Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids

Malou B. Storm, Emilia M. R. Arfaoui*, Phumlile Simelane, Jason Denlinger, Celine Alfredo Dias, Ana Gledis da Conceição, Ara Monadjem, Kristine Bohmann, Michael Poulsen, Kasun H. Bodawatta

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat changes.

Original languageEnglish
Article numbere11486
JournalEcology and Evolution
Volume14
Issue number7
Number of pages14
ISSN2045-7758
DOIs
Publication statusPublished - 2024

Bibliographical note

Publisher Copyright:
© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.

Keywords

  • Civettictis
  • Genetta
  • gut microbiome
  • metabarcoding
  • omnivores
  • southern Africa
  • Viverridae

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