Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

摘要: Maternal transmission and cage effects are powerful confounding factors in microbiome studies. To assess the consequences of microenvironment on mouse gut microbiome, two groups germ-free (GF) wild-type (WT) mice, one gavaged with a microbiota harvested from adult WT mice another allowed to acquire microenvironment, were monitored using Illumina 16S rRNA sequencing over period 8 weeks. Our results revealed that moved GF specific pathogen free (SPF) conditions take several weeks develop not eliminated by initial gavage treatment. Initial influenced, but did eliminate successional pattern which Proteobacteria became less abundant time. An analysis sequences mapped closest sequenced whole genome suggests functional potential microbial genomes changes significantly time shifting an emphasis pathogenesis motility early community assembly metabolic processes at later points. Functionally, naturally their cage, common biome, exhibit effect Dextran Sulfate Sodium-induced inflammation. argue while there long-term founding community, these mitigated time, must both be explicitly considered interpretation experiments.