Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes
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 infl...
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MDPI AG
2024-11-01
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| Series: | Applied Microbiology |
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| Online Access: | https://www.mdpi.com/2673-8007/4/4/109 |
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| author | Zachary L. McAdams Susheel Bhanu Busi Kevin L. Gustafson Nathan Bivens Craig L. Franklin Paul Wilmes Aaron C. Ericsson |
| author_facet | Zachary L. McAdams Susheel Bhanu Busi Kevin L. Gustafson Nathan Bivens Craig L. Franklin Paul Wilmes Aaron C. Ericsson |
| author_sort | Zachary L. McAdams |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-8871f314fc894561bd456a337ebdd18d |
| institution | DOAJ |
| issn | 2673-8007 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Applied Microbiology |
| spelling | doaj-art-8871f314fc894561bd456a337ebdd18d2025-08-20T02:50:52ZengMDPI AGApplied Microbiology2673-80072024-11-01441600161510.3390/applmicrobiol4040109Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled GenomesZachary L. McAdams0Susheel Bhanu Busi1Kevin L. Gustafson2Nathan Bivens3Craig L. Franklin4Paul Wilmes5Aaron C. Ericsson6Molecular Pathogenesis and Therapeutics Program, University of Missouri, Columbia, MO 65201, USAUK Centre for Ecology and Hydrology, Wallingford OX10 8BB, UKDepartment of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201, USAUniversity of Missouri Genomics Technology Core Facility, University of Missouri, Columbia, MO 65201, USAMolecular Pathogenesis and Therapeutics Program, University of Missouri, Columbia, MO 65201, USALuxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, LuxembourgMolecular Pathogenesis and Therapeutics Program, University of Missouri, Columbia, MO 65201, USAHost 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.https://www.mdpi.com/2673-8007/4/4/109gut microbiomemetagenomicsmetatranscriptomicsThe Jackson LaboratoryInotiv |
| spellingShingle | Zachary L. McAdams Susheel Bhanu Busi Kevin L. Gustafson Nathan Bivens Craig L. Franklin Paul Wilmes Aaron C. Ericsson Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes Applied Microbiology gut microbiome metagenomics metatranscriptomics The Jackson Laboratory Inotiv |
| title | Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes |
| title_full | Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes |
| title_fullStr | Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes |
| title_full_unstemmed | Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes |
| title_short | Multi-Omics Analysis of Mouse Fecal Microbiome Reveals Supplier-Dependent Functional Differences and Novel Metagenome-Assembled Genomes |
| title_sort | multi omics analysis of mouse fecal microbiome reveals supplier dependent functional differences and novel metagenome assembled genomes |
| topic | gut microbiome metagenomics metatranscriptomics The Jackson Laboratory Inotiv |
| url | https://www.mdpi.com/2673-8007/4/4/109 |
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