Microbiota in Dental Root Canals in Cases of Apical Periodontitis (Data of Illumina Sequencing). J Endod. 2014 Sep 13. pii: S0099-2399(14)00574-3.

 

 

2013

Ausmees K, Korrovits P, Timberg G, Punab M, Mändar R. (2013). Semen quality and associated reproductive indicators in middle-aged males: the role ofnon-malignant prostate conditions and genital tract inflammation. World J Urol. 2013 Dec;31(6):1411-25.

 

Brilene T, Soeorg H, Kiis M, Sepp E, Kõljalg S, Lõivukene K, Jürna-Ellam M,Kalinina J, Stšepetova J, Metsvaht T, Lutsar I. (2013)  In vitro synergy of oxacillin andgentamicin against coagulase-negative staphylococci from blood cultures ofneonates with late-onset sepsis. APMIS. Sep;121(9):859-64.

 

Lill, M.; Kõks, S.; Soomets, U.; Schalkwyk, LC.; Fernandes, C.; Lutsar, I.; Taba, P. (2013). Peripheral blood RNA gene expression profiling in patients with bacterial meningitis. Frontiers in Neuroscience, 7, 33.

 

Mändar, Reet (2013). Microbiota of male genital tract: Impact on the health of man and his partner. Pharmacological Research, 69(1), 32 - 41.

 

Punab, Margus; Kullisaar, Tiiu; Mändar, Reet (2013). Male Infertility Workup Needs Additional Testing of Expressed Prostatic Secretion and/or Post-Massage Urine . PLoS ONE, 8(12), e82776

 

Sepp, E.; Lõivukene, K.; Julge, K.; Voor, T.; Mikelsaar, M. (2013). The association of gut microbiota with body weight and body mass index in preschool children of Estonia. Microbial Ecology in Health and Disease, 24, 19231

 

Sharafedtinov KK, Plotnikova OA, Alexeeva RI, Sentsova TB, Songisepp E, Štšepetova J, Smidt I, Mikelsaar M. Hypocaloric diet supplemented with probiotic cheese improves body mass index and blood pressure indices of obese hypertensive patients--a randomized double-blind placebo-controlled pilot study. Nutr J. 2013 Oct 12;12:138.

 

Soeorg H, Huik K, Parm U, Ilmoja ML, Metelskaja N, Metsvaht T, Lutsar I. (2013). Genetic relatedness of coagulase-negative Staphylococci from gastrointestinal tract and blood of preterm neonates with late-onset sepsis. Pediatr Infect Dis J. Apr;32(4):389-93.

 

 

 

2012

 

Adamson, V.; Mitt, P.; Pisarev, H.; Metsvaht, T.; Telling, K.; Naaber, P.; Maimets, M. (2012). Prolonged outbreak of Serratia marcescens in Tartu University hospital: a case-control study. BMC Infectious Diseases, 12(1), 281

 

Songisepp, E.; Hütt, P.; Rätsep, M.; Shkut, E.; Kõljalg, S.; Truusalu, K.; Štšepetova, J.; Smidt, I.; Kolk, H.; Zagura, M.; Mikelsaar, M. (2012). Safety of probiotic cheese containing Lactobacillus plantarum Tensia according to a variety of health indices in different age groups. Journal of Dairy Science, 95(10), 5495 - 5509.

 

Mikelsaar, Marika; Hütt, Pirje; Štšepetova, Jelena; Smidt, Imbi; Shkut, Elena; Rätsep, Merle; Zilmer, Mihkel; Songisepp, Epp (2012). Probiotic Heart cheese "Harmony" comprising L. plantarum Tensia influences blood pressure and metabolic health indices (in Russian). Voprossõ pitanija, 81(3), 74 - 81.

 

 

2011

 

Metsvaht T, Ilmoja ML, Parm U, Merila M, Maipuu L, Müürsepp P, Julge K, Sepp E, Lutsar I. Ampicillin versus penicillin in the empiric therapy of ELBW neonates at risk of early onset sepsis. Pediatr Int. 2011 Sep 5. doi: 10.1111/j.1442-200X.2011.03468.x. [Epub ahead of print] PubMed PMID: 21895866.

 

Parm Ü, Metsvaht T, Sepp E, Ilmoja ML, Pisarev H, Pauskar M, Lutsar I. Mucosal surveillance cultures in predicting Gram-negative late-onset sepsis in neonatal intensive care units. J Hosp Infect. 2011 Aug;78(4):327-32. PubMed PMID: 21684633.

 

Parm U, Metsvaht T, Sepp E, Ilmoja ML, Pisarev H, Pauskar M, Lutsar I. Risk factors associated with gut and nasopharyngeal colonization by common Gram-negative species and yeasts in neonatal intensive care units patients. Early Hum Dev. 2011 Jun;87(6):391-9. Epub 2011 Mar 21. PubMed PMID: 21419584.

 

Lutsar I, Trafojer UM, Heath PT, Metsvaht T, Standing J, Esposito S, Meiffredy de Cabre V, Oeser C, Aboulker JP. Meropenem vs standard of care for treatment of late onset sepsis in children of less than 90 days of age: study protocol for a randomised controlled trial. Trials. 2011 Sep 30;12(1):215. [Epub ahead of print] PubMed PMID: 21958494.

 

Hütt P, Kõll P, Stsepetova J, Alvarez B, Mändar R, Krogh-Andersen K, Marcotte H, Hammarström L, Mikelsaar M. (2011). Safety and persistence of orally administered human Lactobacillus sp. strains in healthy adults. Beneficial Microbes 2: 79-90.

 

Borovkova N, Korrovits P, Ausmees K, Türk S, Jõers K, Punab M, Mändar R. (2011). Influence of sexual intercourse on genital tract microbiota in infertile couples. Anaerobe, in press.

 

Sepp E, Štšepetova J, Smidt I, Rätsep M, Kõljalg S, Lõivukene K, Mändar R, Jaanimäe L, Löhr IH, Natås OB, Naaber P. (2011). Intestinal lactoflora in Estonian and Norwegian patients with antibiotic associated diarrhea. Anaerobe, in press.

 

Štšepetova, J.; Sepp, E.; Kolk, H.; Lõivukene, K.; Songisepp, E.; Mikelsaar, M. (2011). Diversity and metabolic impact of intestinal Lactobacillus sp. in healthy adults and the elderly. British Journal of Nutrition, 1 - 10.

 

Uibo, R.; Panarina, M.; Teesalu, K.; Talja, I.; Sepp, E.; Utt, M.; Mikelsaar, M.; Heilman, K.; Uibo, O.; Vorobjova, T. (2011). Celiac disease in patients with type 1 diabetes: a condition with distinct changes in intestinal immunity? Cellular and Molecular Immunology, 8(2), 150 - 156.

Mikelsaar, M. (2011). Human microbial ecology: lactobacilli, probiotics, selective decontamination. Anaerobe, 1 - 5.

 

Kullisaar, T.; Štšepetova, J.; Zilmer, K.; Songisepp, E.; Rehema, A.; Mikelsaar, M.; Zilmer, M. (2011). An antioxidant probiotic reduces postprandial lipemia and oxidative stress. Central European Journal of Biology, 6, 32 - 40.

