Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes

McAdams, Zachary L. ORCID: https://orcid.org/0000-0003-2883-507X; Busi, Susheel Bhanu ORCID: https://orcid.org/0000-0001-7559-3400; Gustafson, Kevin L. ORCID: https://orcid.org/0000-0002-2104-8762; Bivens, Nathan; Franklin, Craig L. ORCID: https://orcid.org/0000-0002-9198-867X; Wilmes, Paul ORCID: https://orcid.org/0000-0002-6478-2924; Ericsson, Aaron C. ORCID: https://orcid.org/0000-0002-3053-7269. 2024 Multi-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes [in special issue: Microbiome in ecosystem, 3rd ed.] Applied Microbiology, 4 (4). 1600-1615. 10.3390/applmicrobiol4040109

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Official URL: https://doi.org/10.3390/applmicrobiol4040109

Abstract/Summary

Host genetics and environmental factors have been associated with effects on the mouse fecal microbiome; however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on targeted-amplicon sequencing data, and functional differences between these communities remain poorly defined. We applied a multi-omic (metagenomic and metatranscriptomic) approach to biomolecules extracted from murine feces representative of two U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes, frequently containing genomic content unique to each supplier. Transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier including carbohydrate, fatty acid, and sulfite metabolism. These data provide a detailed characterization of the baseline differences in the fecal metagenome of mice from two U.S. commercial suppliers, suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony.

Item Type:	Publication - Article
Digital Object Identifier (DOI):	10.3390/applmicrobiol4040109
UKCEH and CEH Sections/Science Areas:	Soils and Land Use (Science Area 2017-)
ISSN:	2673-8007
Additional Information. Not used in RCUK Gateway to Research.:	Open Access paper - full text available via Official URL link.
Additional Keywords:	gut microbiome, metagenomics, metatranscriptomics, The Jackson Laboratory, Inotiv
NORA Subject Terms:	Zoology Biology and Microbiology Data and Information
Related URLs:	Other Other
Date made live:	06 Dec 2024 12:46 +0 (UTC)
URI:	https://nora.nerc.ac.uk/id/eprint/538515

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.3390/applmicrobiol4040109

UKCEH and CEH Sections/Science Areas:

Soils and Land Use (Science Area 2017-)

ISSN:

2673-8007

Additional Information. Not used in RCUK Gateway to Research.:

Open Access paper - full text available via Official URL link.

Additional Keywords:

gut microbiome, metagenomics, metatranscriptomics, The Jackson Laboratory, Inotiv