Creative Minds: The Human Gut Microbiome’s Top 100 Hits

Michael Fischbach

Michael Fischbach

Microbes that live in dirt often engage in their own deadly turf wars, producing a toxic mix of chemical compounds (also called “small molecules”) that can be a source of new antibiotics. When he started out in science more than a decade ago, Michael Fischbach studied these soil-dwelling microbes to look for genes involved in making these compounds.

Eventually, Fischbach, who is now at the University of California, San Francisco, came to a career-altering realization: maybe he didn’t need to dig in dirt! He hypothesized an even better way to improve human health might be found in the genes of the trillions of microorganisms that dwell in and on our bodies, known collectively as the human microbiome.

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Creative Minds: Making a Miniature Colon in the Lab

Gut on a Chip

Caption: Top down view of gut tissue monolayer grown on an engineered scaffold, which guides the cells into organized crypts structures similar to the conformation of crypts in the human colon. Areas between the circles represent the flat lumenal surface.
Credit: Nancy Allbritton, University of North Carolina, Chapel Hill

When Nancy Allbritton was a child in Marksville, LA, she designed and built her own rabbit hutches. She also once took apart an old TV set to investigate the cathode ray tube inside before turning the wooden frame that housed the TV into a bookcase, which, by the way, she still has. Allbritton’s natural curiosity for how things work later inspired her to earn advanced degrees in medicine, medical engineering, and medical physics, while also honing her skills in cell biology and analytical chemistry.

Now, Allbritton applies her wide-ranging research background to design cutting-edge technologies in her lab at the University of North Carolina, Chapel Hill. In one of her boldest challenges yet, supported by a 2015 NIH Director’s Transformative Research Award, Allbritton and a multidisciplinary team of collaborators have set out to engineer a functional model of a large intestine, or colon, on a microfabricated chip about the size of a dime.

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Creative Minds: New Piece in the Crohn’s Disease Puzzle?

Gwendalyn Randolph

Gwendalyn Randolph

Back in the early 1930s, Burrill Crohn, a gastroenterologist in New York, decided to examine intestinal tissue biopsies from some of his patients who were suffering from severe bowel problems. It turns out that 14 showed signs of severe inflammation and structural damage in the lower part of the small intestine. As Crohn later wrote a medical colleague, “I have discovered, I believe, a new intestinal disease …” [1]

More than eight decades later, the precise cause of this disorder, which is now called Crohn’s disease, remains a mystery. Researchers have uncovered numerous genes, microbes, immunologic abnormalities, and other factors that likely contribute to the condition, estimated to affect hundreds of thousands of Americans and many more worldwide [2]. But none of these discoveries alone appears sufficient to trigger the uncontrolled inflammation and pathology of Crohn’s disease.

Other critical pieces of the Crohn’s puzzle remain to be found, and Gwendalyn Randolph thinks she might have her eyes on one of them. Randolph, an immunologist at Washington University, St. Louis, suspects that Crohn’s disease and other related conditions, collectively called inflammatory bowel disease (IBD), stems from changes in vessels that carry nutrients, immune cells, and possibly microbial components away from the intestinal wall. To pursue this promising lead, Rudolph has received a 2015 NIH Director’s Pioneer Award.

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You Won’t Believe What’s In These Pills

Fecal pills

Credit:: Hohmann lab

Clostridium difficile, or more commonly “C. diff,” is a nasty bacterium that claims the lives of 14,000 Americans every year. Most at risk are people with conditions requiring prolonged use of antibiotics, which have the unfortunate side effect of wiping out the natural, good bacteria in the colon—thus allowing bad bugs like C. diff to multiply unchecked. In many folks, C. diff infection can be treated by halting the original antibiotics and switching to other types of antibiotics. But for some people, that doesn’t work—C. diff is either resistant to treatment or makes a hasty comeback.

What’s to be done then? Well, researchers have known for some time that taking microbe-rich stool samples from healthy people and transplanting them into C. diff patients helps to improve their symptoms. The challenge has been figuring out a safe and effective way to do this that is acceptable to patients and doesn’t involve invasive procedures, such as colonoscopy or nasogastric tubes [1,2]. Could there be a simple solution? To put it more bluntly: what about poop pills?

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