 

Metsvaht, T.; Ilmoja, ML.; Parm, U.; Merila, M.; Maipuu, L.; Müürsepp, P.; Julge, K.; Sepp, E.; Lutsar, I. (2011). Ampicillin versus penicillin in the empiric therapy of ELBW neonates at risk of early onset sepsis. Pediatrics International, xx(xx), x - x. [ilmumas]

 

Naaber, Paul; Štšepetova, Jelena; Smidt, Imbi; Rätsep, Merle; Kõljalg, Siiri; Lõivukene, Krista; Jaanimäe, Liis; Löhr, Iren; Natås, Olav; Truusalu, Kai; Sepp, Epp (2011). Quantification of Clostridium difficile in Antibiotic-Associated Diarrhea Patients. Journal of Clinical Microbiology, xx [ilmumas]

 

 

2010

 

Kõll P, Mändar R, Smidt I, Hütt P, Truusalu K, Mikelsaar RH, Shchepetova J, Krogh-Andersen K, Marcotte H, Hammarström L, Mikelsaar M. Screening and evaluation of human intestinal lactobacilli for the development of novel gastrointestinal probiotics. Curr Microbiol. 2010 Dec;61(6):560-6. Epub 2010 May 5. PubMed PMID: 20443005.

 

Kullisaar T, Songisepp E, Aunapuu M, Kilk K, Arend A, Mikelsaar M, Rehema A, Zilmer M. Complete glutathione system in probiotic Lactobacillus fermentum ME-3. Prikl Biokhim Mikrobiol. 2010 Sep-Oct;46(5):527-31. PubMed PMID: 21058502.

 

Lutsar I, Metsvaht T. Understanding pharmacokinetics/pharmacodynamics in managing neonatal sepsis. Curr Opin Infect Dis. 2010 Jun;23(3):201-7. Review. PubMed PMID: 20179595.

 

Metsvaht T, Ilmoja ML, Parm U, Maipuu L, Merila M, Lutsar I. Comparison of ampicillin plus gentamicin vs. penicillin plus gentamicin in empiric treatment of neonates at risk of early onset sepsis. Acta Paediatr. 2010 May;99(5):665-72. Epub 2010 Jan 20. PubMed PMID: 20096030.

 

Mikelsaar M, Štšepetova J, Hütt P, Kolk H, Sepp E, Lõivukene K, Zilmer K, Zilmer M. Intestinal Lactobacillus sp. is associated with some cellular and metabolic characteristics of blood in elderly people. Anaerobe. 2010 Jun;16(3):240-6. Epub 2010 Mar 17. PubMed PMID: 20223288.

 

Pähkla ER, Jõgi E, Nurk A, Pisarev H, Koppel T, Naaber P, Saag M, Lõivukene K. Periodontal disease in mothers indicates risk in their children. Int J Paediatr Dent. 2010 Jan;20(1):24-30. PubMed PMID: 20059590.

 

Parm U, Metsvaht T, Sepp E, Ilmoja ML, Pisarev H, Pauskar M, Lutsar I. Impact of empiric antibiotic regimen on bowel colonization in neonates with suspected early onset sepsis. Eur J Clin Microbiol Infect Dis. 2010 Jul;29(7):807-16. Epub  2010 May 6. PubMed PMID: 20446013.

 

Smidt, I.; Sepp, E.; Rätsep, M.; Kõljalg, S.; Lõivukene, K.; Löhr, I.; Natas, O.; Mändar, R.; Naaber, P. (2010). Quantitative evaluation of Clostridium difficile and intestinal lactobacilli in patients with associated diarrhoea. In: Clinical Microbiology and Infection: 20th European Congress of Clinical Microbiology and Infectious Diseases, Vienna, Austria 10-13 april 2010. , 2010, (2), S575.

 

Suitso, I.; Jõgi, E.; Talpsep, E.; Naaber, P.; Lõivukene, K.; Ots, M.-L.; Michelson, T.; Nurk, A. (2010). Protective effect by Bacillus smithii TBMI12 spores of Salmonella Enteritidis in mice. Beneficial Microbes, 37 - 42.

 

Truusalu K, Kullisaar T, Hütt P, Mahlapuu R, Aunapuu M, Arend A, Zilmer M, Mikelsaar RH, Mikelsaar M. Immunological, antioxidative, and morphological response in combined treatment of ofloxacin and Lactobacillus fermentum ME-3 probiotic in Salmonella Typhimurium murine model. APMIS. 2010 Nov;118(11):864-72. doi: 10.1111/j.1600-0463.2010.02672.x. Epub 2010 Sep 14. PubMed PMID: 20955459.

 

Walsh TJ, Driscoll T, Milligan PA, Wood ND, Schlamm H, Groll AH, Jafri H, Arrieta AC, Klein NJ, Lutsar I. Pharmacokinetics, safety, and tolerability of voriconazole in immunocompromised children. Antimicrob Agents Chemother. 2010 Oct;54(10):4116-23. Epub 2010 Jul 26. PubMed PMID: 20660687; PubMed Central PMCID: PMC2944563.

 

 

2009

 

Metsvaht T., Pisarev H., Ilmoja M. L., Parm U., Maipuu L., Merila M., Muursepp P. & Lutsar I. (2009) Clinical parameters predicting failure of empirical antibacterial therapy in early onset neonatal sepsis, identified by classification and regression tree analysis. BMC Pediatr 9, 72.

 

Sepp E., Stsepetova J., Loivukene K., Truusalu K., Koljalg S., Naaber P. & Mikelsaar M. (2009) The occurrence of antimicrobial resistance and class 1 integrons among commensal Escherichia coli isolates from infants and elderly persons. Ann Clin Microbiol Antimicrob 8, 34.

 

Domeika M., Savicheva A., Sokolovskiy E., Frigo N., Brilene T., Hallen A., Unemo M., Ballard R. C. & Ward M. (2009) Guidelines for the laboratory diagnosis of Chlamydia trachomatis infections in East European countries. J Eur Acad Dermatol Venerol. 23:1353-1363.

 

Türk S, Punab M, Mändar R. Antimicrobial susceptibility patterns of coryneform bacteria isolated from semen. Open Infect Dis J, 2009; 3: 31-36.

 

Lutsar, I., I. Anca, M. Bakir, V. Usonis, R. Prymula, N. Salman, P. Grezesiowski, and M. Greenberg. 2008. Epidemiological characteristics of pertussis in Estonia, Lithuania, Romania, the Czech Republic, Poland and Turkey-1945 to 2005.  Eur J Pediatr. 2009 Apr;168(4):407-15.

 

Hütt P, Andreson H, Kullisaar T, Vihalemm T, Unt E, Kals J, Kampus P, Zilmer M, Mikelsaar M. Effects of a synbiotic product on blood antioxidative activity in subjects colonized with Helicobacter pylori. Lett Appl Microbiol. 2009 Jun;48(6):797-800.

 

Karlsson MO, Lutsar I, Milligan PA. Population pharmacokinetic analysis of voriconazole plasma concentration data from pediatric studies. Antimicrob Agents Chemother. 2009 Mar;53(3):935-44.

 

Kõljalg S, Truusalu K, Vainumäe I, Štšepetova J, Sepp E, Mikelsaar M. Persistence of Escherichia coli clones and phenotypic and genotypic antibiotic resistance in recurrent urinary tract infections in childhood. J Clin Microbiol. 2009 Jan;47(1):99-105.

 

Mikelsaar M, Zilmer M. Lactobacillus fermentum ME-3 - an antimicrobial and antioxidative probiotic. Microb Ecol Health Dis. 2009 Mar 16. [Epub ahead of print] PubMed PMID: 19381356; PubMed Central PMCID: PMC2670518.

 

Prangli AL, Utt M, Talja I, Sepp E, Mikelsaar M, Rajasalu T, Uibo O, Tillmann V, Uibo R. Antigenic proteins of Lactobacillus acidophilus that are recognised by serum IgG antibodies in children with type 1 diabetes and coeliac disease. Pediatr Allergy Immunol. 2009 Jul 2.

