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

Shane E. Somers, Gabrielle L. Davidson, Crystal N. Johnson, Michael S. Reichert, Jodie M.S. Crane, R. Paul Ross, Catherine Stanton, John L. Quinn

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


The gut microbiota have important consequences for host biological processes and there is some evidence that they also affect fitness. However, the complex, interactive nature of ecological factors that influence the gut microbiota has scarcely been investigated in natural populations. We sampled the gut microbiota of wild great tits (Parus major) at different life stages allowing us to evaluate how microbiota varied with respect to a diverse range of key ecological factors of two broad types: (1) host state, namely age and sex, and the life history variables, timing of breeding, fecundity and reproductive success; and (2) the environment, including habitat type, the distance of the nest to the woodland edge, and the general nest and woodland site environments. The gut microbiota varied with life history and the environment in many ways that were largely dependent on age. Nestlings were far more sensitive to environmental variation than adults, pointing to a high degree of flexibility at an important time in development. As nestlings developed their microbiota from one to two weeks of life, they retained consistent (i.e., repeatable) among-individual differences. However these apparent individual differences were driven entirely by the effect of sharing the same nest. Our findings point to important early windows during development in which the gut microbiota are most sensitive to a variety of environmental drivers at multiple scales, and suggest reproductive timing, and hence potentially parental quality or food availability, are linked with the microbiota. Identifying and explicating the various ecological sources that shape an individual's gut bacteria is of vital importance for understanding the gut microbiota's role in animal fitness.

Original languageEnglish
Pages (from-to)3322-3339
Number of pages18
JournalMolecular Ecology
Issue number12
StatePublished - Jun 2023
Externally publishedYes


  • early development
  • environmental variation
  • gut microbiome
  • gut microbiota
  • host state
  • repeatability


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