Association between co-occurrence and appearance of microbes over time and mouse co-location

Background In in vivo experiments, mice are typically co-housed. It is unclear whether co-location has an effect on the fecal microbiota composition. We studied the potential impact of transmission of bacteria between mice sharing a cage on the evolution of the Operational Taxonomic Units (OTUs) present in the gut of the mice over time. Methods We assessed the association between OTU co-occurrence and mouse co-location (across pairs) and between OTU appearance and presence in co-located mice with Fisher-exact test. Logistic models for OTU appearance were fitted using number of co-located mice with OTU or total abundance as covariates. Results The samples for 88 mice at 3 time points had a mean (standard deviation) of 106 (28) OTUs. Across pairs of mice, co-occurrence and co-location were positively associated for 70-77 OTUs. Appearance of OTU was significantly associated with OTU presence in co-located mice for 84 OTUs. There was a significant effect of number of co-located mice with OTU abundance on OTU appearance for 89 (27) OTUs. Conclusions Co-occurrence and appearance of OTUs were associated with mouse co-location for 21%-27% OTUs. These findings need to be taken into account when comparing abundance of OTUs across time points and treatment groups.