Dogs, people wanted for ‘American Gut’ project

Researchers seek our bodies’ microbial secrets

December 31, 2012 (published)
By Edie Lau

Photomicrograph by Dr. V.R. Dowell Jr. / U.S. Centers for Disease Control, 1972
Fusobacterium russii normally inhabits the human intestine, and has been identified in the canine intestine, as well. One study found bacteria of the genus Fusobacterium to be well-represented in the guts of healthy dogs. Learning about the diversity of microbes that live in people and their pets is a goal of the American Gut research project.

Science wants you and your dog.

More specifically, it wants to examine the microbial communities that populate your bodies. Toward that end, it would like samples of your skin, saliva or stool.

A research project going by the name American Gut aims to survey the microscopic life forms that inhabit our bodies. The purpose is to learn how they influence our individual and collective health.

How do the body’s microbial communities — known as microbiomes — compare among people and pets living in the same household? In different households? In different parts of the country? How does diet influence the differences? How about lifestyle and environment?

“Every single individual has its own unique microbiome,” explains Dr. Jan Suchodolski, a veterinarian and researcher in Texas A&M University’s Veterinary Medicine & Biomedical Sciences Gastrointestinal Laboratory. “(From) the bacteria on your fingertips, they can see who typed on a keyboard.”

Suchodolski is one of dozens of researchers from around the world affiliated with American Gut, which aspires to a broad reach in every respect: The more participants, the merrier, because participants are also the project funders. The price to join in ranges from $99 to $25,000, depending on the number and depth of analyses a participant desires.

The everyone-funds-it approach undergirds organizers’ intention to make data open and available to all. Information on individuals’ microbiomes will be kept confidential, but aggregate data will be open-access, according to information posted on the American Gut website.

So far, researchers’ enthusiasm is outpacing participation. The original Jan. 7 deadline for sign-ups recently was postponed to Feb. 1. As of Monday, the project attracted 484 takers and $83,526 toward its funding goal of $400,000.

Undaunted, organizers note: “This is a ‘Flexible Funding’ campaign so the project and all analysis will go forward regardless if the funding goal is reached.”

The entry-level $99 “perk” provides genetic analysis of the microbes from one sample — stool, mouth or skin. Analysis of two samples is available for $180; three for $260; and four for $320.

For $500, a participant gets “A Week of Feces”— a genetic analysis that identifies the microbial inhabitants found in samples of stool produced every day for one week.

Pricier options, ranging from $1,500 to $25,000, involve more detailed analyses using more sophisticated techniques.

Whether one or more people (or dogs) in a given household participate is up to each participant.

Jeff Leach, founder of the Human Food Project, the organization behind American Gut, told the VIN News Service by email last week that among the enrollees are “a couple dozen” pets. “We expect that number to top a couple of hundred by the Feb. 1 deadline for sign-up,” he said.

For participants, information about who lives in their guts and in what abundance has more curiosity value than clinical value at the moment. What it all means for individuals’ health has yet to be worked out.

Exploration of the body’s microbial diversity is a young science, made possible only recently by tools and techniques that enable scientists to detect life through its DNA. Suchodolski said the first scientific paper on the microbiome was published five years ago.

When Suchodolski began his research career studying a disease in dogs called small intestine bacterial overgrowth, the way scientists determined the bacterial composition of a gut sample was through culturing — that is, by encouraging the microbes in the sample to multiply in the laboratory so as to get a good look at them.

“Then the molecular tools came out ... and it turned out that what was being cultured was only a small part (of the total),” Suchodolski said. “We discovered it was so much more diverse and so much more complex.”

His research since then has identified more than 36 bacterial genera in the guts of healthy dogs. A study co-authored by Suchodolski and published in June by PLOS compared the bacterial populations of healthy dogs with dogs suffering from inflammatory bowel disease, a condition characterized by chronic diarrhea, vomiting and intestinal inflammation.

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The researchers found significant differences in the bacterial population of sick dogs versus well dogs.

For example, the populations of Fusobacterium and Bacteroides, the first and second most abundant bacterial genera in the healthy dogs, were much less abundant in sick dogs. Meanwhile, bacteria normally not present or present at very low levels in well dogs made up more than half of the bacterial populations in the guts of sick dogs.

(The researchers used the same genetic analysis that will be applied to most samples in the American Gut project — specifically, amplification and sequencing of RNA from what is known as the16S ribosomal gene.)

In a more recent study, published in November by BMC Veterinary Research, Suchodolski and colleagues found gut microbiome disparities in healthy horses and horses with chronic laminitis, an inflammation of connective tissues in the hoof.

His foray into the bacterial world of the gut has given Suchodolski an appreciation for the system’s complexity, which he compares to a jungle or rainforest.

“The ‘good bacteria, bad bacteria’ (concept) is probably too simplistic,” he said. The pertinent question is whether various types of bacteria are present in numbers that support a healthy body, he said.

Researchers also have seen that people in different parts of the world with markedly different diets have markedly different microbiomes. “Diet is definitely a big influence on the gut,” Suchodolski said.

That suggests the possibility that individuals can, by changing what they eat, change their microbiomes — potentially preventing or correcting disease. The trick is knowing exactly how. Because microbiomes are unique to individuals, the same dietary change in one individual may have a different effect on another, Suchodolski said.

But perhaps given enough information, science can learn to predict outcomes. “Can we measure (an individual’s) microbiome and predict how he will respond to a probiotic? How he’d respond to a high-fat diet? A high-protein diet?” Suchodolski asked rhetorically. “We can change our microbiome, but we need to know in which direction.”

Even when illness is not an issue, the influence of diet on the gut and its microbial occupants may have important effects, as dog owners who pick up regularly after their pets know.

Kelly Swanson, a nutritionist in the Department of Animal Sciences at the University of Illinois at Urbana-Champaign and another American Gut collaborator, said pet food manufacturers are among those keenly interested in the effects of diet on stool quality — namely, volume, consistency and odor.

“It’s definitely an important thing,” Swanson said. “Most responsible owners are having to pick it up, and (that chore) reminds you of it every day.”

Swanson’s research in pet nutrition has led him to the microbiomes of cats and dogs. Much of his work has involved healthy laboratory animals, so he is excited by the opportunity to analyze data from pets in ordinary households.

“I’m almost positive that there are dogs even in urban areas that are exposed to different bacteria than in our lab,” Swanson said. “We’re not in a sterile environment, but we’re pretty clean.”

It’s a less controlled situation, Swanson acknowledged — the researchers are reliant on owners to document their pets’ diets, for example — but the resulting data is more likely to be applicable to the general population.

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