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Background Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciurus hudsonicus) population. Red squirrels are territorial, solitary, and live in a highly seasonal environment and therefore represent a very attractive system to study factors that drive the temporal and spatial dynamics of gut microbiota. Result For the first time, this study revealed significant spatial patterns of gut microbiota within a host population, suggesting limited dispersal could play a role in shaping and maintaining the structure of gut microbial communities. We also found a remarkable seasonal rhythm in red squirrel’s gut microbial composition manifested by a tradeoff between relative abundance of two genera Oscillospira and Corpococcus and clearly associated with seasonal variation in diet availability. Our results show that in nature, environmental factors exert a much stronger influence on gut microbiota than host-associated factors including age and sex. Despite strong environmental effects, we found clear evidence of individuality and maternal effects, but host genetics did not seem to be a significant driver of the gut microbial communities in red squirrels. Conclusion Taken together, the results of this study emphasize the importance of external ecological factors rather than host attributes in driving temporal and spatial patterns of gut microbiota in natural environment. Electronic supplementary material The online version of this article (10.1186/s40168-017-0382-3) contains supplementary material, which is available to authorized users.

North American red squirrels (Tamiasciurus hudsonicus) anticipate when white spruce (Picea glauca), their primary food source, will produce large amounts of cones in infrequent and irregular mast years (Boutin et al. 2006). Cones mature in autumn and are then available as food for red squirrels, but females produce larger, and often multiple, litters the preceding spring and summer in anticipation of the upcoming mast. Because this pulse of the cone food resource follows the birth of the litter, it cannot be a source of energy for the female to produce young; instead, there must be cues for increased reproductive investment by the females prior to mast cone production, perhaps through consumption of buds on the masting trees (Boutin et al. 2006, 2013). Boutin et al. (2006) only studied females; whether male behavior anticipates mast years is still unstudied. At our study area in the Yukon, 2014 was a mast year for spruce cone production in late summer (Lamontagne et al. 2005). J. A. Haines was observing male red squirrel mating behavior during spring 2014, giving her an unanticipated opportunity to document the previously unstudied effects of a mast year on male red squirrels., Data collection was supported by grants provided to S. Boutin, A. G. McAdam, M. M. Humphries, J. E. Lane, and D. W. Coltman from the Natural Sciences and Engineering Research Council of Canada, as well as National Science Foundation grants to A. G. McAdam and B. Dantzer. J. A. Haines was supported by an NSERC Doctoral Postgraduate Scholarship, University of Alberta Canadian Circumpolar Institute Circumpolar/Boreal Alberta Research Funds and Aboriginal Affairs and Northern Development Canada Northern Scientific Training Program Grants, and University of Alberta Faculty of Graduate Studies and Research scholarships., "The Scientific Naturalist", Copyright by the Ecological Society of America. This is an electronic version of an article published as: Haines, J.A., Coltman, D.W., Dantzer, B., Gorrell, J.C., Humphries, M.M., Lane, J.E., McAdam, A.G., & Boutin, S. (2018). Sexually selected infanticide by male red squirrels in advance of a mast year. Ecology, 99(5), 1242-1244. DOI: 10.1002/ecy.2158 Ecology is published by the Ecological Society of America and is available online at: https://esajournals.onlinelibrary.wiley.com/journal/19399170/, and this article is available at: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecy.2158., https://viurrspace.ca/bitstream/handle/10613/6527/Gorrell.Ecology.99.5.pdf?sequence=3