Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics

Li, S.; Zhang, S.; Li, B.; Sha, S.; Kang, J.; Li, P.; Zhang, A.; Ji, Q.; Lv, Q.; Zhang, X.-X.; Ni, H.; Han, X.; Xu, M.; Wang, G.; Zhang, W.; Sun, Y.; Xu, R.; Xin, Y.; Yan, Q.; Ma, Y.

doi:10.1101/2020.01.29.926196

bioRxiv · 10.1101/2020.01.29.926196

Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics

Li, S.·Zhang, S.·Li, B.·Sha, S.·Kang, J.·Li, P.·Zhang, A.·Ji, Q.·Lv, Q.·Zhang, X.-X.·Ni, H.·Han, X.·Xu, M.·Wang, G.·Zhang, W.·Sun, Y.·Xu, R.·Xin, Y.·Yan, Q.·Ma, Y.

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Abstract

The laboratorial mouse harbors a unique gut microbiota with potential value for human microbiota-associated studies. Mouse gut microbiota has been explored at the genus and species levels, but features rarely been showed at the strain level. The identification of 833,051 and 658,438 nonredundant genes of faeces and gut content samples from the laboratorial C57/BL mice showed over half of these genes were newly found compared to the previous mouse gut microbial gene catalogue. Metagenome-assembled genomes (MAGs) was used to reconstruct 46 nonredundant MAGs belonging to uncultured specieses. These MAGs included members across all phyla in mouse gut (i.e. Firmicutes, Bacteroidetes, Proteobacteria, Deferribacteres, Verrucomicrobia, and Tenericutes) and allowed a strain-level delineating of the mouse gut microbiota. Comparison of MAGs with human gut colonies revealed distinctive genomic and functional characteristics of mouses Bacteroidetes and Firmicutes strains. Genomic characteristics of rare phyla in mouse gut microbiota were demonstrated by MAG approach, including strains of Mucispirillum schaedleri, Parasutterella excrementihominis, Helicobacter typhlonius, and Akkermansia muciniphila. ImportanceThe identification of nonredundant genes suggested the existence of unknown microbes in the mouse gut samples. The metagenome-assembled genomes (MAGs) instantiated the specificity of mouse gut species and revealed an intestinal microbial correlation between mouse and human. The cultivation of faeces and gut contents sample validated the existence of MAGs and estimate their accuracy. Full-length 16S ribosomal RNA gene sequencing enabled taxonomic characterization. This study highlighted a unique ecosystem in the gut of laboratorial mice that obviously differed with the human gut flora at the strain level. The outcomes may be beneficial to researches based on laboratorial mouse models.

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Li, S., Zhang, S., Li, B., Sha, S., Kang, J., Li, P., Zhang, A., Ji, Q., Lv, Q., Zhang, X.-X., Ni, H., Han, X., Xu, M., Wang, G., Zhang, W., Sun, Y., Xu, R., Xin, Y., Yan, Q., Ma, Y.. 2020-01-31. Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics. https://doi.org/10.1101/2020.01.29.926196

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