 

 

2008

Koll, P., R. Mandar, H. Marcotte, E. Leibur, M. Mikelsaar, and L. Hammarstrom. 2008. Characterization of oral lactobacilli as potential probiotics for oral health. Oral Microbiol Immunol 23:139-47.

 

Meriste, S., J. M. Jacquet, P. Willems, and I. Lutsar. 2008. Immunologic response to Hib tetanus toxoid conjugated vaccine coadministered with DTPa either mixed or in two separate injections in toddlers not primed with Hib vaccine. Hum Vaccin 4:31-5.

 

Troke, P., K. Aguirrebengoa, C. Arteaga, D. Ellis, C. H. Heath, I. Lutsar, M. Rovira, Q. Nguyen, M. Slavin, and S. C. Chen. 2008. Treatment of scedosporiosis with voriconazole: clinical experience with 107 patients. Antimicrob Agents Chemother 52:1743-50.

 

Truusalu, K., R. H. Mikelsaar, P. Naaber, T. Karki, T. Kullisaar, M. Zilmer, and M. Mikelsaar. 2008. Eradication of Salmonella Typhimurium infection in a murine model of typhoid fever with the combination of probiotic Lactobacillus fermentum ME-3 and ofloxacin. BMC Microbiol 8:132.

 

 

2007

 

Andreson, H., T. Sillakivi, M. Peetsalu, A. Peetsalu, and M. Mikelsaar. 2007. Persistence of Helicobacter pylori infection in patients with peptic ulcer perforation. Scand J Gastroenterol 42:324-9.

 

Olak, J., R. Mandar, S. Karjalainen, E. Soderling, and M. Saag. 2007. Dental health and oral mutans streptococci in 2-4-year-old Estonian children. Int J Paediatr Dent 17:92-7.

 

Metsvaht, T., K. Oselin, M. L. Ilmoja, K. Anier, and I. Lutsar. 2007. Pharmacokinetics of penicillin g in very-low-birth-weight neonates. Antimicrob Agents Chemother 51:1995-2000.

 

Stsepetova, J., E. Sepp, K. Julge, E. Vaughan, M. Mikelsaar, and W. M. de Vos. 2007. Molecularly assessed shifts of Bifidobacterium ssp. and less diverse microbial communities are characteristic of 5-year-old allergic children. FEMS Immunol Med Microbiol 51:260-9.

 

Turk, S., P. Korrovits, M. Punab, and R. Mandar. 2007. Coryneform bacteria in semen of chronic prostatitis patients. Int J Androl 30:123-8.

 

Tamm, E., P. Naaber, M. Maimets, M. Oona, S. Koljalg, and I. Lutsar. 2007. Antimicrobial susceptibility and serogroup/serotype distribution of nasopharyngeal isolates of Streptococcus pneumoniae in healthy Estonian children in 1999-2003. Clin Microbiol Infect 13:824-6.

 

 

2006

 

Altraja A, Naaber P, Tamm E, Meriste S, Kullamaa A, Leesik H. Antimicrobial susceptibility of common pathogens from community-acquired lower respiratory tract infections in Estonia. J Chemother. 2006 Dec;18(6):603-9.

 

Andreson, H., Sillakivi, T., Peetsalu, M., Peetsalu, A., Mikelsaar, M. Persistence of Helicobacter pylori infection in patients with peptic ulcer perforation. Scand. J. Gastroenterol., 2006, 41.

 

Hütt P, Štšepetova J, Lõivukene K, Kullisaar T, Mikelsaar M. Antagonistic activity of probiotic lactobacilli and bifidobacteria against entero- and uropathogens. J Appl Microbiol. 2006 Jun;100(6):1324-32.

 

Korrovits, P., Punab, M., Türk. S., Mändar, R. Seminal microflora in asymptomatic inflamatory (NIH IV category) prostatitis. Eur. Urology, 2006.

 

Lõivukene K, Kermes K, Sepp E, Adamson V, Mitt P, Jurna M, Magi H, Kallandi U, Otter K, Naaber P. The comparison of susceptibility patterns of Gram-negative invasive and non-invasive pathogens in Estonian hospitals. Antonie Van Leeuwenhoek. 2006 Apr-May;89(3-4):367-71.

 

Lõivukene K, Sepp E, Adamson V, Mitt P, Kallandi U, Otter K, Naaber P. Prevalence and antibiotic susceptibility of Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae in Estonian intensive care units in comparison with European data. Scand J Infect Dis. 2006;38(11-12):1001-8.

 

Lõivukene, K., Kermes, K., Sepp, E., Adamson, V., Mitt, P., Kallandi, U., Otter, K., Naaber, P., European Antimicrobial resistance Surveillance System, Estonian Study Group. Surveillance of antimicrobial resistance of invasive pathogens: the Estonian experience. Euro Surveill. 2006 Feb;11(2):47-9.

 

Marcotte H, Koll-Klais P, Hultberg A, Zhao Y, Gmur R, Mandar R, Mikelsaar M, Hammarstrom L. Expression of single-chain antibody against RgpA protease of Porphyromonas gingivalis in Lactobacillus. J Appl Microbiol. 2006 Feb;100(2):256-63.

 

Pähkla ER, Koppel T, Naaber P, Saag M, Loivukene K. The efficacy of non-surgical and systemic antibiotic treatment on smoking and non-smoking periodontitis patients. Stomatologija. 2006;8(4):116-21.

 

Vendt, N., Grünberg, H., Tuure, T., Malminiemi, O., Wuolijoki, E., Tillmann, V., Sepp, E., Korpela, R. Growth during the first 6 months of life in infants using formula enriched with Lactobacillus rhamnosus GG: double-blind, randomized trial. J. Human Nutr. Diet., 2006, 19, 51.

 

 

2005

 

Karjagin, J., Pähkla, R., Karki, T., Starkopf, J. Distribution of metronidazole in muscle tissue of patients with spetic shock and its efficacy against Bacteroides fragilis in vitro. J. Antimicr. Chemother., 2005, 55, 341-346.

 

Kasenõmm, P., Piirsoo, A., Kull, M., Kull, M. Jr, Mikelsaar, M. Selection of indicators for tonsillectomy in adults with recurrent tonsillitis. BMC Ear, Nose and Throat Disorders 2005, 5:7

 

Kõll-Klais P, Mändar R, Leibur E, Marcotte H, Hammarström L, Mikelsaar M. (2005). Oral lactobacilli in chronic periodontitis and periodontal health: species composition and antimicrobial activity. Oral Microbiol Immunol, 2005, 20, 354-361.

 

Kõll-Klais, P., Mändar, R., Leibur, E., Mikelsaar, M. Oral microbial ecology in chronic periodontitis and periodontal health. Micr. Ecol. Health Dis., 2005, 17, 146-155.

 

Mändar R, Raukas E, Türk S, Korrovits P, Punab M. (2005). Mycoplasmas in semen of chronic prostatitis patients. Scand J Urol Nephrol 39: 479-482.

 

Sepp E., Julge K., Mikelsaar M., Björksten B. Intestinal microbiota and immunoglobulin E response in 5-year-old Estonian children. Clin.Exper. Allergy, 35, 1141-1146.

 

Songisepp E., Kals J., Kullisaar T., Hütt P., Mändar R., Zilmer M., Mikelsaar M. Evaluation of the functional efficacy of an antioxidative probiotic in healthy volunteers. Nutrition Journal, 2005, 4:22.

