Fig. 1

The early-life fecal microbiota begins diversifying at postnatal day 15. A Taxonomic classification of stool samples collected from neonates sequenced at the 16S rRNA gene V4 region. Genera represented at greater than 5% abundance in at least one sample are shown. Each bar represents the average abundance of taxa from all samples collected from pups from the litter for a given time point; the n above each bar indicates the number of samples collected for that time point. Color families show phyla-level assignments—blue for Bacteroidetes, orange for Deferribacteres, red for Firmicutes, green for Proteobacteria, and yellow for Verrucomicrobia; grey includes phyla present at less than 5% abundance in all samples. LEfSe analysis was performed to identify discriminatory taxa between pup microbiota samples from P10–P14 versus P15–P20. Cutoff was a logarithmic linear discriminant analysis (LDA) score of 4.0. B Discriminatory taxa displayed based on effect size. C Cladogram of age-discriminant taxa. D Shannon diversity calculated based on operational taxonomic unit (OTU) clustering. E Faith’s phylogenetic diversity was calculated based on the phylogeny of amplicon sequence variants (ASVs). F 16S rRNA gene copies per fecal pellet, detected by qPCR. Medians are indicated by a horizontal line. Results were compared by the Kruskal-Wallis test with Dunn’s test for multiple comparisons. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, ns, not significant; n =12–57, representing samples from mice combined across four litters from two genotypes as in A within indicated age ranges