Into Wild: Animal Microbiomes in Conservation

With the threats of climate change, pollution and habitat loss looming large, the future of many wild animal populations is uncertain at best. An estimated 41,000 plant and animal species face extinction, making the need for realistic, effective conservation strategies more pressing than ever. Developing such strategies requires an understanding of factors that influence the health of threatened organisms, and as it turns out, some of the most important factors are quite small.

Just like in humans, microbial communities living within, and on, animals (i.e., their microbiomes) play integral roles in the well-being of their hosts. Microbes contribute to the adaptability and fitness of animal hosts by regulating processes related to digestion, reproduction, infection resistance and more. They can also negatively impact animal well-being by causing infections and disease. A growing body of research suggests microbial consortia inhabiting everything from animals’ guts to their skin may be useful for informing and supporting conservation practices.

“A lot of people in the conservation world are very excited about microbiomes,” said Dr. Carly Muletz Wolz, a molecular ecologist at the Center for Conservation Genomics at the Smithsonian National Zoo and Conservation Biology Institute. “They’re hoping they can be a tool to boost the success of reintroduction programs, of animals breeding in captivity and of the health of animals already in the wild.”

Yet, saving a life-much less a species-is not easy. Though microbiome analyses show potential in the conservation field, there are challenges, related to everything from sample collection to data generation and interpretation, that scientists must overcome to increase the utility of these tools.

Environmental Changes Impact Animal Microbiomes and Health

The composition of an animal’s microbiome is closely tied with their environment and lifestyle. As such, examining these microbial communities may provide useful insights into how behavioral, dietary and/or environmental changes and disruptions, such as habitat loss and chemical pollution, impact animal health.

Habitat Loss

Habitat loss is one of the largest issues facing wild animal populations today-approximately 46% of global land that was once covered by wild grasslands, forests and shrubs is now used for agriculture. These changes are reflected in animals’ microbiomes. Take the Udzungwu red colobus monkey (one of the most threatened primate species in Africa) as an example. Researchers found that monkeys inhabiting fragmented forest (i.e., forest that has been broken up into smaller patches, largely because of human land use) have reduced gut bacterial diversity compared to those living in protected forest. Another study showed that these variations are accompanied by a loss of metabolic pathways associated with digesting plant-derived chemicals, signaling environmental degradation and a loss of plant diversity in fragmented landscapes.

Temperature Changes

While changes in animal microbiomes, particularly gut microbiomes, are linked to factors like diet and food accessibility, they also shift in response to other environmental variables, like temperature. Animals routinely adapt to seasonal temperature fluctuations, and the frequency and magnitude of such fluctuations are expected to increase due to climate change. Experiments in animals ranging from cattle to lizards show that higher ambient temperatures are associated with reduced microbial diversity and a decrease in certain (often beneficial) gut bacterial species, such as members of the Firmicutes phylum. Studying the effects of temperature-along with other climate change-induced environmental disruptions-on microbiome composition and function may be useful for monitoring how animal populations are faring in a warming world.

Environmental Chemicals

Exposure to chemicals, like pesticides, alters the structure and function of microbial communities in ways that can negatively affect animal health. For instance, glyphosate (the most common pesticide used globally) inhibits growth of bacteria isolated from the gut of Hawaiian green turtles and could adversely affect digestion. The pesticide also perturbs the gut microbial community of honey bees to increase their susceptibility to infection by the bacterial pathogen, Serratia marcescens, which may contribute to declining bee populations.

“Animals, including humans, are exposed to increasingly higher levels of anthropogenic chemicals,” said Dr. Candace Williams, a microbial ecologist in recovery ecology at the San Diego Zoo Wildlife Alliance. “It’s important for us to understand [the] intersection [between] wildlife and these environmental chemicals, and how they influence the long-term survival and fitness of these species.” The microbiome offers a new lens through which to understand these interactions.

Animal Microbiomes Protect Against Pathogens

In addition to habitat loss, climate change and chemical pollution, wild animals must fend off microbial pathogens, and their microbiomes form important barriers against infection. For instance, Batrachochytrium dendrobatidis (Bd), a type of fungus, mercilessly kills amphibians by inhibiting their ability to breathe through their skin.The fungus has spread like wildfire-it is responsible for global population declines of over 500 amphibian species, 90 of which are now presumably extinct.

A dead frog
A frog that succumbed to Bd infection.

However, several bacterial members of the amphibian skin microbiome, such as Janthinobacterium lividum and Pseudomonas fluroscens, protect against infection by Bd. Scientists are figuring out how to use these bacteria as probiotics to inhibit Bd infection in amphibians. Muletz Wolz, who studies the topic, noted that applying probiotics to amphibians in the laboratory has shown great promise. Researchers have recently begun exploring how to apply the bacteria to wild amphibians to slow the spread of the fungus in natural environments.

Harnessing Microbiomes to Promote Animal Health in Captivity

Researchers are just scratching the surface for how to integrate microbiome analyses in the realm of conservation. While some efforts have centered using microbiome-informed strategies to protect animals in the wild, most work so far has focused on modulating the microbiomes of animals born into, or entering, captivity.

