Abstract
The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.
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Acknowledgements
E.C.H. has been supported by an Australian Postgraduate Award. The financial support of Meat and Livestock Australia Limited via a Technical Assistance Grant (to E.C.H. project code B.STU.0257) as well as funds for project D.MHN.0617 (awarded to J.G.M. and P.R.G.) is gratefully acknowledged. This work has also been supported by funds (to M.M.) via CSIRO’s Science Leader scheme and The University of Queensland Diamantina Institute. The Translational Research Institute is supported by a grant from the Australian Government. The CSIRO projects 01200.035/B.CCH.6510 and 01200.038/B.CCH.6610 were funded by the Australian Government Department of Agriculture, and Meat & Livestock Australia Limited as part of the National Livestock Methane Program. P.Ó.C. is supported by a UQ Reginald Ferguson Research Fellowship in Gastroenterology. We are especially grateful for the technical assistance received with the PacBio sequencing of the BMS genome by Paul Lacaze in his past role with Millennium Science and Lawrie Wheeler (Queensland Institute of Technology), as well as gas chromatography analysis support by Mr Jagadish Padmanabha.
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E.C.H. planned and performed research and helped write the paper; D.H.P., J.G.V., C.P.R., C.S.M., S.E.D. and P.Ó.C. assisted with research and helped write the paper. P.R.G. and J.G.M. provided samples enabling Methanosphaera sp. PA5 isolation and helped with the preparation and review of the manuscript; and P.H., G.W.T., and M.M. planned and supervised research and wrote the paper.
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Hoedt, E.C., Parks, D.H., Volmer, J.G. et al. Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME J 12, 2942–2953 (2018). https://doi.org/10.1038/s41396-018-0225-7
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DOI: https://doi.org/10.1038/s41396-018-0225-7
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