 

Usonis V, Meriste S, Bakasenas V, Lutsar I, Collard F, Stoffel M, Tornieporth N. Immunogenicity and safety of a combined hepatitis A and B vaccine administered concomitantly with either a measles-mumps-rubella or a diphtheria-tetanus-acellular pertussis-inactivated poliomyelitis vaccine mixed with a Haemophilus influenzae type b conjugate vaccine in infants aged 12-18 months. Vaccine. 2005; 23: 2602-6

 

 

2004

 

Naaber, P., Smidt, I., Štšepetova, J., Brilene, T., Annuk, H., Mikelsaar, M. Inhibition of Clostridium difficile strains by intestinal Lactobacillus species. J. Med. Microbiol., 2004, 53, 551-554.

 

Naaber, P., Mikelsaar, M. Interactions between lactobacilli and antibiotic-associated diarrhea. In: Advances in Applied Microbiology. Eds. A.I. Laskin, J.W. Bennett, G.M. Gadd. Volume 54. Elsevier Inc., 2004, 231-260.

 

Songisepp, E., Kullisaar, T., Hütt, P., Elias, P., Brilene, T., Zilmer, M., Mikelsaar, M. A new probiotic cheese with antioxidative and antimicrobial activity. J. Dairy Sci., 2004, 87, 2017-2023.

 

Truusalu K, Naaber P, Kullisaar T, Tamm H, Mikelsaar R-H, Zilmer K, Rehema A, Zilmer M, Mikelsaar M. The influence of antibacterial and antioxidative probiotic lactobacilli on gut mucosa in a mouse model of Salmonella infection. Microbial Ecology in Health and Disease 2004, 16:4, 180-187.

 

Kõll-Klais, P., Mändar, R., Leibur, E., Kjaeldgaard M. High levels of salivary lactobacilli in Estonian schoolchildren. Eur. J. Paed. Dent., 2004, 2, 107-109.

 

Maaroos, H.-I., Andreson, H., Lõivukene, K., Hütt, P., Kolk, H., Kull, I., Labotkin, K., Mikelsaar, M. The diagnostic value of endoscopy and Helicobacter pylori tests for peptic ulcer patients in late post-treatment setting. BMC Gastroenterology, 2004, ,4, 27.

 

 

2003

 

Annuk, H., Štšepetova, J., Kullisaar, T., Songisepp, E., Zilmer, M., Mikelsaar, M. Characterization of intestinal lactobacilli as putative probiotic candidates. J. Appl. Microbiol., 2003, 94, 403-412.

 

Kullisaar, T., Songisepp, E., Mikelsaar, M., Zilmer, K., Vihalemm, T., Zilmer, M. Antioxidative probiotic fermented goats' milk decreases oxidative stress-mediated atherogenicity in human subjects. Br. J. Nutr., 2003, 90, 449-456.

 

Lõivukene, K., Naaber, P. Antibiotic susceptibility of clinically relevant anaerobes in Estonia from 1999 to 2001. Anaerobe, 2003, 9, 57-61.

 

Tapfer, H., Liigant, A., Simovart, H.E., Põldoja, E., Kokk, K., Naaber, P., Talvik, R. Dissemination of bacteria in multiple organs associated with apoptosis and macrophage activity in different stages of experimental sepsis. Scand. J. Surg., 2003, 92, 163-170.

 

Kermes K., Punab M., Lõivukene K., Mändar R.. Anaerobic seminal fluid microflora in chronic prostatitis/chronic pelvic pain syndrome patients. Anaerobe 2003, 9, 117-123.

 

Punab M., Lõivukene K., Kermes K., Mändar R. (2003). The limit of leukocytospermia from the microbiological viewpoint. Andrologia, 2003, 35, 271-278.

 

 

2002

 

Andreson H, Lõivukene K, Sillakivi T, Maaroos H-I, Ustav M, Peetsalu A, Mikelsaar M. Association of cagA and vacA genotypes of Helicobacter pylori with gastric diseases in Estonia. J. Clin. Microbiol., 2002, 40, 298-300.

 

Hynes SO, Broutet N, Eurohepygast Study Group, Wadström T, Mikelsaar M, O'Toole PW, Telford J, Engstrand L, Kamiya S, Mentis AF, Moran AP. Phenotypic variation of Helicobacter pylori isolates from geographically distinct regions detected by lectin typing. J. Clin. Microbiol., 2002, 40, 227-232.

 

Kolk H, Maaroos H-I, Kull I, Labotkin K, Lõivukene K, Mikelsaar M. Open access endoscopy in an epidemiological situation of high prevalence of Helicobacter pylori infection: applicability of the guidelines of the European Society for Primary Care Gastroenterology. Family Practice, 2002, 19, 3, 231-235.

 

Krüüner A, Pehme L, Ghebremichael S, Koivula T, Hoffner SE, Mikelsaar M. Use of molecular techniques to distinguish between treatment failure and exogenous reinfection with Mycobacterium tuberculosis. Clin. Infect. Dis., 2002, 35, 146-155.

 

Kõljalg S, Naaber P, Mikelsaar M. Antibiotic resistance as an indicator of bacterial chlorhexidine susceptibility. J. Hosp. Infect., 2002, 51, 106-113.

 

Kasenõmm P, Kull M, Mikelsaar M. Association between tonsillar core microflora and post-tonsillectomy bacteremia. Micr. Ecol. Health Dis., 2002, 14, 122-127.

 

Mikelsaar M, Annuk H, Štšepetova J, Mändar R, Sepp E, Björksten B. Intestinal lactobacilli of Estonian and Swedish children. Micr. Ecol. Health Dis., 2002, 14, 75-80.

 

Kullisaar T, Zilmer M, Mikelsaar M, Vihalemm T, Annuk H, Kairane C, Kilk A. Two antioxidative lactobacilli strains as promising probiotics. Int. J. Food Microbiol., 2002, 72, 215-224.

 

Lõivukene K, Maaroos H-I, Kolk H, Kull I, Labotkin K, Mikelsaar M. Prevalence of antibiotic resistance of Helicobacter pylori isolates in Estonia during 1995-2000 in comparison to the consumption of antibiotics used in treatment regimens. Clin. Microbiol. Infect., 2002, 8, 598-603.

 

 

2001

 

Krüüner A, Danilovitsch M, Pehme L, Laisaar T, Hoffner SE, Katila ML. Tuberculosis as an occupational hazard for health care workers in Estonia. Int. J. Tuberc. Lung Dis., 2001, 2, 170-176.

 

Lockman S, Krüüner A, Binkin NJ, Levina K, Wang YC, Danilovitsch M, Hoffner SE, Tappero JW. Clinical outcomes of Estonian patients with primary multidrug-resistant versus drug-susceptible tuberculosis. Clin. Infect. Dis., 2001, 32, 373-380.

 

Karki T, Truusalu K, Vainumäe I, Mikelsaar M. Antibiotic susceptibility patterns of community- and hospital-acquired Staphylococcus aureus and Escherichia coli in Estonia. Scand. J. Infect. Dis., 2001, 33, 333-338.

 

Mändar R, Lõivukene K, Hütt P, Karki T, Mikelsaar M. Antibacterial susceptibility of intestinal lactobacilli of healthy children. Scand. J. Infect. Dis., 2001, 33, 344-349.

 

Annuk H, Hynes SO, Hirmo S, Mikelsaar M, Wadström T. Characterisation and differentiation of lactobacilli by lectin typing. J. Med. Microbiol., 2001, 50, 1-6.

