Metagenomic Analysis of the Dynamic Changes in the Gut Microbiome of the Participants of the MARS-500 Experiment, Simulating Long Term Space Flight

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  • Authors: Mardanov A.V.1, Babykin M.M.2, Beletsky A.V.1, Grigoriev A.I.3, Zinchenko V.V.2, Kadnikov V.V.1, Kirpichnikov M.P.2, Mazur A.M.1,4, Nedoluzhko A.V.1, Novikova N.D.3, Prokhortchouk E.B.1,4, Ravin N.V.1,4, Skryabin K.G.1,4, Shestakov S.V.2
  • Affiliations:
    1. Centre “Bioengineering”, Russian Academy of Sciences
    2. Lomonosov Moscow State University
    3. Russian Federation State Research Center Institute of Biomedical Problems RAS (IBMP)
    4. Biological Faculty, Lomonosov Moscow State University
  • Issue: Vol 5, No 3 (2013)
  • Pages: 116-125
  • Section: Research Articles
  • URL: http://actanaturae.ru/2075-8251/article/view/10594
  • DOI: https://doi.org/10.32607/20758251-2013-5-3-116-125
  • Cite item

Abstract


A metagenomic analysis of the dynamic changes of the composition of the intestinal microbiome of five participants of the MARS-500 experiment was performed. DNA samples were isolated from the feces of the participants taken just before the experiment, upon 14, 30, 210, 363 and 510 days of isolation in the experimental module, and two weeks upon completion of the experiment. The taxonomic composition of the microbiome was analyzed by pyrosequencing of 16S rRNA gene fragments. Both the taxonomic and functional gene content of the microbiome of one participant were analyzed by whole metagenome sequencing using the SOLiD technique. Each participant had a specific microbiome that could be assigned to one of three recognized enterotypes. Two participants had enterotype I microbiomes characterized by the prevalence of Bacteroides, while the microbiomes of two others, assigned to type II, were dominated by Prevotella. One participant had a microbiome of mixed type. It was found that (1) changes in the taxonimic composition of the microbiomes occurred in the course of the experiment, but the enterotypes remained the same; (2) significant changes in the compositions of the microbiomes occurred just 14-30 days after the beginning of the experiment, presumably indicating the influence of stress factors in the first stage of the experiment; (3) a tendency toward a reversion of the microbiomes to their initial composition was observed two weeks after the end of the experiment, but complete recovery was not achieved. The metagenomic analysis of the microbiome of one of the participants showed that in spite of variations in the taxonomic compositions of microbiomes, the “functional” genetic composition was much more stable for most of the functional gene categories. Probably in the course of the experiment the taxonomic composition of the gut microbiome was adaptively changed to reflect the individual response to the experimental conditions. A new, balanced taxonomic composition of the microbiome was formed to ensure a stable gene content of the community as a whole without negative consequences for the health of the participants.


A. V. Mardanov

Centre “Bioengineering”, Russian Academy of Sciences

Author for correspondence.
Email: shestakovgen@mail.ru

Russian Federation

M. M. Babykin

Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

A. V. Beletsky

Centre “Bioengineering”, Russian Academy of Sciences

Email: shestakovgen@mail.ru

Russian Federation

A. I. Grigoriev

Russian Federation State Research Center Institute of Biomedical Problems RAS (IBMP)

Email: shestakovgen@mail.ru

Russian Federation

V. V. Zinchenko

Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

V. V. Kadnikov

Centre “Bioengineering”, Russian Academy of Sciences

Email: shestakovgen@mail.ru

Russian Federation

M. P. Kirpichnikov

Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

A. M. Mazur

Centre “Bioengineering”, Russian Academy of Sciences; Biological Faculty, Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

A. V. Nedoluzhko

Centre “Bioengineering”, Russian Academy of Sciences

Email: shestakovgen@mail.ru

Russian Federation

N. D. Novikova

Russian Federation State Research Center Institute of Biomedical Problems RAS (IBMP)

Email: shestakovgen@mail.ru

Russian Federation

E. B. Prokhortchouk

Centre “Bioengineering”, Russian Academy of Sciences; Biological Faculty, Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

N. V. Ravin

Centre “Bioengineering”, Russian Academy of Sciences; Biological Faculty, Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

K. G. Skryabin

Centre “Bioengineering”, Russian Academy of Sciences; Biological Faculty, Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

