Using Big Data and Next-Generation Sequencing to Improve Your Pet’s Health

Using Big Data and Next-Generation Sequencing to Improve Your Pet’s Health
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Curiosity has been known to kill the cat, but in this case, the curiosity of one UC Davis researcher may help improve the health of cats (and dogs) through a better understanding of their digestive health.

For individuals curious enough to wonder why their furry companion(s) sometimes suffer from gastrointestinal upsets like diarrhea, vomiting, or constipation, it might be time to collect a sample of their poop to have their gut bacteria examined. These bacteria, which are part of what researchers call the “microbiome,” play important roles in healthy digestion for pets

Just as humans get tested for diseases such as IBD (Inflammatory Bowel Disease), pet owners now have the option of having their cat or dog’s poop examined by trained researchers to determine the composition of gut bacteria. Think of this as the 23andMe for pets, except that instead of looking at ancestry and genes, AnimalBiome sequences poop samples from dogs and cats in order to better understand their digestive health. Supplements and therapies are then developed to help improve these conditions.

Helping pet parents better understand their companions’ digestive health has been a mission for Holly Ganz, PhD, Co-Founder, and CEO of AnimalBiome since she started studying the dog oral microbiome as a researcher at the UC Davis School of Veterinary Medicine in 2011. AnimalBiome started as a “citizen-science project” to examine the microbiome of cats’ digestive systems. This project eventually turned into a “Kittybiome” Kickstarter campaign that was launched in 2015 to help pet owners better understand their cats’ health and biology.

“We launched the KittyBiome Kickstarter to fund our basic research on the microbiome of animals. From this research, I found that many of the cats that participated in KittyBiome had chronic digestive disorders and a number had suspected IBD. Our subsequent market research has shown that 10% of all dogs and cats in the US have chronic digestive disorders. This helped me realize that my idea for a microbiome-based diagnostic could address a large market as well as meet a real need,” Holly explained.

The Kittybiome campaign proved to be successful, with funds reaching seven times more than the targeted goal (the campaign also helped recruit the celebrity cat, Lil Bub, to join the cause!). AnimalBiome has recently launched a “DoggyBiome” Kickstarter campaign to study microbiomes amongst dogs.

“We now want to better understand the amount of variation in the microbiome of dogs. We are hoping to get contributions from many different dog breeds, as well as dogs with different health conditions. By understanding what healthy dogs look like and how sick dogs differ, we can create better diagnostics and potentially therapeutics. Participants in the KittyBiome project included many healthy cats, as well as those with various health conditions. This helped us build a large database on cat microbiomes, as well as their health, diet, and lifestyle. As a result, we are already helping sick cats and now we want to do the same for dogs. This campaign is for dog lovers, pet parents, the curious, scientists and more - it’s for people who are eager to support real innovation for pet health and watch it unfold,” Holly mentioned.
Holly Ganz, CEO and Co-Founder of AnimalBiome

Holly Ganz, CEO and Co-Founder of AnimalBiome

“We have been applying microbiome analysis to better understand human health and disease,” says Jack Gilbert, Professor of Surgery at University of Chicago, Director of the Microbiome Center, and author of Dirt is Good: The advantage of microbes for your child’s developing immune system, “This is leading to the development of novel probiotics to alleviate symptoms of disease, and novel drug based interventions to help prevent or cure disease. Applying this to our furry friends is the next logical step.”

Big Data’s Role In Your Pet’s Health

AnimalBiome might sound too good to be true, as not many commercial solutions have been developed to help detect, prevent, and treat digestive diseases in cats and dogs. But just as next-generation sequencing (NGS) impacts medical and genomic research in humans, Holly realized that the same could be done to detect diseases in animals.

“The convergence of next-generation sequencing and advanced bioinformatics has led to numerous publications on the microbiome, including some of my own, that have identified alterations in microbial communities that were associated with a diseased state. I collaborated on a project with some colleagues in computer science to identify bacterial biomarkers associated with disease in wildlife. We used advanced bioinformatics and machine learning to identify bacterial biomarkers associated with influenza infection in wild mallards that allowed us to predict the disease state with 96 percent accuracy. The development of these methods helped me realize that I could potentially use the gut microbiome of dogs and cats to identify digestive disorders like IBD,” Holly explained.

Of course, next-generation sequencing also generates massive amounts of data that needs to be analyzed in order for conclusions to be drawn. The scale and efficiency of NGS is so large that big-data algorithms are now being applied to reveal hidden patterns in sequencing, analysis, and annotation.

Similar to the NGS process used in humans, once AnimalBiome receives pets’ samples, they use laboratory facilities to extract the DNA from all the bacteria in the sample. Then a small region of the DNA is sequenced from each of them called, “16S rRNA,” which acts as a barcode for each bacterium.

Next, all those thousands of barcodes are taken and sequenced, allowing researchers to gain an understanding of the pets’ samples. Big data algorithms are then used to interpret those thousands of barcodes. Once insights are gained for this data, each pet’s results are presented to pet owners in a simple dashboard. This data reveals specific insights into the microbial community of each pet and has the potential to be informative about their health.

AnimalBiome Dashboard

AnimalBiome Dashboard

“As a researcher who studies bacterial genomes and as someone who absolutely loves cats, dogs, and animals of all sorts, I was really excited to have my cat, Danny, be one of the first AnimalBiome subjects,” says Jennifer Gardy, one of AnimalBiome’s scientific advisors. “Opening up the dashboard and seeing his results was amazing – he’s a pretty healthy cat, and it was so fascinating to see how his microbiome fit with that overall picture of well-being.”

What’s The Cure?

Of course, pet owners and curious individuals might be wondering, “What happens if a dog or cat happens to be diagnosed with IBD or a similar disorder?”

While AnimalBiome recognizes that there is no single cure for chronic digestive disorders, the team is currently testing treatments to cure and even prevent these diseases before they develop. Currently, AnimalBiome is conducting a pilot study of Fecal Microbiota Transplant (FMT) pills to restore the microbiota in pets with digestive problems linked to low microbial diversity.

While the research is still underway and they are still determining how robust their findings are, AnimalBiome is yielding promising results for those cats lucky enough to participate in the study. With a solution like this, pet parents will finally be able to better understand and improve their pet’s health based on big data analysis, which is something to certainly be curious about.

AnimalBiome has over 1,000 cat samples and that database has really helped it progress in developing diagnostics and therapies for cats. AnimalBiome needs your help to build a similar database for dogs. The DoggyBiome project needs samples from dogs of all breeds, young, old, healthy and ailing. Click here to learn more about the Kickstarter campaign.

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