In the case of Tasmanian devils, low microbial diversity in captive populations raised numerous health concerns, as that deficiency could potentially leave animals susceptible to illness and disease.<\/p>\n
\u201cInitially we had concerns that their reduced gut microbiome in captivity would be an issue when they were released, and we wanted to know if we needed to manage this [issue] in captivity or undertake actions for when the [animals] were released\u201d to better protect them in the wild, says Carolyn Hogg, research manager of the Australasian Wildlife Genomics Group at the University of Sydney.<\/p>\n
But for Tasmanian devils reintroduced to the wild, at least, it turned out no intervention was needed. Monitoring of the released devils\u2019 microbiomes, via the collection and analysis of their feces, showed that the animals were able to\u00a0regain a \u201cwild\u201d microbiome, a process beginning after only a few months. \u201cThe results showed we do not need to worry,\u201d Hogg says.<\/p>\n Elsewhere in Australia, microbiome studies of koalas (Phascolarctos cinereus<\/em>) tell a different tale. Findings suggest that koalas likely need to be translocated or released into habitats closely matching their original forest area, possibly due to their microbiome, says Michaela Blyton,\u00a0a\u00a0<\/strong>molecular ecologist and microbiologist at the University of Queensland.<\/p>\n Koalas are endangered in parts of Australia, so releases and translocations are underway to restore populations \u2014 an important conservation method. But released animals often don\u2019t fare well in the wild, says Blyton, and have to be returned to rehabilitation centers; at worst, they may die.<\/p>\n One possible reason: Research by Blyton\u2019s team\u00a0shows that gut microbiome composition\u00a0has an influence on the koala diet, enabling consumption of specific species of eucalyptus, the animal\u2019s principal food source.<\/p>\n \u201cThe gut microbiome is actually an important component defining the ecological niche of [koala] diet, where they can live, and what they can feed on,\u201d she says. \u201cIf the [eucalyptus] species that\u2019s there isn\u2019t appropriate for the microbiome, then they\u2019re stuck. Whereas if you translocate them into a mixed forest, then they have options.\u201d<\/p>\n Understanding the world\u2019s wildlife microbiome \u2014 with its many hundreds of thousands of species \u2014 is still a nascent field, but researchers are already spotlighting how human activities are changing nature at its smallest scale.<\/p>\n A\u00a02023 paper\u00a0found that climate change and increasing temperatures in Southern Africa\u2019s Kalahari Desert are altering the gut microbes of meerkats (Suricata suricatta<\/em>). Researchers used fecal sample data for this small carnivorous mammal stretching back roughly three decades, which offered insights into how the microbe community changed over time.<\/p>\n \u201cWe can see from a taxonomic perspective already, there\u2019s some bacteria that are slowly but surely becoming less abundant in the gut microbiomes,\u201d says Dominik Melville, an evolutionary ecologist at the University of Ulm in Germany and a co-author on the study.<\/p>\n Other researchers have found that proximity to human populations can\u00a0cause alterations in the gut microbiome\u00a0of tigers (Panthera tigris<\/em>) in India, with\u00a0possible knock-on effects for health.<\/p>\n Similarly, numerous frog species\u2019 skin microbiomes are susceptible to alterations in the environment, including changes resulting from\u00a0habitat fragmentation,\u00a0drought\u00a0and\u00a0climate change, potentially leaving these amphibians vulnerable to the deadly\u00a0chytrid fungus\u00a0that has devastated frog species worldwide.<\/p>\n Ongoing tracking of microbiome alterations in animal microbiomes could offer insights into the reasons for some species\u2019 long-term health declines, says Melville. In the case of the meerkats, the impacts of microbiome changes are still unknown, with further studies planned to hopefully find answers.