S. V. Shestakov

Lomonosov Moscow State University

Email: shestakovgen@mail.ru

Russian Federation

  1. Huttenhower C., Gevers D., Knight R., Abubucker S., Badger J.H., Chinwalla A.T., Creasy H.H., Earl A.M., FitzGerald M.G., Fulton R.S. // Nature 2012, V.486, P.207-214
  2. Methe B.A., Nelson K.E., Pop M., Creasy H.H., Giglio M.G., Huttenhower C., Gevers D., Petrosino J.F., Abubucker S., Badger J.H. // Nature 2012, V.486, P.215-221
  3. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T. // Nature 2010, V.486, P.59-65
  4. Kinross J.M., von Roon A.C., Holmes E., Darzi A., Nicholson J.K. // Curr. Gasrtoenterol. Rep. 2008, V.464, P.396-403
  5. Shestakov S.V. // Biology Bulletin Rev 2011, V.1, №2, P.83-93
  6. Blumberg R., Powrie F. // Science Translational Medicine. 2012, V.4, №137, P.137rv7
  7. Claesson M.J., Cusack S., O’Sullivan O., Greene-Diniza R., de Weerd H., Flannery E., Marchesi J., Falush D., Dinanb T., Fitzgeral G. // Proc. Natl. Acad. Sci. USA. 2011, V.8, SSuppl. 1, P.4586-4591
  8. Turnbaugh P.J., Quince C., Faith J.J., Yatsunenko T., Niazi F., Affourtit J., Egholm M., Henrissat B., Knight R., Gordon J.I. // Proc. Natl. Acad. Sci. USA. 2010, V.7, P.7503-7508
  9. Jalanka-Tuovinen J., Salonen A., Nikkila J., Immonen Q., Kekkonen R., Lahti L., Palva A., de Vos W. // PLoS One. 2011, V.6, P.e23035
  10. Tap J., Mondot S., Levenez F., Pelletier E., Caron C., Furet J-P., Ugarte E., Munoz-Tamayo R., Paslier D.L.E., Nalin R., Dore J., Leclerc M. // Environ. Microbiol. 2009, V.11, №10, P.2574-2584
  11. Willing B.P., Dicksved J., Halvorson J., Andersson A.F., Lucio M., Zheng Z., Jarnerot G., Tysk C., Jansson J.K., Engstrand L. // Gastroenterology. 2010, V.139, P.1844-1854
  12. Frank D.N., St.Amand A.L., Feldman R.A., Boedeker E.C., Harpaz N., Pace N.R. // Proc. Natl. Acad. Sci. USA. 2007, V.104, P.13780-13785
  13. Dethlefsen L., Huse S., Sogin M.L., Relman D.A. // PLoS Biol. 2008, V.6, P.e280
  14. Dethlefsen L., Relman D.A. // Proc. Natl. Acad. Sci. USA. 2011, V.108, P.4554-4561
  15. Robinson C.J., Bohannan B.J.M., Young V.B. // Microbiol. Mol. Biol. Rev. 2010, V.74, №3, P.453-476
  16. Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.-Y., Keilbaugh S.A., Bewtra M., Knights D., Walters W.A., Knight R. // Science. 2011, V.334, P.105-108
  17. Claesson M.J., Jeffery I.B., Conde S., Power S.E., O’Connor E.M., Cusack S., Harris H.M.B., Coakley M., Lakshminarayanan M., O’Sullivan O. // Nature 2012, V.488, P.178-184
  18. Lutgendorff F., Akkermans L.M.A., Soderholm J.D. // Curr. Mol. Med. 2008, V.8, P.282-298
  19. Phillips M.L. // Environmental Health Perspectives. 2009, V.117, P.199-205
  20. Sharkey K.A., Mawe G.M. // ature Rev. Gastroenterology, Hepatology. 2012, V.9, P.74-76
  21. Lebedev V.V. // Herald of the Russian Academy of Sciences. 2010, V.80, №11, P.1000-1004
  22. Grigoriev A.I., Egorov A.D. // Man in a space flight. // Airspace biology and medicine. M. Science. 1997. 1997, V.3, №2, P.368-447
  23. Lizko N.N. // Nahrung. 1987, V.31, P.443-447
  24. Lizko N.N. // Vestnik RAMS. 1996, V.8, P.31-34
  25. Ilyin V.K., Batov A.B., Novikova N.D., Mukhamedieva L.N., Poddubko S.V., Gegenava A.V., Mardanov R.G., Solovieva Z.O., Skedina M.A. // Aviakosmicheskaya i Ekologicheskaya Meditsina (Aerospace and Ecological Medicine). 2010, V.44, №4, P.52-57
