A study of elephants, giraffes and other wildlife in Namibia's Etosha National Park underscores the ways in which the environment, biological sex, and anatomical distinctions can drive variation in the gut microbiomes across plant-eating species. Because the gut microbiome plays a critical role in animal health, the work can be used to inform conservation efforts.
"This study is valuable because Etosha gave us the opportunity to sample such a large number of species under different environmental conditions," says Erin McKenney, co-author of a paper on the work and an assistant professor of applied ecology at North Carolina State University. "That gives us meaningful insight into the role the environment plays in shaping the gut microbiome of herbivores.
"Unfortunately, this study may also be important for a second reason," McKenney says. "Etosha is experiencing devastating wildfires affecting a huge section of the park. Because our samples were taken before the wildfires, these findings could inform recovery efforts by helping us understand how species' microbiomes are adjusting to changes in diet that stem from the fire's impact on the landscape."
For this study, the researchers divided Etosha into three zones, depending on the amount of rainfall each zone received. The diversity and abundance of plant species varied from zone to zone, due to the precipitation differences, but nine of the 11 herbivore species were found in all three zones. The researchers were able to collect fresh feces samples from species ranging from African elephants (Loxodonta africana) and Angolan giraffes (Giraffa camelopardalis angolensis) to 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.
"We ended up with 312 fecal samples across the 11 species, which gave us a wealth of microbiome data, and our analysis gave us a deeper understanding of the variables that can influence these microbial ecosystems," says Rylee Jensen, first author of the paper and a recent master's graduate from Northern Michigan University.
"One of the most interesting findings was that there were five types of bacteria that served as environmental indicators," Jensen says. "Specifically, the relative abundance of these five microbes varied in a predictable way from zone to zone. All of these microbes are known for either breaking down lipids, breaking fiber down into nutrients animals can digest, or both. This is interesting because these environmental indicators could be key for helping us monitor environmental changes and how animal species are adapting to those changes."
"Also, one of these environmental indicators is an entire phylum of bacteria that has previously been identified in the gut microbiome of camels," McKenney says. "Camels are herbivores, but they are not closely related to any of the species we surveyed in this study, so to find that phylum here suggests it is a particularly robust indicator of environmental conditions in places where water is at a premium."
The researchers also found a range of microbial differences that could be attributed to biological sex and gut morphology differences across species. However, there were some interesting findings involving the elephants.
"Elephants had two types of 'core' microbes - meaning these microbes were found in more than half of elephant samples - that were uncommon in the other species," Jensen says. "This is likely due to the fact that elephants eat a wider variety of plant materials than the other species. This stood out because we found 22 types of core bacteria overall, and 20 of those types of bacteria were core bacteria for multiple species - but elephants hosted the only two types of core bacteria that were not common in other species. This highlights the role that feeding behavior and environment play on shaping the gut microbiome."
"We're excited about this work, in part, because we were able to collect high-quality samples from species in a region that had not previously been sampled for gut microbiome studies, and we got very fine resolution data," says Diana Lafferty, co-author of the paper and an associate professor of biology at Northern Michigan.
"This is a level of detail and data quality that is often only achieved under captive or clinical conditions," McKenney says.
"And we've essentially established a baseline that can be used to help us understand any changes we see in these species in this region," Lafferty says. "That's particularly important given the critical role that many of these species play in these ecosystems and the critical role gut microbiomes play in animal health."
The paper, "Interspecific variation in gut microbiome diversity across the Etosha National Park herbivore community," appears in the journal PLOS One. 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.
