Individual variation in the avian gut microbiota: the influence of host state and environmental heterogeneity

Abstract

The gut microbiome has important consequences for fitness, yet the complex, interactive nature of ecological factors that influence the gut microbiome has scarcely been investigated in natural populations. We sampled the gut microbiota of wild great tits (Parus major) at different life stages and across multiple conifer and mixed woodland fragments, allowing us to evaluate multiple factors that relate to within-individual gut microbiota acquisition, including habitat type, nest position and life history traits. The gut microbiota varied with both environment and life-history in ways that were largely dependent on age. Notably, it was the nestling, as opposed to the adult gut microbiota that was most sensitive to ecological variation, pointing to a high degree of developmental plasticity. Individual nestling differences in gut microbiota were consistently different (repeatable) from one to two weeks of life, driven entirely by the effect of sharing the same nest. Our findings point to important early developmental windows in which the gut microbiota are most sensitive to environmental variation and suggest reproductive timing, and hence parental quality or food availability, interact with the microbiome.

Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity

“…The sample metadata have been made available at http://datadryad.org (Davidson, Somers, et al, 2020: https://doi.org/10.5061/dryad.bk3j9kd9g), this data frame contains variables describing each individual bird sample in this study, their associated environmental variables and microbiome summary statistics (alpha diversity measures and phylum level relative abundance). Tables of ASV abundances by sample and ASV taxonomy are available at also available at http://datadryad.org (Somers et al, 2022: https://doi.org/10.5061/dryad.fttdz08x2). Sequence data are available in the European Nucleotide Archive under access number PRJEB42330, and ERS5506097 ‐ ERS5506338.…”