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Putting the squeeze on gut microbes

Images of bacteria moving through the gut of a larval zebrafish demonstrated the effects of the gut environment on microbial competition. (Credit: PLOS Biology)

Researchers increasingly recognize that the microbes that colonize our guts play an important role in health and development. New research shows that the physical environment in the gut – including all of the squeezing and pushing that goes on there – have a strong effect on the interactions among competing microbes.

Using a new visualizing technique, Karen Guillemin (University of Oregon), a senior fellow in the Humans & the Microbiome program, and colleagues were able to watch two species of bacteria competing in the gut of a larval zebrafish, and observe the dramatic differences the environment makes in which one survives.

“We were able for the first time to visualize the microbial dynamics within the gastrointestinal tract. Before this it’s been a complete black box,” Guillemin says.

The researchers used a computerized imaging technique to take high resolution, three-dimensional images of the larval zebrafish, which is helpfully transparent. The images were able to show what exactly happened as two species of naturally occurring bacteria competed with one another.

Vibrio cholera is a free-swimming bacteria and is capable of quickly moving around in the gut. Aeromonas veronii in contrast tends to grow in stationary clumps. Previous work had shown that Aeromonas tends to compete well against Vibrio in the test tube. But it seems to experience population crashes in guts of zebrafish. Something was clearly happening inside the fish that wasn’t happening in the test tube.

The imaging studies showed it was the movement of the gut that made the difference. The intestines move food from one end to another using peristalsis, a coordinated squeezing motion. The imaging showed that Vibrio remains unperturbed by this squeezing, simply moving to one side or another of the squeezed portion. The clumps of Aeromonas, on the other hand, are pushed along and eventually excreted by the squeezing. It was the peristalsis, combined with competition from Vibrio, that accounted for the population crashes.

They confirmed that finding by doing the same experiments in a zebrafish that carried a mutation that reduced the movements in the gut. In those larvae, populations of Aeromonas were much more stable.

The Humans & the Microbiome program is examining the many ways that microbes living inside of us affect health and development. The microbiome has been implicated in everything from obesity to mental health. A better understanding could help treat a number of different conditions.

Guillemin says that the new finding might be immediately useful for researchers designing new probiotics, who need to understand which microbes will thrive inside the human gut.

The paper was published in PLOS Biology.

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