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Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

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Abstract

Until recently, human gut microbiota was believed to be colonized by few methanogenic archaeal species. Much higher microbial diversity within the human gut was revealed by the use of molecular approaches as compared to routine microbiological techniques, but still, a lot remains unknown. Molecular techniques has the advantage of being rapid, reproducible, and can be highly discriminative as compared to conventional culturing methods. Some of them provide both qualitative and quantitative information. However, the choice of method should be taken with care to avoid biases. The advent of next-generation sequencing gives much deeper information from which functional and ecological hypotheses can be drawn. In this review, molecular techniques that are currently used together with their possible future developments to study gut methanogenic communities are indicated along with their limitations and difficulties that are encountered during their implementation. Moreover, the high amount of metagenomics data from the human gut microbiome indicate that this environment could be a paradigm for new directions in methanogen diversity studies and help to develop new approaches for other environments as well. Concerning humans, this should help us to better understand the possible association of methanogens with some of the diseased conditions and their peculiar distribution among age groups in human.

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Acknowledgments

This work was supported by a PhD. Scholarship support from the French “Ministère de l’Enseignement Supérieur et de la Recherche” to N.G. J.-F.B and P.P.C. thanks the “Université d’Auvergne” for the funding of a post-doctoral fellowship (attributed to P.P.C). P.W.O.T. was supported by Science Foundation Ireland through a Principal Investigator award, by a CSET award to the Alimentary Pharmabiotic Centre, and by an FHRI award to the ELDERMET project by the Dept. Agriculture, Fisheries and Marine of the Government of Ireland. Authors are thankful to Prof. P. Peyret and Dr. E. Peyretaillade for their valuable suggestions during the preparation of the manuscript.

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. EA 4678 CIDAM, Clermont Université; Université d’Auvergne, Clermont-Ferrand, France

    Prem Prashant Chaudhary, Nadia Gaci & Jean-François Brugère

  2. Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland

    Guillaume Borrel & Paul W. O’Toole

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  1. Prem Prashant Chaudhary
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  2. Nadia Gaci
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  5. Jean-François Brugère
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Correspondence to Jean-François Brugère.

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Chaudhary, P.P., Gaci, N., Borrel, G. et al. Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions. Appl Microbiol Biotechnol 99, 5801–5815 (2015). https://doi.org/10.1007/s00253-015-6739-2

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