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  • Writer's pictureFrederic Delsuc

New paper on the evolution the vertebrate gut microbiome out in mBio!

Updated: Jul 28, 2022

The results of the vertebrate microbiome project in collaboration with Rob Knight's lab at the University of California in San Diego are finally being published in mBio. This paper is based on comparisons of the gut microbiomes of over 900 vertebrate species. We found that not only do birds and bats have more similar gut microbiome compositions, but they seem to be similar in how they change across host evolution compared to nonflying mammals. While most mammal gut microbiomes show some degree of phylosymbiosis (closely related hosts have more similar microbiomes), this is not the case in both bats and birds. This can be visualized as 'hotspots for phylosymbiosis' across the vertebrate tree (see figure below). The strength of phylosymbiosis is relatively high across mammals, but decreases along the branch leading to bats, and the one leading to birds. This suggests that the physiological adaptations related to the convergent evolution of flight in birds and bats has impacted the evolution of their gut microbiomes in a similar way.

I am personally indebted to the Tswalu Foundation, the ZooParc de Beauval, the Parc Zoologique de Montpellier, the Réserve Africaine de Sigean, the Jardin Zoologique de la Citadelle de Besançon, the Zoo Fauverie du Mont Faron, the Jardin Zoologique de Lyon, the Zoo de Lille, and the Parc Animalier de Gramat for facilitating access to hundreds of fecal samples from both wild and captive mammal species for this project.

The sequence data and metadata for this project could be downloaded from the Qiita repository: All analysis notebooks by Jon Sanders can be found on GitHub:


Song S.J.*, Sanders J.*, Delsuc F., Metcalf J.L., Amato K.R., Taylor M.W., Mazel F., Lutz H.L., Winker K., Graves G.R., Humphrey G., Gilbert J.A., Hackett S.J., White K.P., Skeen H.R., Kurtis S.M., Withrow J., Braile T., Miller M., McCracken K., Maley J., Blanto, J.M., McKenzie V.J. & Knight R. (2020). Comparative analyses of vertebrate gut microbiomes reveal convergence between birds and bats. mBio 11:e02901-19. doi:10.1128/mBio.02901-19

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