<\/p>\n \u201cWhat we do know in meerkats is that at the same time as these [microbiome] bacteria have declined, and maximum temperatures have increased in the Kalahari, the survival [rate] has gone down within the meerkat population,\u201d he says. But he adds, \u201cIt\u2019s likely we\u2019re looking at an indirect effect.\u201d<\/p>\n A deepened understanding of the inner workings of animal gut microbes could not only help biologists better track wildlife health, but offer solutions. One promising application is the concept of \u201cmicrobial rewilding\u201d as a\u00a0direct conservation intervention\u00a0to bolster reintroduction success rates.<\/p>\n \u201cThe idea of microbial rewilding is that we should be rewilding the microbiomes, along with rewilding the animal, [before reintroduction] because these communities [living inside] the animal are completely inextricable,\u201d says Sally Bornbusch, at the Smithsonian\u2019s National Zoo and Conservation Biology Institute in the U.S.<\/p>\n Fecal microbiota transplants (FMTs), a technique practiced with success on some medical conditions in people, offer one potential route of rewilding gut microbes.<\/p>\n The technique uses feces taken from a healthy animal and packages it into a pill, or some other form, for transplant into an unhealthy animal or one whose gut biome has been altered by captivity. Though the idea of a so-called\u00a0poop pill\u00a0may sound gross on first hearing, the consumption of feces (or coprophagy) is not uncommon\u00a0among some wildlife species, says Bornbusch.<\/p>\n \u201cWhat everyone loves to say is, \u2018everything poops,\u2019\u201d she notes. \u201cScreened feces is an accessible form of microbial therapy that we can harness for medical treatments.\u201d<\/p>\n Bornbusch has collaborated on projects that used poop pills to deliver microbes to about a dozen animal species, and has seen no adverse effects; the goal, she says, is to restore a robust, healthy microbial community.<\/p>\n In one such project, rescued and malnourished elephant seal pups (genus\u00a0Mirounga<\/em>) were given fecal microbiota transplants from healthy pups to help them recover. \u201cPreliminary results show that it may improve the rehabilitation process for these orphaned and stranded elephant pups before they\u2019re released back out into the wild,\u201d Bornbusch says.<\/p>\n In Australia, Blyton notes that FMTs could improve the health of koalas (populations of which are suffering a chlamydia epidemic), and also boost reintroduction efforts. Her team\u2019s research has already demonstrated that the koala gut microbiome can be\u00a0altered\u00a0using poop pills, changes that then allow the animals to eat a wider range of differing eucalyptus, potentially aiding reintroductions.<\/p>\n Other projects have used fecal microbiota transplants to help cheetahs\u00a0(Acinonyx jubatus)<\/em>\u00a0recover healthy microbiomes after antibiotic treatments.<\/p>\n An ongoing pilot project in the U.S. is testing FMTs to help rewild black-footed ferrets (Mustela nigripes<\/em>) and especially to see if animals that have gone through a successful soft release can help captive-bred ferrets. The question Bornbusch hopes to answer is whether this treatment will \u201clessen morbidity and mortality during the soft release phase.\u201d<\/p>\n Laurie Marker, executive director of the Cheetah Conservation Fund, sees great potential in cheetah microbiome research, as the species is notoriously plagued by health problems. With numbers in the wild dwindling, the reintroduction of captive cheetah populations is likely to be a key conservation strategy in future.<\/p>\n For now, however, research is mainly shedding light on captive populations because obtaining microbiome samples via feces found in the wild is challenging, given that scat samples degrade if not collected quickly and stored.<\/p>\n \u201cAs we learn more about the wild population and what their actual healthy microbiomes look like, we can start understanding how to keep cheetahs healthy in captivity,\u201d says Marker.<\/p>\n There is still a long way to go before microbial treatments become a regular part of the conservation toolkit for maintaining health or aiding reintroductions, says Melville, who notes that the research is still in its infancy, with more in-depth work needed before informed decisions can be made. \u201cWe often don\u2019t understand enough about commensal, pathogenic and symbiotic taxa in the microbiome of wild animals,\u201d he explains.