Raulo, A. M. | bioRxiv Science

bioRxiv2023

Social and environmental transmission spread different sets of gut microbes in wild mice

Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here, we used a novel RFID-based tracking system to collect long-term high resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterising their gut microbiota. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges respectively. Strikingly, microbes with distinct biological attributes drove these different transmission signals. While aerotolerant spore-forming bacteria drove the effect of shared space use, a mix of taxa but especially anaerobic bacteria underpinned the social networks effect on gut microbiota similarity. These findings provide the first evidence for parallel social and environmental transmission of gut microbes that involve biologically distinct subsets of the mammalian gut microbiota. List of contributionsO_LIAura Raulo designed the study, helped develop the new RFID tracking technology, collected the data from Wytham, completed all laboratory analyses on gut microbiota profiling prior to sequencing, developed analytical methods, analysed the data and wrote the manuscript C_LIO_LIPaul Burkner helped design the Bayesian probabilistic modeling framework and provided feedback on the manuscript C_LIO_LIJarrah Dale helped collect field data using RFID loggers C_LIO_LIHolly English helped collect field data using RFID loggers and provided feedback on home range analyses C_LIO_LIGenevieve Finerty helped with home range analysis and the analysis of microhabitat variation and provided feedback on the manuscript C_LIO_LICurt Lamberth led development of RFID tracking devices and helped collect field data from Wytham C_LIO_LIJosh Firth supervised the research project, developed social network analysis methods and provided feedback on the analyses and the manuscript C_LIO_LITim Coulson supervised the research project and provided feedback on the analyses and the manuscript C_LIO_LISarah Knowles supervised the research project, helped develop the tracking technology and design the study, collected data from Wytham, planned and supervised laboratory methods, developed analytical methods and provided feedback on analyses and the manuscript. C_LI

ecology↗

bioRxiv2021

Synchronous seasonality in the gut microbiota of wild wood mouse populations

O_LIThe gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, what factors drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. C_LIO_LIHere, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent set of core gut microbes is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. C_LIO_LIBetween 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild UK mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. C_LIO_LIAlthough broadly similar at high taxonomic levels and despite being only 50km apart, the two wild populations did not share a single bacterial amplicon sequence variant (ASV). Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite strong taxonomic divergence in the microbiota, the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, seasonal convergence in the gut microbiota among individuals occurred in late winter/early spring. C_LIO_LIThese findings reveal highly repeatable seasonal gut microbiota dynamics across distinct populations of this species, despite divergent taxa being involved. Providing a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity. C_LI

ecology↗