Bacterial community assembly of specific pathogen-free neonatal mice
Abstract Background Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We addres...
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BMC
2025-02-01
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| Series: | Microbiome |
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| Online Access: | https://doi.org/10.1186/s40168-025-02043-8 |
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| author | Elizabeth A. Kennedy James S. Weagley Andrew H. Kim Avan Antia Anna L. DeVeaux Megan T. Baldridge |
| author_facet | Elizabeth A. Kennedy James S. Weagley Andrew H. Kim Avan Antia Anna L. DeVeaux Megan T. Baldridge |
| author_sort | Elizabeth A. Kennedy |
| collection | DOAJ |
| description | Abstract Background Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters. Results The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species. Conclusions Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract |
| format | Article |
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| institution | Kabale University |
| issn | 2049-2618 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
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| series | Microbiome |
| spelling | doaj-art-fa8815d2cd914f5e9e8cdd7f672b0b3d2025-02-09T12:46:44ZengBMCMicrobiome2049-26182025-02-0113111410.1186/s40168-025-02043-8Bacterial community assembly of specific pathogen-free neonatal miceElizabeth A. Kennedy0James S. Weagley1Andrew H. Kim2Avan Antia3Anna L. DeVeaux4Megan T. Baldridge5Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of MedicineDivision of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of MedicineDivision of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of MedicineDepartment of Molecular Microbiology, Washington University School of MedicineDivision of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of MedicineDivision of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of MedicineAbstract Background Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters. Results The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species. Conclusions Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstracthttps://doi.org/10.1186/s40168-025-02043-8MicrobiotaMicrobiomeMother-infant transmissionDevelopmentEarly-lifeSeeding |
| spellingShingle | Elizabeth A. Kennedy James S. Weagley Andrew H. Kim Avan Antia Anna L. DeVeaux Megan T. Baldridge Bacterial community assembly of specific pathogen-free neonatal mice Microbiome Microbiota Microbiome Mother-infant transmission Development Early-life Seeding |
| title | Bacterial community assembly of specific pathogen-free neonatal mice |
| title_full | Bacterial community assembly of specific pathogen-free neonatal mice |
| title_fullStr | Bacterial community assembly of specific pathogen-free neonatal mice |
| title_full_unstemmed | Bacterial community assembly of specific pathogen-free neonatal mice |
| title_short | Bacterial community assembly of specific pathogen-free neonatal mice |
| title_sort | bacterial community assembly of specific pathogen free neonatal mice |
| topic | Microbiota Microbiome Mother-infant transmission Development Early-life Seeding |
| url | https://doi.org/10.1186/s40168-025-02043-8 |
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