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Journal of Biosciences

, Volume 42, Issue 1, pp 113–119 | Cite as

Molecular analysis of the human faecal archaea in a southern Indian population

  • Sandya B Rani
  • Ramadass Balamurugan
  • Balakrishnan S Ramakrishna
Article

Abstract

Archaea are an important constituent of the human gut microbiota, but there is no information on human gut archaea in an Indian population. In this study, faecal samples were obtained from different age groups (neonatal babies, pre-school children, school-going children, adolescents, adults and elderly) of a southern Indian population, and from a tribal population also resident in southern India). 16S rRNA gene sequences specific to Archaea were amplified from pooled faecal DNA in each group, sequenced, and aligned against the NCBI database. Of the 806 adequate sequences in the study, most aligned with 22 known sequences. There were 9 novel sequences in the present study. All sequences were deposited in the GenBank nucleotide sequence database with the following accession numbers: KF607113 - KF607918. Methanobrevibacter was the most prevalent genus among all the age groups accounting for 98% in neonates, 96% in post-weaning, and 100% each in preschool, school and adult population. In the elderly, Methanobrevibacter accounted for 96% and in tribal adults, 99% of the clones belonged to Methanobrevibacter genus. Other genera detected included Caldisphaera, Halobaculum, Methanosphaeraand Thermogymnomonas. Methanobrevibacter smithii predominated in all age groups, accounting for 749 (92.9%) of the 806 sequences. Archaea can be found in the faeces of southern Indian residents immediately after birth. Methanobrevibacter smithii was the dominant faecal archeon in all age groups, with other genera being found at the extremes of age.

Keywords

Gut microbiota methanogen microbial diversity 

Notes

Acknowledgements

This study was funded by grant no. BT/PR-10769/FNS/20/384/2008 from the Department of Biotechnology, New Delhi, India.

