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  • November 30, 2016

Gut bacteria changes may predict infection and inflammation

Gut bacteria changes may predict infection and inflammation


One of the most surprising revelations about human biology to emerge in recent years is that the microbes in our gut vastly outnumber our body’s own cells. Plus, it seems they play an important role in our health; when they get sick, we get sick. Now, a new study shows how a computer-assisted model can predict gut infection and inflammation before symptoms emerge by tracking changes in gut microbiota signatures over time.

Writing in the journal PLoS ONE, researchers from Brigham and Women’s Hospital (BWH),

an affiliate of Harvard Medical School in Boston, MA, suggest their findings will eventually help

doctors reach a better understanding of how foreign bacteria disrupt our gut microbiota, and from

that find better treatments for gastrointestinal (GI) infection and inflammation.

Senior author Lyn Bry, associate professor of Pathology at Harvard Medical School, and

director of the BWH Center for Clinical and Translational Metagenomics, says:

“Our gut contains 10 times more bacterial cells than there are human cells in our body. The

behavior of these complex bacterial ecosystems when under attack by infection can have a big

impact on our health.”

Gut bacteria show different signatures at different stages of infection

For the study, the team used new computer algorithms developed by co-first author Georg

Gerber, who is also director of the BWH Center for Clinical and Translational Metagenomics, and

Director of BWH’s Computational Unit.

Gut and stomach
By tracking changes in gut microbiota signatures over time, a computer-assisted model can predict gut infection and inflammation before symptoms emerge.

The team used the algorithms to analyze what happens to gut bacteria in mice during different

stages of infection by the pathogen Citrobacter rodentium. The pathogen causes symptoms

that are similar to food poisoning in humans.

In mice with healthy immune systems, the pathogen follows four distinct stages: early

colonization, followed by symptomatic infection, which is then followed by a response from the

immune system where the pathogen is cleared from the system, and finally, a “convalescence” phase,

where tissue damage is repaired.

The whole process takes around 2 months.

For their study, the team produced time-series genetic signatures of the gut bacteria at

various points in the mice’s gut over the 2 months of the infection process. Then, using the

algorithms in a computational framework, they analyzed both local and overall changes in the

bacterial colonies to identify dynamic changes that correspond to the various phases of infection

and inflammation.

Families of gut microbes disrupted in different ways during course of infection

The researchers saw the normal bacteria were disrupted in several different ways, in different

locations in the gut, as the infection unfolded and was resolved.

For example, they found the genetic signatures of bacterial colonies belonging to the genus

Mucispirillum showed these appeared to subside early in the infection process, before

symptoms emerged. And they do not return to normal levels until the final convalescence phase,

well after the pathogen has been cleared away.

Mucispirillum inhabits the mucus layer in the colon, and it is known that the

pathogen actively destroys the microenvironment of that part of the gut.

“Full regeneration of the mucus layer occurs some time after the pathogen’s clearance,

providing a possible explanation for the observed delay in Mucispirillum’s

recolonization of distal colon,” note the authors, adding that the corresponding signature “could

thus provide a marker for health of the surface mucus layer in distal colon, with potential

application to other models of inflammatory colitis.”

Signatures of other bacteria types, such as those belonging to the families

Clostridiales and Lactobacillales showed these populations increased after the

pathogen disappeared.

Plus, the team thought it was interesting that some of these increases occurred in parts of

the gut where the pathogen had not damaged any host cells.

Microbial signatures could help detect subtle versions or early stages of gut diseases

Prof. Bry says that from a clinical perspective, “these new microbial signatures we identified

could help clinicians detect early stages of inflammation or subtle persistent disease in

patients with gastrointestinal disorders, such as inflammatory bowel disease.”

She adds that several of the time-dependent signatures they identified could also be used to

study other types of inflammation and infection.

Various grants and funds helped finance the study, including contributions from the National

Institutes of Health, Netherlands Organization for Scientific Research, Stanley L. Robbins

Memorial Research award, and organizations linked to Harvard.

Meanwhile, Medical News Today recently learned of a study that found gut bacteria diversity improves with

exercise, highlighting another interesting way that our friendly gut flora affect our


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