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We began analyzing https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02043-8, but it redirected us to https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02043-8. The analysis below is for the second page.

Title[redir]:
Bacterial community assembly of specific pathogen-free neonatal mice | Microbiome | Full Text
Description:
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

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Keywords {🔍}

pubmed, samples, article, google, scholar, microbiota, central, cas, bacterial, gut, microbiome, maternal, mice, neonatal, fig, fecal, identified, community, diversity, body, sites, analysis, taxa, mouse, human, earlylife, sequencing, pups, life, early, data, microbes, pup, based, proteus, age, rrna, gene, infants, weaning, taxonomic, sequences, abundance, multiple, ligilactobacillus, development, collected, asv, strains, dam,

Topics {✒️}

ultra-fast single-node solution 1-mm-diameter zirconia/silica beads dominguez-bello mg v4-16s rrna gene short-read shotgun sequencing fast gapped-read alignment nsf grant dge-1745038/dge-2139839 dual-index sequencing strategy limited strain-level descriptions maternal body-site samples ncbi-genome-download fecal–oral microbial transmission interferon-λ determine persistence specific pathogen-free conditions human rotavirus-induced diarrhoea p10–p14 versus p15–p20 de jesus-laboy km broader strain-level resolution early-life bacterial microbiota lyse&spin collection tubes early-life murine microbiome high-throughput sequencing reads infant microbiota transmission infant microbial transmission 16s rrna gene challenges administered pre-weaning dominant early-life taxa illumina miseq instrument van houten ma optimal experimental design strain-specific functional adaptation milk-based diet selects early-life fecal samples coverage statistics—contigs arising low-biomass sites low biomass sites 16s rrna v4 privacy choices/manage cookies specific pathogen-free shotgun metagenomic sequencing maternal body sites maternal body sites shotgun-sequenced mouse samples 16s rrna genes authors scientific editing identify early-life microbes multiple body sites oral contact events lda effect size fecal-oral transmission

Questions {❓}

  • Specific pathogen-free (SPF) animal status as a variable in biomedical research: have we come full circle?
  • Weaning: what influences the timing?
  • Org/records/10456555?

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Video Abstract

Background

Newborn human infants gradually acquire a diverse set of microbes starting at the time of delivery [4.89s.