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.
Gut microbiota methanogen microbial diversity
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This study was funded by grant no. BT/PR-10769/FNS/20/384/2008 from the Department of Biotechnology, New Delhi, India.
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
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
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
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 One9 e87734CrossRefPubMedPubMedCentralGoogle Scholar
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
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 One4 e7063CrossRefPubMedPubMedCentralGoogle Scholar
Dridi B, Raoult D and Drancourt M 2011 Archaea as emerging organisms in complex human microbiomes. Anaerobe.17 56–63CrossRefPubMedGoogle Scholar
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
McNeil NI 1984 The contribution of the large intestine to energy supplies in man. Am J Clin Nutr.39 338–342Google Scholar
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
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
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. Gastroenterology105 1281–1285CrossRefPubMedGoogle Scholar
Ramakrishna BS 2007 The normal bacterial flora of the human intestine and its regulation. J. Clin. Gastroenterol.41 S2–S6CrossRefGoogle Scholar
Ramakrishna BS 2013 Role of the gut microbiota in human nutrition and metabolism. J. Gastroenterol. Hepatol.28 9–17CrossRefPubMedGoogle Scholar
Rutili A, Canzi E, Brusa T and Ferrari A 1996 Intestinal methanogenic bacteria in children of different ages. New Microbiol.19 227–243PubMedGoogle Scholar
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. USA104 10643–10648CrossRefPubMedPubMedCentralGoogle Scholar
Schleper C, Jurgens G and Jonuscheit M 2005 Genomic studies of uncultivated archaea. Nat. Rev. Microbiol.3 479–488CrossRefPubMedGoogle Scholar
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
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 One4 e7401CrossRefPubMedPubMedCentralGoogle Scholar
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