<\/p>\n Last year, the IUCN, the global wildlife conservation authority, formed a specialist group calling for integration of microbial research, including the microbiome, into global\u00a0conservation action, and underlined the need for further study.<\/p>\n \u201cThis is still a very interesting, up-and-coming field that has huge potential,\u201d says Melville. \u201cBy learning more about wildlife microbiomes, we\u2019re also learning a lot more about our relationship with our [human] gut microbiota. And that is often, I think, overlooked or not discussed.\u201d<\/p>\n Cheng, Y., Fox, S., Pemberton, D., Hogg, C., Papenfuss, A. T., & Belov, K. (2015). The Tasmanian devil microbiome \u2014 Implications for conservation and management.\u00a0Microbiome<\/em>,\u00a03<\/em>(1), 76. doi:10.1186\/s40168-015-0143-0<\/a><\/p>\n Zhu, L., Wang, J., & Bahrndorff, S. (2021). Editorial: The wildlife gut microbiome and its implication for conservation biology.\u00a0Frontiers in Microbiology<\/em>,\u00a012<\/em>. doi:10.3389\/fmicb.2021.697499<\/a><\/p>\n Blyton, M. D., Pascoe, J., Hynes, E., Soo, R. M., Hugenholtz, P., & Moore, B. D. (2023). The koala gut microbiome is largely unaffected by host translocation but rather influences host diet.\u00a0Frontiers in Microbiology<\/em>,\u00a014<\/em>. doi:10.3389\/fmicb.2023.1085090<\/a><\/p>\n Risely, A., M\u00fcller\u2010Klein, N., Schmid, D. W., Wilhelm, K., Clutton\u2010Brock, T. H., Manser, M. B., & Sommer, S. (2023). Climate change drives loss of bacterial gut mutualists at the expense of host survival in wild meerkats.\u00a0Global Change Biology<\/em>,\u00a029<\/em>(20), 5816-5828. doi:10.1111\/gcb.16877<\/a><\/p>\n Anusha, G., Khan, A. S., Krishnan, G., & Umapathy, G. (2025). Anthropogenic factors shape the gut microbiota of tigers in Indian tiger reserves.\u00a0Global Ecology and Conservation<\/em>,\u00a063<\/em>, e03874. doi:10.1016\/j.gecco.2025.e03874<\/a><\/p>\n Jim\u00e9nez, R. R., Alvarado, G., Sandoval, J., & Sommer, S. (2020). Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog.\u00a0BMC Microbiology<\/em>,\u00a020<\/em>(1). doi:10.1186\/s12866-020-01979-1<\/a><\/p>\n Buttimer, S., Moura\u2010Campos, D., Greenspan, S. E., Neely, W. J., Ferrante, L., Toledo, L. F., & Becker, C. G. (2024). Skin microbiome disturbance linked to drought\u2010associated amphibian disease.\u00a0Ecology Letters<\/em>,\u00a027<\/em>(1), e14372. doi:10.1111\/ele.14372<\/a><\/p>\n Rollins-Smith, L. A., & Le Sage, E. H. (2023). Heat stress and amphibian immunity in a time of climate change.\u00a0Philosophical Transactions of the Royal Society B<\/em>,\u00a0378<\/em>(1882). doi:10.1098\/rstb.2022.0132<\/a><\/p>\n Bornbusch, S. L., Clarke, T. A., Hobilalaina, S., Reseva, H. S., LaFleur, M., & Drea, C. M. (2022). Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta<\/em>) in Madagascar.\u00a0Scientific Reports<\/em>,\u00a012<\/em>(1), 22388. doi:10.1038\/s41598-022-26861-0<\/a><\/p>\n Contos, P., Gibb, H., Murphy, N. P., Jellinek, S., & Wood, J. L. (2025). Rebuilding microbiomes: Facilitating animal-microbe interactions through ecological restoration and rewilding.\u00a0Journal of Environmental Management<\/em>,\u00a0375<\/em>, 124344. doi:10.1016\/j.jenvman.2025.124344<\/a><\/p>\n Blyton, M. D., Soo, R. M., Whisson, D., Marsh, K. J., Pascoe, J., Le Pla, M., \u2026 Moore, B. D. (2019). Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala.\u00a0Animal Microbiome<\/em>,\u00a01<\/em>(1), 6. doi:10.1186\/s42523-019-0008-0<\/a><\/p>\n Bornbusch, S. L., Crosier, A., Gentry, L., Delaski, K. M., Maslanka, M., & Muletz-Wolz, C. R. (2024). Fecal microbiota transplants facilitate post-antibiotic recovery of gut microbiota in cheetahs (Acinonyx jubatus<\/em>).\u00a0Communications Biology<\/em>,\u00a07<\/em>(1), 1689. doi:10.1038\/s42003-024-07361-5<\/a><\/p>\n![\"A](\"https:\/\/imgs.mongabay.com\/wp-content\/uploads\/sites\/20\/2026\/03\/26151400\/Image_1-scaled.jpg\" "\\"\\"")
Journey into the microbial wild<\/h2>\n
Conservation implications<\/h2>\n
Citations:<\/strong><\/h2>\n