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. 2024 Jan-Dec;16(1):2393791.
doi: 10.1080/19490976.2024.2393791. Epub 2024 Sep 4.

MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes

Nayeon Kim  1 , Chan Yeong Kim  1 , Junyeong Ma  1 , Sunmo Yang  1 , Dong Jin Park  2 , Sang-Jun Ha  2 , Peter Belenky  3 , Insuk Lee  1   4
Affiliations

MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes

Nayeon Kim et al. Gut Microbes. 2024 Jan-Dec.

Abstract

Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.

Keywords: Gut microbiome; metagenome-assembled genomes; mouse gut microbiome; reference microbiome.

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Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Overview of mouse gut microbial genomes in MRGM.
Figure 2.
Figure 2.
Functional annotations of mouse gut microbial proteins in MRGM.
Figure 3.
Figure 3.
Enhanced taxonomic diversity of mouse gut microbiota.
Figure 4.
Figure 4.
Assessment of taxonomic profiling with MRGM.
Figure 5.
Figure 5.
Taxonomic divergence between human and mouse gut microbiota.
Figure 6.
Figure 6.
Functional divergence between human and mouse gut microbiota.
Figure 7.
Figure 7.
Comparison of secondary metabolite potentials between human and mouse gut microbiota.
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