References

  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W and Lipman DJ 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  2. Auguet JC, Barberan A and Casamayor EO 2010 Global ecological patterns in uncultured Archaea. ISME J. 4 182–190CrossRefPubMedGoogle Scholar
  3. Baker GC and Cowan DA 2004 16S rDNA primers and the unbiased assessment of thermophile diversity. Biochem. Soc. Trans. 32 281–221Google Scholar
  4. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, et al. 2010 Enigmatic, ultrasmall, uncultivated Archaea. Proc. Natl. Acad. Sci. USA 107 8806–8811CrossRefPubMedPubMedCentralGoogle Scholar
  5. Balamurugan R, Janardhan HP, George S, Chittaranjan SP and Ramakrishna BS 2008 Bacterial succession in the colon during childhood and adolescence: molecular studies in a southern Indian village. Am. J. Clin. Nutr. 88 1643–1647CrossRefPubMedGoogle Scholar
  6. Balamurugan R, Aarthi CM, Chittaranjan SP and Ramakrishna BS 2009 Molecular detection of the ruminal bacterium, Butyrivibrio fibrisolvens, in feces from rural residents of southern India. Microb. Ecol. Health Dis. 21 38–43CrossRefGoogle Scholar
  7. Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Haché C, Bourdages R and Duchaine C 2014 Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One 9 e87734CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cavicchioli R 2011 Archaea--timeline of the third domain. Nat. Rev. Microbiol. 9 51–61CrossRefPubMedGoogle Scholar
  9. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM and Tiedje JM 2005 The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33 D294–D296CrossRefPubMedGoogle Scholar
  10. Dridi B, Henry M, El Khechine A, Raoult D and Drancourt M 2009 High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4 e7063CrossRefPubMedPubMedCentralGoogle Scholar
  11. Dridi B, Raoult D and Drancourt M 2011 Archaea as emerging organisms in complex human microbiomes. Anaerobe. 17 56–63CrossRefPubMedGoogle Scholar
  12. Forterre P, Brochier C and Philippe H 2002 Evolution of the Archaea. Theor. Popul. Biol. 61 409–422CrossRefPubMedGoogle Scholar
  13. Kabeerdoss J, Ferdous S, Balamurugan R, Mechenro J, Vidya R, Santhanam S, Jana AK and Ramakrishna BS 2013 Development of the gut microbiota in southern Indian infants from birth to six months: a molecular analysis. J Nutr Sci. 2, e18CrossRefPubMedPubMedCentralGoogle Scholar
  14. Lagier JC, Million M, Hugon P, Armougom F and Raoult D 2012 Human gut microbiota: repertoire and variations. Front. Cell Infect. Microbiol. 2 136CrossRefPubMedPubMedCentralGoogle Scholar
  15. McNeil NI 1984 The contribution of the large intestine to energy supplies in man. Am J Clin Nutr. 39 338–342Google Scholar
  16. Mihajlovski A, Dore J, Levenez F, Alric M and Brugere JF 2010 Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age-associated increase of the diversity. Environ. Microbiol. Rep. 2 272–280CrossRefPubMedGoogle Scholar
  17. Miller TL, Wolin MJ, Conway de Macario E and Macario AJ 1982 Isolation of Methanobrevibacter smithii from human feces. Appl. Environ. Microbiol. 43 227–232PubMedPubMedCentralGoogle Scholar
  18. Palmer C, Bik EM, DiGiulio DB, Relman DA and Brown PO 2007 Development of the human infant intestinal microbiota. PLoS Biol. 5 e177CrossRefPubMedPubMedCentralGoogle Scholar
  19. Pochart P, Lemann F, Flourie B, Pellier P, Goderel I and Rambaud JC 1993 Pyxigraphic sampling to enumerate methanogens and anaerobes in the right colon of healthy humans. Gastroenterology 105 1281–1285CrossRefPubMedGoogle Scholar
  20. Pozuelo M, Panda S, Santiago A, Mendez S, Accarino A, Santos J, Guarner F, Azpiroz F, et al. 2015 Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome. Sci. Rep. 5 12693. doi: 10.1038/srep12693 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Rajilić-Stojanović M and de Vos WM 2014 The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol. Rev.. doi: 10.1111/1574-6976.12075 PubMedPubMedCentralGoogle Scholar
  22. Ramakrishna BS 2007 The normal bacterial flora of the human intestine and its regulation. J. Clin. Gastroenterol. 41 S2–S6CrossRefGoogle Scholar
  23. Ramakrishna BS 2013 Role of the gut microbiota in human nutrition and metabolism. J. Gastroenterol. Hepatol. 28 9–17CrossRefPubMedGoogle Scholar
  24. Rutili A, Canzi E, Brusa T and Ferrari A 1996 Intestinal methanogenic bacteria in children of different ages. New Microbiol. 19 227–243PubMedGoogle Scholar
  25. Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, et al. 2007 Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl. Acad. Sci. USA 104 10643–10648CrossRefPubMedPubMedCentralGoogle Scholar
  26. Schleper C, Jurgens G and Jonuscheit M 2005 Genomic studies of uncultivated archaea. Nat. Rev. Microbiol. 3 479–488CrossRefPubMedGoogle Scholar
  27. Stewart JA, Chadwick VS and Murray A 2006 Carriage, quantification, and predominance of methanogens and sulfate-reducing bacteria in faecal samples. Lett. Appl. Microbiol. 43 58–63CrossRefPubMedGoogle Scholar
  28. Vanderhaeghen S, Lacroix C and Schwab C 2015 Methanogen communities in stools of humans of different age and health status and co-occurrence with bacteria. FEMS Microbiol. Lett. 362, fnv092. doi: 10.1093/femsle/fnv092 CrossRefPubMedGoogle Scholar
  29. Wang Y and Qian PY 2009 Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One 4 e7401CrossRefPubMedPubMedCentralGoogle Scholar
  30. Wright ES, Yilmaz LS and Noguera DR 2012 DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl. Environ. Microbiol. 78 717–725CrossRefPubMedPubMedCentralGoogle Scholar
  31. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, et al. 2014 Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12 635–645CrossRefPubMedGoogle Scholar

Copyright information

© Indian Academy of Sciences 2017

Authors and Affiliations

  • Sandya B Rani
    • 1
  • Ramadass Balamurugan
    • 1
  • Balakrishnan S Ramakrishna
    • 1
  1. 1.The Wellcome Trust Research LaboratoryChristian Medical CollegeVelloreIndia

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