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Illuminating the links between gut microbiome composition and diet in two omnivorous African viverrids
  • +7
  • Malou Storm,
  • Emilia Langkjær,
  • Kasun Bodawatta,
  • Phumlile Simelane,
  • Jason Denlinger,
  • Celina Dias,
  • Ana da Conceição,
  • Ara Monadjem,
  • Kristine Bohmann,
  • Michael Poulsen
Malou Storm
University of Copenhagen
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Emilia Langkjær
University of Copenhagen

Corresponding Author:[email protected]

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Kasun Bodawatta
Kobenhavns Universitet
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Phumlile Simelane
University of Eswatini
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Jason Denlinger
Gorongosa National Parkk
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Celina Dias
Gorongosa National Park
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Ana da Conceição
Gorongosa National Park
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Ara Monadjem
University of Eswatini
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Kristine Bohmann
University of Copenhagen Faculty of Health and Medical Sciences
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Michael Poulsen
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Abstract

Microbial communities in guts flexibly adjust to changes in host dietary intakes, but the relationship between diet and gut microbiome is still poorly studied in wild animals. DNA metabarcoding approaches are frequently used to characterise diets or gut microbiomes of diverse species. However, to date, no study has combined these approaches to investigate diet-gut microbiome associations in wild mammals with diverse and fluctuating dietary intakes, such as omnivores. Here, we do this for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. We characterised bacterial communities and identified taxonomic groups within diet by sequencing vertebrate, invertebrate and plant markers on faecal samples. This led us to establish diet compositions that diverged from what has previously been found using visual identification methods for these species. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal-based diets in C. Civetta, and higher proportions of plants consumed by Genetta spp. Diet similarity correlated with gut microbiome similarity in Genetta spp., indicating that plant consumption may be an important driver of gut microbiome structure. The novel insights we provide into the omnivorous diet of C. civetta and Genetta spp. highlight the importance of detailed identification of the dietary guild of species, not only for ecology and conservation, but also when researching how diet shapes the gut microbiome.