The Meta-Gut: Conservational Clues Provided by Hippo Poop

Image Courtesy of Luna Aguilar.

Conservation ecology is on everyone’s mind today and with good reason. With global warming and imminent extinctions making daily news, the preservation of ecological biodiversity has never felt more urgent. To this end, conservation ecologists have made an effort to identify the key players in the most ecologically diverse ecosystems in the world, hoping to find clues about the relationships between organisms and nonliving factors that make such ecosystems high-functioning.

Kenya’s Mara River Valley is a prime example. The fish, birds, and hippos in the Kenyan Masai Mara are interdependent for survival, but recent evidence suggests researchers have overlooked the key players: microbiota. The ecological stability of the Masai Mara is characterized by the relationship between these two biotic spheres, described by community coalescence theory. The basis of this relationship, as it turns out, can be found in hippo poop.

The Meta-Gut

Thousands of hippos in Kenya’s Mara River Valley excrete an estimated 9.3 tons of feces each day. This waste contains gut microbiomes with trillions of bacteria and archaea, which may even function outside the animal itself. Christopher Dutton GRD ’19, a postdoctoral associate in the Department of Ecology and Evolutionary Biology at Yale, and collaborators such as Amanda Subalusky GRD ’16, who is also a postdoctoral associate in the same department, have found that the microbiome of hippos may play an unanticipated role in regulating biological and chemical processes within their larger ecosystem. “Is it possible that these pools could actually, in a way, be functioning like an extension of the hippo gut?” Dutton said. “It’s kind of crazy to think that gut microbiota can be driving what’s happening in this whole river.” This continual exchange of organic matter between hippos and their environment has led to the proposition of a novel conceptual framework known as the “meta-gut.”

Hippo Pools: What Makes Them Special?

All animals carry specialized microorganisms in their digestive tract which help facilitate biologically essential processes such as the metabolism of carbohydrates and the synthesis of amino acids, fatty acids, and vitamins. As hippos wallow in the Mara River, they unload their gut microbiota through the excretion of waste, introducing nutrients and microbes into the river. The meta-gut suggests that this continual loading of organic matter results in an environmental patch within an ecosystem that shares similar characteristics to the gut environment of the host animal. In other words, the river ecosystem inherits characteristics of the hippo gut.

Even without expensive genomic technologies, Dutton and his colleagues had deduced that the constitution of the pools that had high hippo density – high-subsidy hippo pools – differed from pools further upstream. High-subsidy hippo pools were anoxic, or oxygen-depleted, with higher concentrations of methane, hydrogen sulfide, and minerals such as magnesium and calcium, as well as lower concentrations of oxygen and nitrates (compared to the oxic conditions of low-subsidy hippo pools and the Mara River itself). Genomic technology allowed the researchers to correlate these findings with the microbial communities found in both the hippo gut and high-subsidy hippo pools and identify the key microbes causing these biochemical differences in the pools.

Specifically, Dutton and his colleagues used 16S rRNA sequencing technology to compare RNA genomes across samples from areas in the Mara River with high and low hippo population density. 16S rRNA sequencing confers two benefits over other sequencing technologies. First, each organism has 16S rRNA specific to its species, making the 16S rRNA a highly-identifiable label. Second, since rRNA itself is a relatively short-lived biological molecule like RNA, researchers were able to characterize which members of the microbial communities in hippo feces actually play active roles in shaping the ecosystems the hippos inhabit.

Hippo Gut Influences on the Biogeochemical Cycles of the Mara
The idea of the meta-gut may revolutionize our understanding of the abiotic and biotic components in an ecosystem. Within high-subsidy hippo pools, certain biochemical differences were clear. For one, active microbial communities common to the hippo gut and hippo pools were strongly associated with higher concentrations of biochemical oxygen demand, methane, nitrous oxide, and hydrogen sulfite, suggesting that hippo gut microbes may be driving these chemical changes in the river. Secondly, as tons of hippo feces sink into the water, the river environment becomes anoxic. This chemical change may allow for the successful transfer of hippo microbiota into the river, and survival after, as microbes from within the gut are adapted to anaerobic environments present in the digestive tract of animals.
As this organic unloading occurs, the microbial communities from the hippo gut can colonize the digestive tracts of other animals, including fish and insects, in the Mara River Valley. Multiple species of fish in tropical rivers consume hippo feces and, in doing so, may participate in the larger meta-gut. “If some of the hippo microbiota is colonizing the guts of fish and insects, you have to start asking yourself questions like, ‘Is it possible that the fish that are living with hippos and consuming their feces are somehow gaining some type of physiological advantage from the gut microbiota that they’re taking?'” Dutton asked. If such processes are possible, migrating gut microbiota from one species to another can confer important biological advantages for adaptation.