 

Mändar R, Lõivukene K, Ehrenberg A, Smidt I, Raukas E, Kask V, Mikelsaar M. Amniotic fluid microflora in asymptomatic women at mid-gestation. Scand. J. Infect. Dis., 2001, 33, 60-62.

 

Sillakivi T, Aro H, Ustav M, Peetsalu M, Peetsalu A, Mikelsaar M. Diversity of Helicobacter pylori genotypes among Estonian and Russian patients with perforated peptic ulcer, living in South Estonia. FEMS Microbiol. Letters, 2001, 195, 29-33.

 

Naaber P, Tamm E, Pütsepp A, Kõljalg S, Maimets M. Nasopharyngeal carriage and antibacterial susceptibility of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in Estonian children. Clin. Microbiol. Infect., 2000, 12, 6, 675-686.

 

Sillakivi T, Peetsalu M, Mikelsaar M, Peetsalu A. An attempt at Helicobacter pylori eradication with intravenous clarithromycin in perforated peptic ulcer patients. Scand. J. Gastroenterol., 2001, 36, 1119-1120.

 

Krüüner A, Hoffner SE, Sillastu H, Danilovits M, Levina K, Svenson SB, Ghebremichael S, Koivula T, Källenius G. Spread of drug-resistant pulmonary tuberculosis in Estonia. J. Clin. Immunol., 2001, 39, 9, 3339-3345.

 

Björksten B, Sepp E, Julge K, Voor T, Mikelsaar M. The intestinal microflora during the first year of life and the development of allergy. J. Allergy Clin. Immunol. 2001, 108, 516-520

 

 

2000

 

Annuk H., Vainumäe I., Aimla K., Ausmees K., Kullisaar T., Kask S., Mikelsaar M. Antagonistic activity of lactobacilli against urinary Escherichia coli. Microecol. Therapy, 1999, 28, 169-175.

 

Mikelsaar M., Türi E., Türi M., Smidt I. Interaction of Lactobacillus fermentum and Escherichia coli in guinea pig testes model. Micr. Ecol. Therapy, 1999, 28, 319-326.

 

Naaber P., Smidt I., Tamme K., Liigant A., Tapfer H., Mikelsaar M., Talvik R. Translocation of indigenous microflora in an experimental model of sepsis. J. Med. Microbiol., 2000, 49, 431-439.

 

Lõivukene K., Kolk H., Maaroos H.-I., Kasenõmm P., Aro H., Ustav M., Mikelsaar M. Metronidazole and clarithromycin susceptibility and the subtypes of vacA of Helicobacter pylori isolates in Estonia. Scand. J. Infect. Dis., 2000, 32, 59-62.

 

Sepp E., Naaber P., Voor T., Mikelsaar M., Björksten B. Development of intestinal microflora during the first month of life in Estonian and Swedish infants. Micr. Ecol. Health Dis., 2000, 12, 22-26.

 

Naaber P, Kõljalg S, Maimets M. Antibiotic Usage and Resistance Trends in Estonian University Hospitals. International Journal of Antimicrobial Agents; 2000; 16: 309-315

 

 

1999

 

Kõljalg, S., Sults, I., Raukas, E., Truu, J., Ustav, M., Mikelsaar, M. Distribution of Acinetobacter baumannii in a neurointensive care unit. - Scand. J. Infect. Dis., 1999, 31, 145-150.

 

Björksten, B. Naaber, P., Sepp, E., Mikelsaar, M. The intestinal microflora in allergic Estonian and Swedish 2-year-old children. - Clin. Exp. Allergy, 1999, 29, 342-346.

 

Annuk, H., Hirmo, S. Türi, E., Mikelsaar, M., Arak, E., Wadström, T. Effect on cell surface hydrophobicity and susceptibility of Helicobacter pylori to medicinal plant extracts - . FEMS Microbiology Letters, 1999, 172, 41-45.

 

Türi, E., Türi, M., Annuk, H., Arak, E. Action of aqueous extracts of bearberry and cowberry leaves and wild camomille and pineapple-weed flowers on Escherichia coli surface structures. - Pharmac. Biol., 1999, 37, 2, 127-133.

 

 

1998

 

Kaila, M., Isolauri, E., Sepp, E., Mikelsaar, M., Salminen, S. Fecal recovery of a human Lactobacillus strain (ATCC 53103) during dietary therapy of rotavirus diarrhea in infants. - Bioscience Microflora, 1998, 17, 2, 149-151

 

Krüüner, A., Sillastu, H., Danilovitsch, M., Levina, K., Svenson, S.B., Källenius, G., Hoffner, S.E.. Drug resistant tuberculosis in Estonia. - The Official Journal of the International Union Against Tuberculosis and Lung Disease "Tubercle and Lung Disease", 1998, 2, 2, 130-133.

 

Mäkinen, K.K., Olak, J., Russak, S., Saag, M., Seedre, T., Vasar, R., Vihalemm, T., Mikelsaar, M., Mäkinen, P.-L.. Polyol-combinant saliva stimulants: a 4-month pilot study in young adults. - Acta Odontologica Scandinavia, 1998, 56, 1-5.

 

Naaber, P., Mikelsaar, R.-H., Salminen, S., Mikelsaar, M.. Bacterial translocation, intestinal microflora and morphological changes of intestinal mucosa in experimental models of Clostridium difficile infection. - Journal of Medical Microbiology, 1998, 47, 591-598

 

 

1997

 

Naaber P, Klaus K, Sepp E, Björksten B, Mikelsaar M. Colonization of infants and hospitalized patients with Clostridium difficile and lactobacilli. Clinical Infectious Diseases 1997, 25, Suppl 2, 189-190.

 

Sepp E., Julge K., Vasar M., Naaber P., Björksten B., Mikelsaar M. Intestinal microflora of Estonian and Swedish infants. Acta Paediatrica, 1997, 86, 956-961.

 

Türi M, Türi E, Kõljalg S, Mikelsaar M. Influence of aqueous extracts of medicinal plants on surface hyrophobicity of Escherichia coli strains of different origin. APMIS, 1997, 105, 956-962.

 

Naaber P., Maimets M., Mikelsaar M. Prevalence and properties of Clostridium difficile in hospitalized patients of Estonia. - Reviews in Medical Microbiology, Chapman & Hall, 1997, 8, Suppl 1, 60-61

 

Oona M, Rägo T, Maaroos H-I, Mikelsaar M, Lõivukene K, Salminen S, Korhonen H. Helicobacter pylori in children with abdominal complaints: has immune bovine colostrum some influence on gastritis? Alpe Adria Microbiology Journal, 1997, 6, 49-57.

 

Ormisson A, Sepp E, Siigur U, Varendi H, Mikelsaar M. Impact of early life nutrition on growth and intestinal microflora composition in low-birth-weight infants. Scand. J. Nutrition, 1997, 41, 71-74

 

 

1996

 

Kõljalg S., Vuopio-Varkila J., Mikelsaar M., Wadström T. Cell surface properties of Acinetobacter baumannii. - APMIS, 1996, 104, 659-665.

 

Mikelsaar M., Mändar R., Maaroos H.-I., Päär S., Rägo T., Kisand K., Aleljung P., Wadström T. Helicobacter pylori gastritis in children: clinical, bacteriological, and morphological study. - Microecology and Therapy, 1996, 22, 44-53

 

Mändar R., Mikelsaar M. Transmission of mother's microflora to the newborn at birth. - Biology of the Neonate, 1996, 69, 30-35

 

Naaber P., Lehto E., Salminen S., Mikelsaar M. Inhibition of adhesion of Clostridium difficile to Caco-2 cells. - FEMS Immunology and Medical Microbiology, 1996, 14, 205-209.

