An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

Lesker, Till Robin; Durairaj, Abilash Chakravarthy; Galvez, Eric; Lagkouvardos, Ilias; Baines, John F.; Clavel, Thomas; Sczyrba, Alexander; McHardy, Alice C.; Strowig, Till

doi:10.1016/j.celrep.2020.02.036

Cited by 95 publications

(145 citation statements)

References 69 publications

(112 reference statements)

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“…We next used mouse gut related bacterial genomes (Wannemuehler et al, 2014;Lagkouvardos et al, 2016;Brugiroux et al, 2017;Liu et al, 2020;) from IMG and NCBI Refseq and 14 high-quality genomes (completeness >90% and contamination <5%) assembled from reads accessible from PRJEB10572 (Lagkouvardos et al, 2016) (Supplementary Table 3) to generate a Mouse Gut Cultured Bacteria gene set (MiCB). Together with MGGC (Xiao et al, 2015), FDGC (Xiao et al, 2017) and iMGMC (Lesker et al, 2020), downloaded from GigaDB and the GitHub repository, respectively, all gene catalogs were integrated to construct an expanded non-redundant mouse gut bacterial gene catalog (EMGC)( Figure 1). The expanded catalog comprises 5,862,027 genes, which is more than twice the number of genes in the MGGC (Xiao et al, 2015) and one million genes more than the iMGMC catalog (Lesker et al, 2020) (Table 1).…”

Section: Construction and Evaluation Of Emgcmentioning

confidence: 99%

“…Together with MGGC (Xiao et al, 2015), FDGC (Xiao et al, 2017) and iMGMC (Lesker et al, 2020), downloaded from GigaDB and the GitHub repository, respectively, all gene catalogs were integrated to construct an expanded non-redundant mouse gut bacterial gene catalog (EMGC)( Figure 1). The expanded catalog comprises 5,862,027 genes, which is more than twice the number of genes in the MGGC (Xiao et al, 2015) and one million genes more than the iMGMC catalog (Lesker et al, 2020) (Table 1). Thus, 18.93 % of the genes in EMGC are not represented in either the iMGMC or MGGC ( Supplementary Figure 1).…”

Section: Construction and Evaluation Of Emgcmentioning

confidence: 99%

“…MAGs, and by linking MAGs to reconstructed 16S rRNA gene sequences they provided a pipeline enabling improved prediction of functional potentials based on 16S rRNA gene amplicon sequencing (Lesker et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Here we constructed an expanded mouse gut metagenome catalog (EMGC) by integrating 3 published gene catalogs, including the gene catalog of mouse gut metagenome (MGGC) released in 2015 comprising 2,571,074 genes (Xiao et al, 2015), a Feed & Diet Gene Catalog for mice (FDGC) (Xiao et al, 2017), the integrated mouse gut metagenome catalog (iMGMC) (Lesker et al, 2020), 72 available sequenced mouse gut-related bacterial genomes (Wannemuehler et al 2014;Lagkouvardos et al, 2016;Brugiroux et al, 2017;Liu et al, 2020), 14 high-quality genomes assembled from published sequencing data of isolates (Lagkouvardos et al, 2016), and 88 newly shotgun sequenced samples. Our new nonredundant reference gene catalog comprises 5,862,027 genes and was annotated by NR (released on 5 th Jan 2019) and KEGG (release 89) databases (Kanehisa & Goto, 2000).…”

Section: Introductionmentioning

confidence: 99%

“…Our new nonredundant reference gene catalog comprises 5,862,027 genes and was annotated by NR (released on 5 th Jan 2019) and KEGG (release 89) databases (Kanehisa & Goto, 2000). Finally, we generated 902 MGSs from the gene abundance profiles for 326 laboratory mice of EMGC, and compared these MGSs with the high-quality MAG collection (Lesker et al, 2020) and the recent collection of bacteria isolated from the mouse gut (Liu et al, 2020). By combining these individual datasets we increased the number of sequenced bacterial genes of the mouse gut microbiome by more than one million genes, and significantly increased the mapping ratio of read obtained by shotgun sequencing of samples from mouse gut fecal samples providing a resource for future studies on the mouse gut microbiota.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

An expanded gene catalog of the mouse gut metagenome

Zhu

Ren

Huang

et al. 2020

Preprint

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High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of mouse gut metagenomes limits the size and numbers of identified genes in existing catalogs. We therefore established an expanded gene catalog of genes in the mouse gut metagenomes (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse-gut-related bacterial genomes and 3 existing gene catalogs. EMGC increases the number on non-redundant genes by more than one million genes compared to the so far most extensive catalog. More than 50% of the genes in EMGC were taxonomically assigned and 30% were functionally annotated. 902 Metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as an efficient and resource-saving reference dataset for future metagenomic studies in mice.

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Section: Construction and Evaluation Of Emgcmentioning

confidence: 99%

Section: Construction and Evaluation Of Emgcmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

An expanded gene catalog of the mouse gut metagenome

Zhu

Ren

Huang

et al. 2020

Preprint

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Characterization of the gastrointestinal microbiome of the Syrian hamster (Mesocricetus auratus) and comparison to data from mice

Böswald,

Popper,

Matzek

et al. 2024

FEBS Open Bio

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Syrian hamsters (Mesocricetus auratus) have been increasingly used as rodent models in recent years, especially for SARS‐CoV‐2 since the pandemic. However, the physiology of this animal model is not yet well‐understood, even less when considering the digestive tract. Generally, the gastrointestinal microbiome influences the immune system, drug metabolism, and vaccination efficacy. However, a detailed understanding of the gastrointestinal microbiome of hamsters is missing. Therefore, we analyzed 10 healthy 11‐week‐old RjHan:AURA hamsters fed a pelleted standard diet. Their gastrointestinal content was sampled (i.e., forestomach, glandular stomach, ileum, cecum, and colon) and analyzed using 16S rRNA gene amplicon sequencing. Results displayed a distinct difference in the bacterial community before and after the cecum, possibly due to the available nutrients and digestive functions. Next, we compared hamsters with the literature data of young‐adult C57BL/6J mice, another important animal model. We sampled the same gastrointestinal regions and analyzed the differences in the microbiome between both rodents. Surprisingly, we found strong differences in their specific gastrointestinal bacterial communities. For instance, Lactobacillaceae were more abundant in hamsters' forestomach and ileum, while Muribaculaceae dominated in the mouse forestomach and ileum. Similarly, in mouse cecum and colon, Muribaculaceae were dominant, while in hamsters, Lachnospiraceae and Erysipelotrichaceae dominated the bacterial community. Molecular strains of Muribaculaceae in both rodent species displayed some species specificity. This comparison allows a better understanding of the suitability of the Syrian hamster as an animal model, especially regarding its comparability to other rodent models. Thereby, this work contributes to the characterization of the hamster model and allows better experimental planning.

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Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals

Yang

Zhang

et al. 2022

Ecology and Evolution

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The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole‐metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high‐fat and ‐calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.

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An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

Cited by 95 publications

References 69 publications

An expanded gene catalog of the mouse gut metagenome

An expanded gene catalog of the mouse gut metagenome

Characterization of the gastrointestinal microbiome of the Syrian hamster (Mesocricetus auratus) and comparison to data from mice

Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals

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