Study Sheds New Light on What Drives Evolution of Gut Microbiomes
For Immediate Release
A study of wild African herbivores offers new insight into how environmental conditions – not just diet and anatomy – can influence the evolution of gut microbes that play a critical role in animal health and well-being.
“There’s a concept in ecology called phylosymbiosis, which is basically the idea that as species evolve and diverge from each other, their gut microbiomes will also diverge in a predictable way,” says Erin McKenney, co-author of a paper on the work and an assistant professor of applied ecology at North Carolina State University. “But studies have found that this is not always the case, and it’s not clear why.”
“Our work here was focused on determining whether there was evidence of phylosymbiosis among herbivore species in an arid ecosystem – and whether we could identify any factors that may play a role in fostering or inhibiting phylosymbiosis,” says Rylee Jensen, corresponding author of the paper and a recent master’s graduate from Northern Michigan University.
For this study, researchers collected fresh feces samples from 11 herbivore species in Namibia’s Etosha National Park, which is a relatively dry ecosystem. The species include African elephants, Angolan giraffes, wildebeests, two species of zebra and a variety of antelope species. The research team used DNA extraction and sequencing to identify what kinds of bacteria were present in the feces, which gave them information about the types and abundance of bacteria present in the gut microbiome of each animal.
“The findings were interesting, because there was a stark contrast,” Jensen says. “We found little or no evidence of phylosymbiosis in six of the species. However, there were patterns of phylosymbiosis for five of the species: red hartebeest, blue wildebeest, gemsbok, impala and springbok. All five species are bovids – cow-like ruminants whose digestive tract includes complex stomachs with multiple chambers.
“The five species exhibiting phylosymbiosis are also the five species that are most closely related in an evolutionary context, so it makes sense that we would see phylosymbiosis there,” Jensen says. “However, previous work done in more temperate African ecosystems did not find evidence of phylosymbiosis among bovid species. This suggests the actual environment itself may be playing a role in masking or revealing phylosymbiosis in the gut microbiome.”
“Areas that receive more rainfall also tend to have more lush and diverse vegetation, which may support greater gut microbial diversity,” McKenney says. “Drier environments – like Etosha – may strip away gut microbial species that are not specifically adapted to the herbivore hosts and the limited vegetation available. In other words, it may be easier to detect phylosymbiosis in dry ecosystems, because the vast majority of the microbes present will be adapted to the species and its diet – there is less noise in the system.”
“And this may be particularly pronounced for bovids, which have distinct microbial communities relative to other herbivores,” says Jensen.
“In addition, as ecosystems around the world continue to shift as a consequence of human-mediated climate chaos, such as desert expansion and the drying of environments that were historically wetter, the microbial community within Etosha’s herbivore guild may serve as a bellwether for what we might expect to find among herbivore communities in ecosystems that are becoming more arid,” says Diana Lafferty, co-author of the paper and an associate professor at Northern Michigan University.
“This study raises a lot of questions that can be explored in future work, particularly with regard to the role that environmental factors play in shaping the evolution of gut microbiomes,” McKenney says. “Given some of the dramatic ecological shifts we are experiencing due to climate change, these questions are more important than ever.”
The paper, “Phylogenetic influence on gut microbiome diversity within an African herbivore community,” is published open access in the journal BMC Ecology and Evolution. The paper was co-authored by Claudine Cloete, chief conservation scientist at Etosha Ecological Institute; James Beasley, the Terrell Distinguished Professor of Wildlife Management at the University of Georgia; and Madeline Melton, a Ph.D. student at UGA.
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Note to Editors: The study abstract follows.
“Phylogenetic influence on gut microbiome diversity within an African herbivore community”
Authors: Rylee Jensen and Diana J. R. Lafferty, Northern Michigan University; Erin A. McKenney, North Carolina State University; James C. Beasley and Madeline Melton, University of Georgia; and Claudine C. Cloete, Etosha Ecological Institute
Published: Dec. 20, 2025, BMC Ecology and Evolution
DOI: 10.1186/s12862-025-02489-2
Abstract:
Background: The microbial community within the gastrointestinal tract, known as the gut microbiome (GMB), is a complex micro-ecosystem that is modulated by the life history and physiological traits of the host as well as environmental conditions experienced by the host. In addition, phylogeny can be an important driver of GMB variability across mammalian species, with closely-related species sharing more similar microbial communities than distantly-related species, an eco-evolutionary pattern known as phylosymbiosis. In this study, we examined GMB diversity across 11 species of large herbivores in Etosha National Park (ENP), Namibia, to determine whether host species exhibit phylosymbiosis and whether different herbivore families host distinct microbial communities. The large herbivore community of ENP is an excellent model system because the herbivore species represent distinct evolutionary lineages and have evolved a variety of gut morphologies, dietary niches, and habitat requirements, all of which shape gut microbial diversity.
Results: While we found no evidence of phylosymbiosis across the greater ENP herbivore community, phylosymbiosis was detected among bovid species based on a positive correlation between microbial relative abundance and host evolutionary divergence times. Our results also revealed distinct microbial membership (e.g., Bacteroides, Treponema, and Alistipes) that distinguished bovid species from elephants and giraffes.
Conclusions: Our study provides new insights into the impact of phylogeny on GMB diversity in a closely-related African herbivore community. In particular, phylosymbiosis patterns observed in bovids but not all herbivore species demonstrates that microbial communities are dynamic and respond to a mixture of host evolutionary strategies and corresponding adaptations.
