Around the world with guts on the mind

Article: Valerie J. McKenzie, Se Jin Song, Frédéric Delsuc, Tiffany L. Prest, Angela M. Oliverio, Timothy M. Korpita, Alexandra Alexiev, Katherine R. Amato, Jessica L. Metcalf, Martin Kowalewski, Nico L. Avenant, Andres Link, Anthony Di Fiore, Andaine Seguin-Orlando, Claudia Feh, Ludovic Orlando, Joseph R. Mendelson, Jon Sanders, Rob Knight; The Effects of Captivity on the Mammalian Gut Microbiome,  Integrative and Comparative Biology, Volume 57, Issue 4, 1 October 2017, Pages 690 – 704,

A buzz about gut microbiomes

Next time you walk into a supermarket – especially the dairy section – take notice of the number of probiotic yogurts and cheeses. That yogurt cup contains more than just fruit at the bottom. It is filled with live bacteria – a buzzing community of organisms. When you take a spoonful, those bacteria join a larger group of bacteria already thriving in your intestinal track (but read this). Probiotics that help breakdown food and promote nutrient absorption are aptly dubbed “healthy” bacteria. The interest in curating a “healthy” gut microbiome has taken off over the past decade, largely due to a better understanding of how critical gut microbiomes are for overall health. These bacteria play an important role in food digestion and immune system function, among having other benefits.

For zookeepers whose job it is to keep captive animals healthy, it is no surprise that gut microbiome research is a major interest. Captive animals might have an appetite, but if they aren’t able to absorb key nutrients, their long-term health will be in jeopardy. To get a better sense of what a “healthy” microbiome of a captive organism looks like, they needed to understand what gut microbiomes look like in wild populations.

Collect ’em while they’re hot

 A group of scientific researchers set out to study gut microbiomes of wild and captive mammals. The lead author, Dr. Valerie McKenzie, works as an Associate Professor at the University of Colorado Boulder and collaborated with researchers from around the globe. The scientists carefully selected a wide variety of mammals – from aardvarks to cheetahs. They targeted forty-one different species.

Through collaborations with zoo employees and research technicians, they collected fecal samples – what scientists call poop – from eight zoos around the world and from wild mammal populations across 4 continents. In an effort to standardize collecting practices, field technicians followed strict protocols. For one, they collected samples within minutes of defecation. This isn’t too taxing when you are working at the National Zoo in Washington, D.C., but presents a more interesting challenge roaming grasslands in South Africa tracking a cheetah or wildebeest. They carefully stored samples and then headed back to the lab.

Cheetah on the open plains. Photo Credit: Roma Neus (Creative Commons Attribution 3.0 Unported, CC BY 3.0)

What’s in the steaming piles?

 To quantify the types and abundance of gut bacteria, scientists sequenced and analyzed DNA – or genetic makeup – from the fecal samples. Captive animals hosted far fewer bacterial species in their gut than wild species. This didn’t surprise scientists too much. It is well known that human gut microbiomes differ greatly depending on lifestyle. Since living on the open plains of South Africa looks quite different than in a zoo, this matched scientists’ hypotheses.

But the white and black rhinoceros surprised them! For these creatures, the trend was reversed: white and black rhinoceros had greater diversity in gut bacteria compared to their wild counterparts. Captive animals don’t interact with a wide variety of other organisms so they co-opt fewer microbes from new sources.

Scientists want to know more than just the number of species in the samples. Through DNA sequencing efforts, they can identify the names of the species present. One group of bacteria, Prevotella, tend to occur less frequently in captive mammals compared to wild mammals. Prevotella also decreases when humans shift diets from predominantly vegetarian to animal-based foods. Based on this, researchers hypothesized that captive mammals have higher protein diets compared to diets in the wild.

Although captive animals lose some gut bacteria associated with health, they show increases in other beneficial gut bacteria. For instance, Christensenellaceae, a microorganism associated with This family of microbes is easily passed down from parents to offspring. The difference in gut microbes between wild and captive organisms might not always be a bad thing, rather the gut community of the captive animals are likely changing over time in response to the built environment.

Cheetah in a captive environment. Photo Credit: Max Pixel (CC0 1.0 Universal, CC0 1.0)

Next stop

Those who work with captive mammals can use this study to better assess the gut microbiome of animals in their care. Although a range of gut microbial compositions can be considered “healthy,” it’s important to understand how diet and environment could change these quantities of bacteria. Research centered on classifying and quantifying microbiome will continue to be important as zookeepers work to keep animals healthy in zoos and conservation breeding facilities. The field is changing faster than the number of yogurts in the dairy section. Scientists hope to continue studying captive and wild animals to gain a better understanding of what factors drive these differences.

Featured Image

Featured Image Attribution: Chris Wood, Oxford Medical Illustration and Nicola Fawcett (Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)


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Claire Wilson

I completed my M.S. in Biological and Environmental Sciences from the University of Rhode Island in 2016. As a community ecologist, I studied the interaction between invasive insects and a native plant. I recently moved to Washington, DC to support student/faculty development in the microbial sciences and am driven to increase science literacy. Although I'm enjoying working at the intersection of research, education, and communication, I miss long days in the field. Away from work and freelance writing, you can find me running in Rock Creek park, dodging city bikers, and scheming my next backpacking trip.

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