Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as well as exposure to a natural environment, increased microbiota diversity and altered community composition. Community composition in mice exposed to high temperatures and humidity diverged as much from the microbiota of mice housed outdoors as from the microbiota of control mice. Additionally, infection with the nematode Trichuris muris modulated how the microbiota responded to environmental transitions: The dynamics of several families were buffered by the nematodes, while invasion rates of two taxa acquired outdoors were magnified. These findings suggest that gut bacterial communities respond dynamically and simultaneously to changes within the host’s body (e.g., the presence of nematodes) and to changes in the wider environment of the host.

IgG and worm counts

File: IgG_WormCount.csv. This file contains the Trichuris muris-specific IgG optical density values and the final worm counts of individual mice at the experimental endpoint (i.e., 28 days post-infection). Mice are distinguished by their ID number.

Metadata and sequencing information

File: Metadata_Sequencing.csv. This file contains information on the environment, infection groups, deworming treatment, mass, and cage and outdoor wedge distributions of individual mice throughout the experiment. Up to six timepoints of data were collected for each mouse. Individual mice are distinguished by their ID number. The sample_ID names match the ID names in the 16S rRNA sequence files available from the NCBI Sequence Read Archive database. The number and proportion of sequencing reads (Forward: R1; Reverse: R2) and information on the yields and the quality of reads for each fecal sample that was sequenced are also presented.