 

Mikelsaar M., Sepp E., Mändar R., Ormisson A. Criteria for evaluation of the faecal microflora. - Microecology and Therapy, 1995, 23, 149-150

 

Mändar R., Mikelsaar M. Vaginal microflora during pregnancy. - Alpe Adria Microbiology Journal, 1996, 5, 1, 41-50

 

Naaber P., Mikelsaar M. Antibiotic-compromised murine model of Clostridium difficile infection. - Microecology and Therapy, 1995, 25, 201-205

 

Sepp E., Tamm E., Torm S., Lutsar I., Mikelsaar M., Salminen S. Impact of a lactobacillus probiotic on the faecal microflora in children with shigellosis. - Microecology and Therapy, 1995, 23, 74-80.

 

 

1995

 

Karki, T., Lenzner, H., Lenzner, A. Quantitative composition of the human lactoflora and methods for its examination. Microecology and Therapy. Herborn-Dill, Germany, 1995, 21, 157-162.

 

Türi, M., Sepp, E., Mikelsaar, M. Putative virulence markers for Escherichia coli strains of different origin. Alpe Adria Microbiology Journal, Milano, 1995, 4, 4, 253-263. Ó Excerpta Medica EMBASE.


Mändar R, Saag H, Peil P, Mikelsaar M. Bacterial vaginosis during pregnancy. Microecology and Therapy, 1995; 23: 24-31.

PAPERS IN ESTONIAN

 
Kõljalg S, Naaber P, Lõivukene K, Kermes K, Allik M, Sepp E. Streptococcus pyogenes’e esinemissageduse oluline tõus. Eesti Arst, 2023, 102, Lisa 1. OÜ Celsius Healthcare, 65-65.


Türk, S.; Kermes, K.; Lõivukene, K.; Raukas, E.; Korrovits, P.; Punab, M.; Mändar, R. (2010). Sperma mikrofloora kroonilise prostatiidi korral. Eesti Arst, 89(2), 83 - 94.

 

Kasenõmm, P., Piirsoo, A., Kull, M. jn., Kull, M., Mikelsaar, M. (2005). Kroonilise tonsilliidi patogeneesi uuringud kui alus tonsillektoomia objektiivsete kriteeriumite leidmiseks. Eesti Arst, 84 (8), 531-541.

 

Kõll-Klais, P.; Mändar, R.; Mikelsaar, M.; Leibur, E. (2003). Suuõõne mikroobiökoloogia kroonilise parodontiidi puhul. Eesti Arst, 82(11): 759 -767.

 

Sepp E, Kõljalg S, Truusalu K, Štšepetova L, Metsvaht T, Sau L, Jürna M, Mägi H, Allik M, Mikelsaaar M. (2003). Staphylococcus epidermidis ja Klebsiella pneumoniae - võimalikud hospitaalinfektsioonide tekitajad Eesti lasteintensiivarvi osakondades. Eesti Arst 82(4): 239-248.

 

Järv H, Naaber P, Kaur S, Eisen M, Silm H. Varbaküünte seenhaigus Eestis ? võrdlus Euroopa maadega. Eesti Arst 2002; 81: 338-342

 

Krüüner A. Mycobacterium tuberculosis'e levik, mikrobioloogilise diagnostika võimalused ja ravimiresistentsus Eestis. Eesti Arst, 2001, 3, 131-139.

 

Songisepp E., Mikelsaar M. Rukkileiva juuretise kvaliteeti kindlustavad leivajuuretise piimhappebakterid. Põllumajandus, 2000, 4,5, 5-7.

 

Lõivukene K., Kolk H., Maaroos H.-I., Mikelsaar M. Helicobacter pylori tüvede metronidasool- ja klaritromütsiintundlikkus Eesti patsientide seas. Eesti Arst, 2000, 8, 453-459.

 

Kõljalg S., Karki T., Olsson-Liljequist B. Metsitsilliin-resistentse Staphylococcus aureus'e esinemissagedus Eestis. Eesti Arst, 2000, 8, 466-470.

 

Mikelsaar M. Esilekerkivad infektsioonid. Eesti Arst, 2000, 8, 471-480.

 

Kasenõmm, P. Krooniline retsidiveeruv tonsilliit. Eesti Arst, 2000, 8, 481-485.

 

Mändar R. Antibakteriaalsete preparaatide mõju normaalsele mikrofloorale. Eesti Arst, 2000, 8, 486-491.

 

Karki T. Antibiootikumid ja antibiootikumresistentsus. Eesti Arst, 2000, 8, 492-498

 

Annuk H., Raukas M., Türi E., Türi M., Arak E. Leesikalehtede (Uvae ursi folium) vesitõmmiste toime Escherichia coli agregatiivsele aktiivsusele I. - Eesti Rohuteadlane, Tartu , 1997, 3, 3-5.

 

Annuk H., Raukas M., Türi E., Türi M., Arak E. Leesikalehtede (Uvae ursi folium) vesitõmmiste toime Escherichia coli agregatiivsele aktiivsusele II. Eesti Rohuteadlane, 1997, 4, 3-5.

 

Sepp E., Lõivukene K., Naaber P., Kermes K., Julge K., Vasar M., Björksten B., Mikelsaar M. Tervete ja allergiliste laste mikrofloora erinevused. Eesti Rohuteadlane, 1997, lisa, 62-63.

 

Sepp E., Metsvaht T. Vastsündinute bakterieemiate struktuur ja laboratoorne diagnoosimine Tartu Lastekliiniku intensiivraviosakonna andmeil.Eesti Arst, 1997, 6, 513-519.

 

Karki T., Vares P., Kõljalg S., Kirm A. Elektrokeemiliselt töödeldud vesilahuste bakteritsiidsest toimest in vitro. - Eesti Rohuteadlane, Tartu , 1997, lisa, 15-17.

 

Krüüner A., Danilovits M., Türi E. Ravimiresistentsete Mycobacterium tuberculosis'e tüvede osatähtsusest tuberkuloosi etioloogias Eestis. - Eesti Rohuteadlane, Tartu , 1997, lisa, 23-24.

 

Kõljalg S., Sults I., Raukas E., Mikelsaar M. Acinetobacter baumannii persisteerimine neurointensiivravi osakonnas. - Eesti Rohuteadlane, Tartu, 1997, lisa, 26-27.

 

Mikelsaar M., Karki T., Kirsberg E., Kõljalg S., Kermes K., Mägi H., Ivanova M., Rauk S., Timmas T., Jõks U. Uroinfektsioonidega Eesti patsientide Escherichia coli tüvede tundlikkus antibiootikumidele. - Eesti Rohuteadlane, Tartu , 1997, lisa, 35-36.

 

Mändar R., Lõivukene K., Türi M., Mikelsaar M. Eesti ja Rootsi lastelt isoleeritud laktobatsillitüvede tundlikkus antibiootikumide suhtes. - Eesti Rohuteadlane, Tartu, 1997, lisa, 37-38.

 

Mikelsaar M. Hospitaalinfektsioon tänapäeval. Eesti Arst, 1996, 3, 237-245

 

Karki T., Lenzner H., Lenzner A. Lactobacillus casei toime seedekulgla laktofloorasse. Eesti Arst, 1996, 1, 30-34.

 

Karki, T. Etüülalkohol ja inimese seedekulgla laktofloora. Eesti Arst, Tallinn, 1995, 5, 390-393.

