Earlier this year, I brought you the story of how my cats—Tux, Tuffy, and Nigel—donated their poo to science. While that was—if you'll excuse the pun—mainly for shits and giggles, Tuffy ended up following up on that research, although not by choice. I put him in a follow-up study to see if a fecal microbiome transplant could cure his inflammatory bowel disease. The little chap's gut flora showed a textbook response to the microbiome restoration supplement, and it did what drastic changes to his diet and twice-daily doses of powerful steroids couldn't: it ended the chronic diarrhea that was absolutely no fun for anyone involved.

Here, kitty

As DNA and RNA sequencing has gotten faster and cheaper, they've allowed scientists to delve deeper into cataloguing the communities of microbes that live on our skin and in our guts. And the results have been quite interesting. For example, location matters. While everyone's microbiome—like their genome—is unique, the assortment of bacteria that live behind my ears is far more similar to those living behind someone else's ears than they are to the bacteria that live on my hands.

While that may just be academically interesting, many hope that a better understanding of the microbiome will lead to improvements in human health. By combining microbiome data with medical histories, it's possible to correlate different conditions with different microbial populations. And although that's resulted in some overstated claims, what's become clear is that the microbiome can have real consequences to our health—particularly if the microbiome changes following exposure to antibiotics, antibacterial soaps, or environmental chemicals.

But this isn't just limited to humans; all animal species have a collection of associated microbes. In fact, many of the most compelling results linking microbes to health have come in mice. The Kittybiome project is a crowdfunded research program that uses DNA sequencing to get a sense of the species of gut bacteria found in cats. Its goals are to better understand how different microbe populations might affect cat health and to provide a fun way of doing some science outreach to the public.

Doggybiome Not content to let cats (and their owners) take all the glory, AnimalBiome is now expanding its work to include the dog. The AnimalBiome team is Not content to let cats (and their owners) take all the glory, AnimalBiome is now expanding its work to include the dog. The AnimalBiome team is recruiting canine volunteers , some of whom it hopes will be "golden poo" donors: healthy dogs who can provide samples that can be used to treat sick dogs.

In 2016, I enrolled our cats in Kittybiome. Nigel and Tuffy turned out to have below-average diversities of intestinal flora. While this didn't really appear to have any consequences for Nigel, it may well have been a factor in Tuffy's IBD, which developed in the latter half of 2016.

What on Earth is a fecal transplant?

A lot of microbiome research has focused on the gut. Our intestines are packed with bacteria that work hand in hand with our immune system to limit the growth of pathogens and control GI disorders like Crohn's disease, IBD, and ulcerative colitis. Studies in animals have suggested that the gut microbiome has a powerful role in obesity. While connecting those dots is a useful scientific endeavor in and of itself, the real excitement concerns the potential to use the microbiome as a tool. Enter the fecal transplant, a technique that involves collecting feces from a healthy donor and introducing it into the GI tract of a patient.

Fecal transplants have already shown positive results in treating chronic diarrhea in humans and puppies. And, because the Kittybiome project revealed a much greater incidence of chronic diarrhea among pet cats than previously thought, Holly Ganz (the founder and CEO of AnimalBiome, the company behind the project) decided to see if the approach could be beneficial to our feline friends. With nothing else to lose, we decided to give it a try with Tuffy.

Kittybiome

Kittybiome

Kittybiome

Kittybiome

Kittybiome

Kittybiome

While some of you might be recoiling in horror at the thought, transferring poop was no messier than giving a cat any other pill. The dirty work happened back in the Bay Area, where Ganz and her team identified a number of healthy donor cats, then freeze-dried their feces and packaged it into capsules. Tuffy's microbiome supplement started at the beginning of March and lasted three weeks. Even though the capsules were quite small, the poor little guy did not particularly enjoy having them forced down his throat several times a day. But it wasn't like he enjoyed the standard treatment for IBD, having a liquid steroid squirted into his mouth morning and night.

For the first couple of weeks, the transplant appeared to be having no effect. But during week three, we began to see changes. His need to use the litter box decreased dramatically (from every 2-3 hours down to once or twice a day), and we witnessed a spectacular improvement in consistency as measured by the Bristol Stool Scale. (Yes, that's a thing.) And this phenotypic response was mirrored in the DNA sequencing results, which showed a reaction that Ganz described as textbook. As you can see from the charts, there were big increases in a number of taxa that are known to combat inflammation and aid digestion. Instead of the very low levels prior to the beginning of the transplant, by the end, Tuffy was at the high end of the range for healthy cats.

So long and thanks for all the fish

While I wish that I could end this piece on a happy note, in this case that's just not possible. While his GI distress cleared up, Tuffy never regained his lost muscle mass. In fact, despite our best efforts to supplement his diet with his favorite foods (McDonalds hamburger patties and ham baby food, in case you're curious), Tuffy's weight loss continued. For a cat who once tipped the scales at 15lbs, by mid-May he was down to 6lbs. And then he stopped eating.

Jonathan Gitlin

Jonathan Gitlin

Jonathan Gitlin

Jonathan Gitlin

As our wonderful vet explained, cats can crash very quickly. After soldiering on and enduring what must have been a miserable year—the twice-daily medications, the trips to the vet, the diarrhea and pain—he'd evidently had enough.

He had just one joy left—basking in the sunlight. We had just moved house, and Tuffy (along with our other cats) now had a safe, walled garden in which they could spend unsupervised time outside. He got to chase a squirrel. (Don't worry, he didn't catch it.) Unsteady on his feet and almost spent of energy, he still climbed the stairs during the night to our bedroom, to sleep under the covers a few last times.

By Memorial Day, it was clear to all that it was time. After a peaceful day spent outside in the sun, our vet came to the house and we said our final goodbyes. Tuffy slipped into unconsciousness in my arms, and passed away at 3:15pm. He was a good cat, arriving as an extremely terrified barn rescue in 2002 and brave and gregarious over the following years, brightening our lives all the while.

Writing these final three paragraphs have been tough, but it's comforting to know that he made his own contribution to science, one that will live on.