  26. Ushakov I.B. // Abst. Intern. Symp. Results of the experiments simulating manned mission to Mars (MARS-500). Moscow. 2012. 2012, P.46-65
  27. Morukov B.V., Belakovsky M.S., Demin E.P., Suvorov A.V. // Abst. Intern. Symp. Results of the experiments simulating manned mission to Mars (MARS-500). Moscow. 2012. 2012, P.44
  28. Salonen A., Nikkila J., Jalanka-Tuovinen J., Immonen O., Rajilic-Stojanovic M., Kekkonen R.A., Palva A., de Vos W. // J. Microbiol. Methods. 2010, V.81, P.127-134
  29. Cole R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G. M., Tiedje J. M. // Nucleic Acids Research 2009, V.37, P.D141-D145
  30. Simpson J.T., Wong K., Jackman S.D., Jones S.J.M., Birol I. // Genome Res. 2009, V.19, №6, P.1117-1123
  31. Rho M., Tang H., Ye Y. // Nucleic Acid Res. 2010, V.38, №20, P.e191
  32. Kent W.J. // Genome Res. 2002, V.12, P.656-664
  33. Benson D.A., Karsch-Mizrachi I., D.J.Lipman I.O., J.Ostell I.O., E.W.Sayers. I.O. // Nucleic Acid Research. 2011, V.39, P.D32-D37
  34. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., Yamanishi Y. // Nucleic Acids Research 2008, V.36, SSuppl. 1, P.D480-D484
  35. Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H-Y., Cohoon M., de Crecy-Lagard V., Diaz N., Disz T., Edwards R. // Nucleic Acids Research 2005, V.33, №17, P.5691-5702
  36. Apweiler R., Martin M.J., O’Donovan C., Magrane M., Alam-Faruque J., Antunes R., Barrell D., Bely B., Bimgley M., Binns D. // Nucleic Acids Research 2011, V.39, P.D214-D219
  37. Langmead B., Trapnell C., Pop M., Salzberg S.L. // Ultrafast // Genome Biol. 2009, V.10, №3, P.R25
  38. Eckburg P.B., Bik E.M., Bernstein C.N., Purdom E., Dethlefsen L., Sargent M., Gill S.R., Nelson K.E., Relman D.A. // Science. 2005, V.308, P.1635-1668
  39. Claesson M.J., O’Sullivan O., Wang Q., Nikkila J., Marchesi J.R., Smidt H., de Vos W.M., Ross R.P., O’Toole P.W. // PLoS One. 2009, V.4, P.e6669
  40. O’Toole P.W., Claesson M.J. // Intern. Dairy J. 2010, V.20, P.281-291
  41. Arumugam M., Raes. J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., Fernandes G.R., Tap J., Bruls T., Batto J.-M. // Nature 2011, V.473, P.174-180
  42. Huse S.M., Ye Y., Zhou V., Fodor A.A. // PLoS One. 2012, V.7, P.e34242
  43. Jeffrey I.B., Claesson J., O’Toole P.W. // arure Microbiol. Rev. 2012, V.10, P.591-592
  44. Frank D.N., Pace N.R. // Curr. Opin. Gastroenterol. 2008, V.24, P.4-10
  45. Ley R.E., Turnbaugh P.J., Klein S., Gordon J.I. // Nature 2006, V.444, P.1022-1023
  46. Schwiertz A., Taras D., Schafer K., Beijer S., Bos N.A., Donus C., Hardt P.D. // Obesity. 2009, V.18, P.190-195
  47. Jerenberg C., Lofmark S., Edlund C., Jansson J.K. // ISME J. 2007, V.1, P.55-61
  48. Bratlie M., Johansen J., Sherman B.T., Huang D.W., Lempicki R.A., Drablos F. // BMC Genomics. 2010, V.11, P.588
  49. Anderson J.K., Smith T.G., Hoover T.R. // Trends Microbiol. 2010, V.118, №1, P.30-37
  50. Smillie C.S., Smith M.B., Friedman J., Cordero O.X., David L.A., Alm E.J. // Nature 2011, V.480, P.241-244

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Copyright (c) 2013 Mardanov A.V., Babykin M.M., Beletsky A.V., Grigoriev A.I., Zinchenko V.V., Kadnikov V.V., Kirpichnikov M.P., Mazur A.M., Nedoluzhko A.V., Novikova N.D., Prokhortchouk E.B., Ravin N.V., Skryabin K.G., Shestakov S.V.

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