 

Naaber, P. Clostridium difficile põhjustatud diarröa. Mikrobioloogilise diagnoosimise esmane kogemus Tartus. Eesti Arst. Tallinn, 1995, 1, 11-15.

 

Reinaste, R., Türi, M. Bensalkooniumkloriidsalvide antimikroobne aktiivsus. Eesti Rohuteadlane, Tartu, 1995, VI, 4, 147-149,

 

Türi, E., Türi, M. Ravimtaimede toimemehhanismist Escherichia coli suhtes. Eesti Rohuteadlane, Tartu, 1995, VI, 4, 149-151.

 

Mikelsaar, M. Kas inimkond vabaneb kunagi nakkushaigustest? Akadeemia. Tartu, 1995, 7 aastakäik, 1693-1711.

CREP

CREP_intro_end CREP (Collection of Reproductive Tract Microorganisms) is a collection of microbial strains and microbiota samples of reproductive tract. The collection is a part of the Competence Centre on Health Technologies. The collection was founded in 2009. The strains and microbiota samples were collected from reproductive tract of healthy, diseased and infertile women, men and couples. The collection contains both lactic acid bacteria and opportunistic pathogens. The main research activities are related to probiotic development for reproductive tract disorders, and analysis of the microbiota composition in case of different health conditions.

CREP Guidelines

CREP_rules_eng Guidelines for management and use of the scientific collection
Collection of Reproductive Tract Microorganisms
at Competence Centre on Health Technologies
 
General
CREP (Collection of Reproductive Tract Microorganisms) is a collection of microbe strains and microbiota samples extracted from reproductive tract. The collection is a part of the Competence Centre on Health Technologies (Tervise TAK). Microbe strains and microbiota samples preserved in the collection have been extracted from healthy or infertile individuals, as well as people with inflammatory diseases. Samples have been collected from males, females and male-female couples. The collection contains beneficial lactobacilli and opportunistic pathogens. Main focus of the collection is on the development of probiotics for management of the reproductive tract diseases, as well as analysis of the microbiota composition in case of different health conditions.
The collection follows the recommendations of international organisations, such as ECCO (European Culture Collections' Organization), WFCC (World Federation of Culture Collections), CABRI (Common Access to Biological Resources and Information), OECD Best Practice Guidelines for Biological Resource Centre, and Nagoya protocol.
All biological materials and isolates in the collection are documented. Strict rules are followed for accessing and using of the collection (Recommendation Rec(2006)4 of the Committee of Ministers of member states on research on biological materials of human origin, article 14).
Collection is registered in the World Data Center for Microorganism (WDCM) database as collection no. 1091. Collection belongs to the Estonian National Collection of Microbiology, with a modern database system and a unified website. The collection can be found on the Estonian Electronic Microbial dataBase (EEMB). The collection catalogue is publicly accessible: http://eemb.ut.ee/ and http://eemb.ut.ee/eng.
 
Management and structure of collection
The collection consists of microbe strains and microbiota samples that are collected during scientific research or bought and information in a digital database.
New strains and microbiota samples are added to collection according to the agreement of the acceptance of biological material.
When submitting new samples to the collection, information about the sample is added to the digital database. The database is also updated when new information is obtained about the samples. The updates are managed by the collection administrator who collects necessary information from other staff, researchers and students.
Each preserved item has a unique ID-code which consists on the collection acronym and a number combination.
Biological materials are assigned a code and preserved according to the regulations of the Council of the European Union (Recommendation Rec(2006)4 of the Committee of Ministers of member states on research on biological materials of human origin).
The head and administrator of the collection are responsible for proper usage of the collection and database.
The collection is located in microbiology lab of CCHT, Ravila 19, Tartu 50411, Estonia.
 
Storage of the samples
The microbe strains and microbiota samples are stored at -80°C in multiple parallels in multiple freezers. Isolated strains are preserved in sterile cryovials containing SKIM-milk medium or in special chemically treated cryosolutions.
The collection is preserved in locked refrigerators. The collection is accessible only for the assigned person, in absence of those persons only to an assigned substitute. No third party has access to the collection.
Conditions for preservation (the temperature and continuous maintenance of the freezers) are managed by the head of the collection. Freezers are equipped with fault detection systems. In case of a malfunction, a message automatically is sent to the person assigned to the collection.
Samples are handled and utilized according to the “Regulations for handling infectious material” legislation (in force since  31.10.2013 nr. 119, RTL 2003, 115, 1831).
 
Use and availability of biobank
Main task of the collection is to support and promote research and development in the field of microbial communities of the reproductive tract through the collection, processing, storage and making available of the microbial strains and microbiota samples and the related information.
The strains and microbiota samples as well as the information about them are accessible for scientific research and development, according to the MTA (material transfer agreement) in accordance with the Nagoya protocol rules.
The collection catalogue is publicly accessible.
 

CREP Team

Research fellows, students and technicians work at the CREP collection.
The collection website and database are managed and developed by Hugo M䮤ar  hugo.mandar [at] ut.ee.
More information about CREP can be found here.

CREP Contacts

Collection of Reproductive Tract Microorganisms

Competence Centre on Health Technologies

Ravila 19

Tartu 50411

Estonia

 

E-mail:

tiiu.roop [at] ut.ee

reet.mandar [at] ut.ee

 

CREP Publikatsioonid / Publications

CREP_public_eng Patent application

Vaginal Lactobacillus crispatus strains as probiotics for urogenital health. Tervisetehnoloogiate Arenduskeskus AS. Authors: Reet Mändar, Pirje Hütt, Imbi Smidt, Jelena д𥰥tova, Eleri Lapp, Mariheleen Rostok, Gertu Sõerunurk, Tiiu Rööp, Dagmar Hoidmets, Hardi Tamm, Marit Kolk, Sander Piiskop, Triin Palmiste, Kairi Koort, Andres Salumets. Priority number: 1816425.1. Priority date: 9.10.2018.

PhD dissertations

Kristo Ausmees, 2014, (sup) Reet Mändar, Margus Punab. Reproductive function in middle-aged male: associations with prostate, lifestyle and couple infertility status.
Silver Türk, 2009, (sup) Reet Mändar; Tiiu Kullisaar, Etiopathogenetic aspects of chronic prostatitis: role of mycoplasmas, coryneform bacteria and oxidative stress.

MSc dissertations

Evelin Mutli, 2020, (sup) Triin Laisk; Reet Mändar; Kairi Koort, Korduva vaginiidi geneetilised riskifaktorid Eesti populatsioonis.
Kristiina Sõsa, 2019, (sup) Kairi Koort; Silver Türk. Viljatute paaride suguteede mikrobioomi bioinformaatiline analüüs.
Triin Palmiste, 2017, (sup) Kairi Tammoja, Jelena д𥰥tova. Probiootilise potentsiaaliga vaginaalsete Lactobacillus crispatus tüvede proteoomi analüüs.
Juliana Baranova, 2017, (sup) ܬle Parm, Jelena д𥰥tova, Reet Mändar. Kehavälisel viljastamisel kasutatava materjali mikrobioloogiline kontroll.
Ave Ahelik, 2013, (sup) Reet Mändar, Tiiu Kullisaar, Sulev Ingerpuu. Oksüdatiivne stress viljatutel paaridel (Oxidative stress in infertile couples).
Eleri Lapp, 2013, (sup) Reet Mändar. Kehavälise viljastamise ebaedu põhjused: suguteede põletikud, tervislik seisund ja tervisekäitumine mõlemal partneril (Reasons for in vitro fertilisation (IVF) failure: reproductive tract infections, general state of health and health behaviour of both partners).
Riinu Kiiker, 2013, (sup) Reet Mändar, Jaanis Juhanson. Ureaplasmad ja laktobatsillid viljatute paaride suguteede mikrobiootas ning seksuaalvahekorra mõju tupe mikroobikooslusele (Ureaplasmas and lactobacilli in the genital tract microbiota of infertile couples and influence of sexual intercourse on vaginal microbial community).
Natalja Borovkova, 2010, (sup) Reet Mändar, Margus Punab. Seksuaalvahekorra mõju naissuguteede mikrofloorale viljatutel paaridel.

