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PMID: 19759898 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.

PloS one ·Vol. 4 ·No. 9 ·2009-09-17 ·Pages e7063

Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M

Abstract

The low and variable prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae DNA in human stool contrasts with the paramount role of these methanogenic Archaea in digestion processes. We hypothesized that this contrast is a consequence of the inefficiencies of current protocols for archaeon DNA extraction. We developed a new protocol for the extraction and PCR-based detection of M. smithii and M. stadtmanae DNA in human stool. Stool specimens collected from 700 individuals were filtered, mechanically lysed twice, and incubated overnight with proteinase K prior to DNA extraction using a commercial DNA extraction kit. Total DNA was used as a template for quantitative real-time PCR targeting M. smithii and M. stadtmanae 16S rRNA and rpoB genes. Amplification of 16S rRNA and rpoB yielded positive detection of M. smithii in 95.7% and M. stadtmanae in 29.4% of specimens. Sequencing of 16S rRNA gene PCR products from 30 randomly selected specimens (15 for M. smithii and 15 for M. stadtmanae) yielded a sequence similarity of 99-100% using the reference M. smithii ATCC 35061 and M. stadtmanae DSM 3091 sequences. In contrast to previous reports, these data indicate a high prevalence of the methanogens M. smithii and M. stadtmanae in the human gut, with the former being an almost ubiquitous inhabitant of the intestinal microbiome.

MeSH Terms
Adolescent Adult Aged Aged, 80 and over Child Child, Preschool DNA, Archaeal/analysis Feces Female Gene Expression Regulation, Bacterial Humans Infant Infant, Newborn Infections/epidemiology,microbiology Intestines/microbiology Male Methanobacteriaceae/metabolism Methanobrevibacter/metabolism Microbiological Techniques Middle Aged RNA, Ribosomal, 16S/metabolism Reverse Transcriptase Polymerase Chain Reaction/methods
Chemicals
DNA, Archaeal RNA, Ribosomal, 16S
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Dridi Bédis
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes UMR CNRS 6236 IRD 3R198, IFR 48, Faculté de Médecine, Université de la Méditerranée and Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
Henry Mireille
El Khéchine Amel
Raoult Didier
Drancourt Michel
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Article Info
Journal
PloS one
Abbr.
PLoS One
ISSN
1932-6203
DOI
10.1371/journal.pone.0007063
Published
2009-09-17
Epub
2009-00-17
Pages
e7063
Language
English
Region
United States
NLM ID
101285081
PMCID
PMC2738942
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pone.0007063 PMC Full Text View journal details
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