Going with the gut

By Anand Kumar, D.V.M., Ph.D.

A new gut bacteria cocktail could transform our approach to chronic disease

If all disease begins in the gut, as Hippocrates declared more than 2,000 years ago, then surely the cures for those diseases must be tied to the gut, as well.

The gut – a.k.a. the gastrointestinal tract that starts at the mouth and ends at the anus – contains trillions of bacterial cells. A majority are good bacteria that reside in the nearly 30 feet of the large and small intestines. These good bacteria are responsible for a person’s overall health.

But sometimes a harmful bacterium called Clostridium difficile (C. diff) infects the gut, with symptoms that range from diarrhea to inflammation of the colon. Doctors typically treat the infection with antibiotics, but spores from C. diff often linger in the gut and re-infect the patient.

If the infection occurs more than twice, doctors often recommend a fecal transplant: They transplant poop from a person with a healthy gut into the gut of the infected patient. Sounds crazy, but the idea is that the healthy bacteria in the transplanted poop will fight off the C. diff infection. The process works about 95 percent of the time.

Although fecal transplants are fairly routine, not all doctors can perform them and not all hospitals are equipped to handle them. In the United States, only 34 states have hospitals that can perform fecal transplants—and the number of practitioners in those states is limited.

On top of that, finding a good poop donor is challenging – typically, only three out of 100 people meet the donation requirements. Even so, donor samples aren’t screened for all pathogens, so although the transplant might cure a C. diff infection, it might cause another type of infection. Or the transplant might carry a behavior or condition, such as diabetes or depression, from the donor to the recipient – that’s how powerful gut bacteria are.

But what if scientists could identify and isolate the bacteria in a fecal sample that inhibit C. diff and then put just those bacteria into a pill or drink? That’s exactly what my colleagues and I are working on at Los Alamos National Laboratory: pulling together bacteria into a super-powerful cocktail that washes out the infection. The work exploits the Laboratory’s extensive biological research efforts developed in support of our national security mission.

Working with a syringe in an anaerobic glove box, scientists extract healthy gut bacteria from a donated fecal sample. They randomly place two to five gut bacteria together with C. diff pathogen in millions of microdroplets – essentially microscopic bubbles where the gut bacteria and pathogen can interact – and then identify the microdroplets where C. diff growth is suppressed. The gut bacteria in those microdroplets are then identified through sequencing and are mixed together into a cocktail that can be taken orally.

Not only is the cocktail safer than a fecal transplant, but it’s a heck of a lot more comfortable (no tubes through the nose or colon) and affordable (transplants, which costs thousands of dollars, typically aren’t covered by insurance).

Although the cocktail is not yet in clinical testing, we hope that one day it will be available over the counter. Then, people can take it as a precaution against C. diff or to treat an existing infection. Another precaution is a healthy diet full of colorful vegetables and unprocessed foods – Hippocrates would surely agree.

Dr. Kumar works with a pathogenic bacteria sample within a biosafety level 2 facility at Los Alamos National Laboratory.

Anand Kumar, D.V.M., Ph.D., works in the Biosecurity and Public Health group at Los Alamos National Laboratory. He is an Entrepreneurial Fellow under a joint initiative of the University of California and Los Alamos that helps early-career scientists pursue commercializing their technologies.


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Los Alamos National Laboratory uses scientific and engineering expertise to solve the nation's toughest national security challenges.