Monographies

Türk S, Kullisaar T, Korrovits P, Ausmees K, Punab M, Mändar R. (2011). Some etiopathogenetic aspects of chronic prostatitis: mycoplasmas, coryneform bacteria and oxidative stress. Charleston, CreateSpace, 98 p.
Korrovits P, Punab M, Mändar R. (2011). Asymptomatic inflammatory prostatitis. Charleston, CreateSpace, 68 p.
 
Papers

The research papers composed by supplying or using the CREP collection can be found here.


EEMB

Eesti Elektrooniline Mikroobide andmeBaas

Estonian Electronic Microbial dataBase

HUMB contains strains from E.coli ...
HUMB contains strains from lactobacillus - ME3
HUMB contains strains from whatever you need...
HUMB contains strains from E.coli - do now worry!
EEMB: Introduction & contacts

(Estonian Electronic Microbial dataBase)
is an electronic database of Estonian National Collection of Microbes that currently hosts three collections of microorganisms:

  • CELMS (Collection of Environmental and Laboratory Microbial Strains) at Institute of Molecular and Cell Biology, University of Tartu
  • HUMB (Human Microbiota Biobank) at Department of Microbiology, University of Tartu
  • CREP (Collection of Reproductive Tract Microorganisms) at Competence Centre on Health Technologies  
   

  • reet.mandar [at] ut.ee (Reet Mändar)
  • hugo.mandar [at] ut.ee (Hugo Mändar)   

CELMS: Introduction & contacts

CELMS is a collection of non-medical environmental and laboratory microbial strains situated at the Institute of Molecular and Cell Biology, University of Tartu. The collection was founded in 1995. Since year 2008 the collection is registered at WFCC-MIRCEN World Data Centre for Microorganisms (registry number 926).

 

CELMS is a member of ECCO (European Culture Collections’ Organisation). The collection is financed by the Estonian Ministry of Education and Research. Majority of strains have been isolated from polluted areas with strong oil shale mining and chemical industry impact. Since year 2008 bacterial isolates from different regions of the Baltic Sea have been added to the collection. Main tasks of the collection are extension of collection with new strains and type cultures, characterization of strains and distribution of microorganisms for purpose of research and education. Our main research activities are related to use molecular methods for characterization of microbial strains and diversity of functional genes.

Department of Genetics Institute of Molecular and Cell Biology
University of Tartu
23 Riia Street
Tartu 51010
Estonia

E-mail: signe.viggor@ut.ee (Signe Viggor)
Phone +372 7 376 038

CREP: Introduction & contacts
CREP_intro_end CREP (Collection of Reproductive Tract Microorganisms) is a collection of microbial strains and microbiota samples of reproductive tract. The collection is a part of the Competence Centre on Health Technologies. The collection was founded in 2009. The strains and microbiota samples were collected from reproductive tract of healthy, diseased and infertile women, men and couples. The collection contains both lactic acid bacteria and opportunistic pathogens. The main research activities are related to probiotic development for reproductive tract disorders, and analysis of the microbiota composition in case of different health conditions.

Collection of Reproductive Tract Microorganisms

Competence Centre on Health Technologies

Ravila 19

Tartu 50411

Estonia

 

E-mail:

tiiu.roop [at] ut.ee

reet.mandar [at] ut.ee

 

HUMB: Introduction & contacts
EEMB_humb_introduction_2021 About the Biobank


    Human Microbiota Biobank (HUMB) is located in the Department of Microbiology, Institute of Biomedicine and Transitional Medicine. The biobank contains more than 20,000 microbial strains of human origin and more than 3,000 microbiota samples. The collection has joined two international networks (WDCM, ECCO).Main goal of the collection is to support and promote research and development in the field of microbiota. An important area of work is the screening of the properties of beneficial bacteria of human body, leading to the development of novel probiotics. Another important area of work involves the causative agents of opportunistic infections, their spectrum of drug susceptibility and virulence factors.
The biobank was started in 1994, when the first microbiota samples and lactobacilli strains were obtained in frame of the Estonian-Swedish allergy study. In the following years, the biobank has been supplemented with thousands of microbiota samples and microbial strains through numerous research projects. Particularly valuable are the beneficial bacteria derived from the human microbiota - lactobacilli and bifidobacteria, but the collection also contains a large number of opportunistic bacteria. Hundreds of specimens are added to collection each year, originating from intestinal tract, oral cavity, respiratory tract, genital tract and skin. The collection also preserves several patented probiotic lactobacilli, as well as standard cultures purchased from other collections for quality control and comparative testing.
The information system of the collection is based on the MySQL platform. The PHPRunner software package (XLineSoft) has been used to create the database user interface, and the dbForge Studio for MySQL (Devart) software package has been used to build the database architecture, create and test procedures and functions. A modern cPanel environment is used to organize database security, platform and content updates, and archiving. Data is managed via a web browser. The basic data of the catalog is visible to the average user, the entire structure of the catalog is visible and editable by registered users. Work on the development of the database and website is organized in cooperation with the Institute of Physics of the University of Tartu.


Research and development

The biobank is constantly engaged in research - determining the properties of microbial strains, isolating and analyzing DNA, analyzing microbial communities, updating and organizing the database. An important part of the collection's work is the screening of the properties of beneficial bacteria (including lactobacilli and bifidobacteria) from the gastrointestinal tract, genital tract and oral cavity, one of the results of which is the development of novel probiotics. There has been a huge growth in the world in the development of functional foods and probiotic products for health promotion and prophylaxis of certain diseases. The research and development needed for this requires laboratory and clinical trials regulated by EU rules, which must confirm the efficacy and safety of the selected bacterial strains. Lactobacillus fermentum ME-3 (DSM 14241) is patented by the University of Tartu and is used in several products developed in cooperation with companies: 'Hellus' brand of dairy products (Tere AS), cheese 'Andre Salute' (Andre Juustufarm OÜ), probiotic yoghurt ice cream (Balbiino AS), probiotic Madagascar chocolate (Chocolala OÜ), it is also marketed as a Reg'Activ food supplement (OÜ NoraVita).

Another important field of the collection's work is to elucidate the sources of the causative agents of opportunistic infections, their drug susceptibility and virulence factors. This will allow to map their spread and to update the treatment guidelines. These works are based on a sub-collection of opportunistic bacteria associated with clinical infections, that have been collected in collaboration with various clinics and foreign partners. Using and / or supplementing the HUMB collection, national treatment guidelines have been developed, numerous doctoral and master's theses have been defended, and more than 400 scientific publications have been completed.
Biobank is open for scientific cooperation.

Please contact us to receive additional information about the strains:

tiiu.roop [at] ut.ee
eet.mandar [at] ut.ee

Human Microbiota Biobank

Department of Microbiology

University of Tartu

Ravila 19

Tartu 50411

Estonia

 

 

E-mail:

tiiu.roop [at] ut.ee

reet.mandar [at] ut.ee



Please contact us to receive additional information about the strains.

We can perform also several additional tests for the strains.