Zoos and other conservation centers often house assurance populations of endangered species-these are “backup” populations that can be reintroduced into the wild to bulk up natural communities and ensure species survival and longevity. However, for reintroduction to be a success, “we need to have healthy animals,” noted Muletz Wolz. “And for breeding we need to have healthy individuals that want to make more babies.”

Unfortunately, many animals do not breed well under human care. The reasons why aren’t always clear, but microbiomes may have something to do with it. Indeed, the microbiomes of captive animals differ from wild individuals, as conditions influencing microbiome composition and function (e.g., diet, habitat, exposure to humans) vary from natural environments. These changes may be tied to aspects of animal fitness, including reproductive success.

For example, Williams and her colleagues at the San Diego Zoo have found that in captive southern white rhinoceros-a threatened species that breeds poorly in captivity-fertility is associated with gut microbial metabolism of dietary compounds, called phytoestrogens. Because they look and act like endogenous estrogen in the body, phytoestrogens can lead to hormonal imbalances and contribute to reduced breeding success. The Zoo found that switching captive rhinos to a low-phytoestrogen diet resulted in some pregnancies. Yet, “not all rhinos increased fertility after the diet change-some stayed infertile,” Williams noted. These disparate outcomes likely relate to differences in the composition and metabolic function of the gut microbiome between fertile and infertile rhinos. That is, the gut microbes in infertile rhinos may produce phytoestrogen metabolites that mess with the rhinos’ hormonal circuitry and negatively impact their fertility. The next step is to determine the specific identities and metabolic functions of these microbes as they relate to breeding success.

southern white rhinos
Poor breeding in captivity threatens the sustainability of southern white rhino assurance populations.

Source: San Diego Zoo Wildlife Alliance

Animal Microbiomes in Conservation Science: Challenges and Roadblocks

There is a lot left to learn about host-microbe interactions in animals, and their value in conservation.

“We are so far behind in the animal world, compared to the human world, in understanding of these interactions,” said Williams. “And not only are we far behind in terms of having baseline data for many of these species that we work with, [but] we are up against a wall of extinction.” In fact, “less than 1% of threatened species have had their microbiome examined.” This means that, for most species, scientists still don’t know what a “normal” microbiome looks like. Which microbes are good, which are bad-and when? The answers to these questions vary from one species to the next.

Part of the challenge of studying wild animal microbiomes is generating data in the first place. Researchers often have access to a limited number of animals, both in captivity and in the wild. With only a handful of samples (if that), it is difficult to gain a comprehensive picture of the microbiome of a species/population. The sampling process itself can also be a challenge, particularly in the wild-try collecting microbial samples from the epidermis of sharks, and you’ll get the picture.

captive red wolf
A captive red wolf.

Even when researchers have data in hand, applying their findings in “the real world” is another challenge. “How feasible is it to go spray 1000 animals with a probiotic [in the wild]?” Muletz Wolz asked, referring to the use of probiotics to control fungal infections in amphibians. Answer: not very. Even in captivity, where conditions are more easily controlled, microbiome-informed efforts to promote animal health may be challenging. She highlighted a recent story about red wolves, where even captive wolves that ate a diet like their wild counterparts (i.e., whole meat) had a different microbiome than wild wolves. This story underscores that, even if an intervention seems easy to implement, such as altering diet, there may be additional barriers and environmental complexities that undermine its efficacy.

The Future of Animal Microbiomes in Wildlife Conservation

Most microbiome studies in animals use DNA sequencing to determine which microbes (namely bacteria) are present, and how they may correlate with phenotypes of interest (e.g., reproductive success). Yet, “we have to move beyond these very correlative studies,” Williams stated. “A multidisciplinary approach is extremely necessary to understand the function of these microbes within these communities in different contexts to understand whether certain microbes may be beneficial or detrimental in the hosts that we study.” This can be achieved by adopting experimental frameworks that couple DNA sequencing with, for instance, metabolomics.

It may also be beneficial to isolate and cultivate microbes directly from samples, particularly if the goal is to isolate bacteria to administer as a probiotic. “You can’t make a probiotic if you don’t have any culture,” Muletz Wolz explained. In other words, you can’t give a DNA sequence to an animal to make them feel better. Moving forward, researchers will need to “figure out how to connect the culturing and the sequencing to make advancements.”

Progress will also rely on extensive collaborations between scientists across disciplines. Muletz Wolz emphasized the need “to get the microbiologists and conservation people working more together, particularly [in the context of] reintroductions…There are very few studies tracking animals that go from being reared in captivity and released and following them as they live in the wild.”

Nevertheless, despite the challenges, Williams is excited about what the future holds. “We are making the change from [the idea that] ‘microbes aren’t involved in anything,’ to understanding that they are really critical for maintaining healthy individuals, in our care and in the wild.”


Research in this article was presented at ASM Microbe, the annual meeting of the American Society for Microbiology, held June 9-13, 2022, in Washington, D.C.

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