Host phylogeny, diet, and habitat differentiate the gut microbiomes of Darwin’s finches on Santa Cruz Island

Wesley T. Loo, Jefferson García-Loor, Rachael Y. Dudaniec, Sonia Kleindorfer, Colleen M. Cavanaugh*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    34 Citations (Scopus)
    62 Downloads (Pure)


    Darwin’s finches are an iconic example of an adaptive radiation with well-characterized evolutionary history, dietary preferences, and biogeography, offering an unparalleled opportunity to disentangle effects of evolutionary history on host microbiome from other factors like diet and habitat. Here, we characterize the gut microbiome in Darwin’s finches, comparing nine species that occupy diverse ecological niches on Santa Cruz island. The finch phylogeny showed moderate congruence with the microbiome, which was comprised mostly of the bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria. Diet, as measured with stable isotope values and foraging observations, also correlated with microbiome differentiation. Additionally, each gut microbial community could easily be classified by the habitat of origin independent of host species. Altogether, these findings are consistent with a model of microbiome assembly in which environmental filtering via diet and habitat are primary determinants of the bacterial taxa present with lesser influence from the evolutionary history between finch species.

    Original languageEnglish
    Article number18781
    Pages (from-to)1-12
    Number of pages12
    JournalScientific Reports
    Publication statusPublished - 11 Dec 2019

    Bibliographical note

    Copyright the Author(s) 2019. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.


    Dive into the research topics of 'Host phylogeny, diet, and habitat differentiate the gut microbiomes of Darwin’s finches on Santa Cruz Island'. Together they form a unique fingerprint.

    Cite this