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Gut Microbiomes Across Nine Kruger Mammals Clustered More Strongly by Dietary Group Than Species

African wild dog in Kruger National Park, South Africa
Research: Disease, parasites & microbiology, Ecology

Gut microbiomes from nine wild mammal species living in Kruger National Park clustered more strongly by broad dietary and digestive group than by host species. The study compared carnivores, ruminant herbivores and non-ruminant herbivores living in the same ecosystem, while also finding biologically meaningful differences among species within those groups.

Nine species separated into three broad microbiome groups

The researchers sampled African lions (Panthera leo), spotted hyenas (Crocuta crocuta), African wild dogs (Lycaon pictus), common warthogs (Phacochoerus africanus), African bush elephants (Loxodonta africana), black rhinoceroses (Diceros bicornis), white rhinoceroses (Ceratotherium simum), African buffaloes (Syncerus caffer) and impalas (Aepyceros melampus). They sequenced the V3–V4 region of the bacterial 16S rRNA gene from 94 faecal samples, a genetic marker widely used to identify and compare bacterial communities. Eighty-nine samples passed quality filtering for the main analyses.

The microbiomes formed strong clusters corresponding to carnivores, non-ruminant herbivores and ruminants. A machine-learning classifier assigned samples to those three groups with about 93% accuracy. Species differences remained within each dietary group, but were smaller than the broad differences among the three groups.

Microbial diversity followed digestive strategy

Using the Shannon diversity index — which combines the number of microbial types with how evenly they are represented — non-ruminant herbivores had the highest median diversity at 6.89. Ruminants followed at 6.54 and carnivores at 5.83. The authors link the richer communities of hindgut fermenters such as elephants, rhinoceroses and warthogs to the broad range of plant material fermented in the large intestine, whereas ruminants depend on a more specialised foregut fermentation system.

The taxonomic composition also reflected diet. Carnivore microbiomes were enriched in bacterial groups associated with protein- and bile-rich digestive environments, including Fusobacteriaceae and Clostridiaceae. Herbivores had more groups associated with fibre degradation, including Rikenellaceae and Oscillospiraceae.

Broad dietary groups did not erase species differences

Black and white rhinoceroses provided one of the clearest examples. Both are hindgut fermenters, but black rhinoceroses browse leaves and woody plants whereas white rhinoceroses are grazers. Their bacterial communities differed at genus level in ways the authors interpret as consistent with the different plant substrates reaching the hindgut.

Spotted hyenas also differed from lions and African wild dogs. Clostridia UCG-014 was the strongest bacterial discriminator for hyenas. Predicted functional profiles also separated the species, which the authors cautiously relate to the hyena’s greater use of carrion, bone and fat-rich food. These metabolic functions were inferred from 16S profiles rather than measured directly, so they describe predicted microbial capacities, not demonstrated rates of metabolism.

The study therefore shows a hierarchy of influences rather than a simple diet-versus-species choice: broad feeding and digestive strategy explained the largest microbiome differences, while species-specific ecology still produced distinct signatures within those groups.

Sources and image credit

  1. Green, S., Thongthum, T., Pietrucci, D., et al. (2026). Dietary ecology structures gut microbiome assembly in sympatric wild mammals from Kruger National Park, South Africa. Animal Microbiome.Primary open-access Article in Press published 18 September 2026. Full 21-page article checked. Ninety-four faecal samples from nine wild mammal species were sequenced and 89 retained after quality filtering. Dietary group was the strongest organiser of microbiome composition; non-ruminant herbivores had the highest microbial diversity, and focal comparisons identified distinct black-versus-white rhinoceros and spotted-hyaena profiles.

Image: African wild dog (Lycaon pictus) on the H11 Road west of Skukuza, Kruger National Park, Mpumalanga, South Africa, photographed 25 February 2022. Photo: Bernard DUPONT. Source: Wikimedia Commons. CC BY-SA 2.0. Representative image of one of the nine study species in the study park; not an identified sampled animal. · CC BY-SA 2.0 · Source

About this content: This story was produced with AI assistance within an editorial workflow developed by Wildlife Vagabond. Editorial responsibility remains with Wildlife Vagabond.How AI is used

Disease, parasites & microbiology

SPECIES IN THIS STORY

Species in this story

Lion Panthera leo Explore species Spotted Hyena Crocuta crocuta Explore species African Wild Dog Lycaon pictus Explore species Common Warthog Phacochoerus africanus Explore species African Bush Elephant Loxodonta africana Explore species Black Rhinoceros Diceros bicornis Explore species White Rhinoceros Ceratotherium simum Explore species African Buffalo Syncerus caffer Explore species Impala Aepyceros melampus Explore species

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