Genomic stability and functional flexibility in intestinal microbiota of gnotobiotic mouse model

In the face of constant microbial mutagenesis and recombination the intestinal microbiota remains reasonably stable in healthy adults taking a consistent diet and no medications. Given that reproducible animal models are essential for mechanistic understanding of host-microbial mutualism, we carried out a 6-year gnotobiotic experiment in mice colonised with 12 representative fully-sequenced taxa to determine the boundaries of microbiota stability and its mechanisms. Non-synonymous mutations that reached a significant allele frequency with corresponding variant RNA expression were mainly single-nucleotide polymorphisms (SNPs) in genes annotated for nutrient acquisition or replication. Comparatively few synonymous mutations fixed in any taxon of the consortium – usually in linkage with a non-synonymous variant – consistent with constant dilution of most neutral mutations through intestinal transit and fecal shedding. Microbial subspecies also evolved with emblematic variants for nutrient acquisition. Dietary shifts caused not only transcriptional adaptation to macronutrient and micronutrient changes, but also rapid selection and expression of SNPs present previously only at low frequency, consistent with their selective advantage on the new diet. Gnotobiotic stability is therefore maintained by removal of variants with no selective advantage by shedding, and flexible adaptation at both genomic and transcriptomic levels to dietary fluctuations.