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Diversity of Human-Associated Methanobrevibacter smithii Isolates Revealed by Multispacer Sequence Typing

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Abstract

Methanobrevibacter smithii is the main archaea in human, detoxifying molecular hydrogen resulting from anaerobic bacteria fermentations into gaseous methane. Its identification relies on gene sequencing, but no method is available to discriminate among genetic variants of M. smithii. Here, we developed a multispacer sequence typing (MST) for genotyping the genetic variants of M. smithii. Four intergenic spacers recovered from the M. smithii reference genome were PCR amplified and sequenced in three M. smithii reference strains and in a collection of 22 M. smithii isolates from the oral cavity in two individuals and the gut of 10 additional individuals. Sequencing yielded 216 genetic polymorphisms including 89 single nucleotide polymorphisms (41.2 %), 83 insertions (38.4 %), and 44 deletions (20.4 %). Combining these genetic polymorphisms yielded 15 genotypes with an index of discrimination of 0.942 (confidence interval 0.9–0.984; P < 0.05). Five M. smithii isolates made from the oral cavity yielded five different genotypes; seven gut isolates yielded nine different genotypes; genotypes MST5 and MST6 were found both in the oral cavity and the gut. Multiple genotypes were identified in some individuals at the same anatomical site. MST is a sequencing-based method which discriminates several genetic variants within M. smithii. Individuals may harbor several contemporary genetic variants of M. smithii in the oral cavity and gut. MST will allow studying population dynamics of M. smithii and tracing its circulation between individuals and their environment.

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Acknowledgments

VN was supported by a Grant of “Mediterranean Infection Institute,” Marseille, France. The work was supported by Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Marseille, France. The authors acknowledge the Ethic Committee of Institut Fédératif de Recherche 48 for reviewing the ethics of the Project.

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Authors and Affiliations

  1. Aix Marseille Université, URMITE, Faculté de Médecine, UM 63 UMR_S1095 UMR 7278, Méditerranée Infection, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France

    Vanessa D. Nkamga, Hong T. T. Huynh, Gérard Aboudharam & Michel Drancourt

  2. Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Nice, Hôpital de l’Archet II, 151 Route de St Antoine de Ginestière, BP 3079, 06202, Nice Cedex 3, France

    Raymond Ruimy

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  1. Vanessa D. Nkamga
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  2. Hong T. T. Huynh
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  3. Gérard Aboudharam
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  4. Raymond Ruimy
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  5. Michel Drancourt
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Correspondence to Michel Drancourt.

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284_2015_787_MOESM1_ESM.pptx

Supplementary Figure S1: Alignment of four intergenic sequences in three references for M. smithii and 22 clinical isolates. S1a, spacer 1 sequence alignment, S1b, spacer 2 sequence alignment; S1 c, spacer 3 sequence alignment; S1d, spacer 4 sequence alignment. Color code: red color indicates absolute consensus; blue color indicates partial, majoritary consensus; black color indicates partial, minority consensus (PPTX 495 kb)

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Nkamga, V.D., Huynh, H.T.T., Aboudharam, G. et al. Diversity of Human-Associated Methanobrevibacter smithii Isolates Revealed by Multispacer Sequence Typing. Curr Microbiol 70, 810–815 (2015). https://doi.org/10.1007/s00284-015-0787-9

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  • DOI: https://doi.org/10.1007/s00284-015-0787-9

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