Hippo Pools Over Time and Space

These biological advantages and the meta-gut itself are not constant over time. Characterizing the hippo pool microbiome before and after flushing flows (large torrents of water that essentially recycle the water of the hippo pools) showed that the hippo pool’s microbiome best matched the hippo gut’s microbiome in the intervals between flushing. Evidently, it takes time for the meta-gut to be established. Moreover, the flushing flow experiment also provided clues to how the hippo pools impacted upstream parts of the river. Directly after flushing, the hippo pools most resembled the upstream river regions, indicating that there are some innate free-living microbial communities that are common in all parts of the river. However, the microbes that most contributed to the biochemical and ecological stability of the high-subsidy pools were directly derived from hippo feces and were largely contained to the hippo pools.

The Hippo Gut and Ecological Stability

Thus, there’s more to the Masai Mara hippos than meets the eye. When hippos and their neighbors swim around in feces, not only are the animals propagating their own gut microbiota, but that of an entire ecosystem. Our current understanding of ecosystems, and the organisms that comprise the biodiversity of the ecosystem, are largely limited to what we can see and touch. However, the team’s work with the hippos’ gut microbiota, and consequently, the river ecosystem microbiota, point to the importance and ubiquity of microorganisms. Without them, the entire river ecosystem could collapse. “When species cohabitate, I think it’s really important that we acknowledge that every organism living in the Masai Mara is sharing their microbes,” Dutton said. “The more diversity you have on the landscape, the more of a chance that you’re going to get the correct colonization in your gut that helps you survive.”

But even if the hippo meta-gut is crucial to the river ecosystem, why should this matter to us? If the ecosystem functions, as far as the planet-conscious person is concerned, there isn’t much harm. And yet, the preservation of biodiversity, beyond just the preservation of ecosystems, is one of the central goals of ecology. Dutton explained the difference between a partially functioning ecosystem and an effectively functioning ecosystem. “Biodiversity is so important, specifically [when we’re] looking at the effective functioning of ecosystems,” Dutton said. “When we throw ecosystems out of whack, that’s when we start to get these problems of excess carbon in the atmosphere from CO2, methane, and nitrous oxide.” Thus, the preservation of the gut microbiome of the larger species, like hippos and beavers, in the Masai Mara is just as important to the functioning of geochemical systems as the preservation of the observable species themselves.

Future Steps

Next, Dutton wants to specifically identify the taxa of the hippos’ gut microbiota involved in nitrogen and carbon recycling that ultimately contribute to the growth and survival of plants, animals, and our planet. He will work with the hippos at an experimental stream facility at Disney and do detailed sampling of the biochemistry in microbial communities. Specifically, Dutton is excited about using metatranscriptomics, a technique that sequences the active genetic code in a cell to indicate what functions the cell is carrying out in real-time. Identifying the communities of microbiota that are functioning will enable the team to distinguish between the species that are present in the feces and those that play significant roles in the functioning of the meta-gut ecosystem.

Ultimately, the hippo meta-gut is a microcosm of all ecosystems, where the role of the microbiota has been largely underestimated. The respective focuses of ecologists and microbiologists studying this have been largely divergent until the concept of meta-guts was shown to be critical to the geochemical cycles that improve the welfare of the entire ecosystem and, ultimately, the entire planet. Thus, as we focus on the warming of the planet and the accumulation of carbon in the atmosphere, we must consider the preservation of biodiversity, from the smallest species to the largest. Though it might seem unexpected to think that part of the solution to climate change and ecological preservation is lodged in hippo poop, a better appreciation of the interspecies relations in an ecosystem and the roles they play will fill a critical gap in our understanding of life on our planet.

Further Reading

Castledine, Meaghan, et al. “Community Coalescence: An Eco-Evolutionary Perspective.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 375, no. 1798, 23 Mar. 2020, p. 20190252, 10.1098/rstb.2019.0252. Accessed 27 May 2021.


Dutton, Christopher L., et al. “The Meta-Gut: Community Coalescence of Animal Gut and Environmental Microbiomes.” Scientific Reports, vol. 11, no. 1, 30 Nov. 2021, 10.1038/s41598-021-02349-1. Accessed 2 Jan. 2022.