if only it was a mouthswab —

My cats poop for science

A study is looking at the microbiome of our pets, and my cats are taking part.

The three stooges at rest. They have no idea they're doing their part to further scientific knowledge.
Enlarge / The three stooges at rest. They have no idea they're doing their part to further scientific knowledge.
Elle Cayabyab Gitlin

Ever wondered about the bacteria in your cat's gut? It's probably not something that crops up in most people's daily lives, but some of us care. The evidence for that is Kittybiome, a crowdfunding project that's trying to survey the biological diversity in cats' intestines. Suitably intrigued, and keen to do my bit, I backed the project. And that's how I came to be staking out the litter box over the summer, armed with nitrile gloves and three poop-collection kits. You know, for science.

It's all about what's known as the "microbiome"—the populations of microbes that we carry around on our skin and in our guts. Equipped with ever-cheaper and faster DNA sequencing, scientists are now able to catalogue these communities of microbes, which we are finding can have a powerful influence on health and disease. While much of the microbiome research to date has, understandably, focused on the relationship between these microbes and humans, animals have their own microbiomes. Which is where Holly Ganz and her colleagues come in; they're applying the techniques refined in humans to understand more about the cats and dogs with whom many of us share our lives.

Ganz, now founder and CEO of Animalbiome, told Ars that "It started as a citizen science project that I started with Jonathan Eisen and a couple of other researchers." She was studying the microbiome of animals at the Genome Center at UC, Davis, when she realized that getting people to contribute microbiome samples from their cats could be a fun way to get the public to participate in research. "So we did a Kickstarter, partly because academic funding is increasingly hard to obtain and partly because veterinary grants are small and hard to get."

This approach—albeit not with pets—had been tried successfully before, in the shape of the American Gut Project. The Kittybiome Kickstarter ended up raising seven times more than the target and recruited celebrity cat Lil Bub along the way. Participants were recruited through the Kickstarter and received collection kits (like the ones I used) for a sufficient donation. All they had to do was collect some cat poop, drop it in a sterile sample container, and mail it in. You know, for science.

You can see some of Tux, Tuffy, and Nigel's results in the gallery. The type of sequencing used only detects bacteria, not viruses or parasites (the sequencing only analyzes so-called "hypervariable regions" of bacterial 16S ribosomal RNA). Compared to similar cats in the study, all three of my cats turned out to have below-average richness of bacteria inside them; both Tuffy and Nigel also had below-average diversity of their gut bacteria. As we'll discover, that may have contributed to Tuffy contracting inflammatory bowel disease in the second half of 2016.

But despite living in the same house and eating the same food, all three have distinct microbiomes, with different combinations of microbial lineages.

More than just scientific curiosity

As the microbiome data started coming in from pets (along with health info supplied by their owners), the project grew from something that was mainly science outreach into a more health-focused endeavor.

"In the process of running the samples and looking at the data, and in talking to people about their pets, we found that digestive problems were a lot more common in cats than we realized," Ganz told me. "It turned out that maybe as many as 10 percent of cats in the US have chronic digestive problems, and dogs are similar. We also found that, when we looked at the microbiome data, all of the cats reported as having chronic diarrhea all had microbiomes that looked lacking in diversity. There was a lot of variation, but they were all pretty different than your average cat."

Ganz also found that some healthy cats also had odd-looking microbiomes. "We came to think of those as "apparently healthy," she explained. "It might be that having a low diversity in your gut is fine if you don't get stomach flu or you have to take antibiotics, which is when you run into trouble." While no one has conclusively demonstrated that microbiomes have these effects yet, it would be consistent with findings from other ecosystems.

Realizing this problem and that people were desperate for a solution, Ganz suggested that desperate owners of IBD cats might consider a fecal microbiome transplant. This approach has worked in humans and also puppies with chronic diarrhea, and it's even being tested in humans to treat obesity. But vets able and willing to perform the procedure are few and far between. As anyone who has been to the vet recently knows well, veterinary medicine isn't usually cheap. That's when Ganz decided to found AnimalBiome, which is continuing the work cataloguing both cat and dog microbiomes as well as developing new therapeutics for pets with dodgy tummies.

One such therapy is a fecal microbiome transplant, which is currently in a pilot trial. "We reached out to find people who had healthy cats and dogs in the prime of life," she explained. (The cats and dogs have to fully mature, because the microbiome changes when they're weaned onto solid food, then changes again once they reach their dotage.) The donor animals had to be free of health problems, couldn't have received antibiotics in the past six months, and had to be free of parasites, viruses, and common pathogens like salmonella and E. coli.

Participating owners of the recipient animals collect several poop samples (over time) as their pets undergo a microbiome transplant. "We don't have enough data yet to know how microbiome composition affects the outcome, so we're collecting microbiome samples from everyone to see if certain donors are better," Ganz told me. "We have this joke in the office about 'golden poo' and that maybe some donors will be much more effective than others. But it could be that just having a different community is enough. We don't know the answer yet."

But Ganz's initial handful of results were promising: the first seven cats all showed a dramatic improvement within a few days of starting their poop pills. I'm hoping for a first-hand demonstration of that; despite daily doses of the powerful steroid prednisolone, Tuffy's IBD remains intractable. He started his fecal microbiome transplant last week, and, with any luck, you'll be able to read about its progress in a forthcoming follow-up.

Channel Ars Technica