The group of bacteria called Enterobacteriaceae, which includes Klebsiella pneumoniae, Shigella, E. coli and others, is present at low levels as part of a healthy human gut microbiome. But at high levels (caused, for example, by increased inflammation in the body or eating contaminated food), these microbes can cause illness and disease. In extreme cases, too many Enterobacteriaceae in the intestine can be life-threatening.
Researchers have used computational approaches, including artificial intelligence, to analyze the composition of the gut microbiome of more than 12,000 people in 45 countries from their stool samples. They found that a person’s microbiome “signature” can predict whether their gut is likely to be colonized by Enterobacteriaceae. The results are consistent across different health states and geographic locations.
The researchers identified 135 species of gut microbes that are commonly found in the absence of Enterobacteriaceae and that likely protect against infections.
Among the protective species of the intestine, a group of bacteria called Faecalibacterium stands out, which produce beneficial compounds called short-chain fatty acids by breaking down the fiber in the foods we eat. This appears to protect against infection by a variety of disease-causing Enterobacteriaceae.
Researchers suggest that eating more fiber in our diet will encourage the growth of good bacteria and displace bad bacteria to significantly reduce the risk of disease.
In contrast, taking probiotics (which do not directly change the environment in the gut) is less likely to affect the likelihood of Enterobacteriaceae infection.
The results are published today in the magazine. nature microbiology.
“Our results suggest that what we eat is potentially very important in controlling the likelihood of infection with a variety of bacteria, including E.coli and Klebsiella pneumoniae, because this changes our intestinal environment to make it more hostile to invaders,” said Dr. Alexandre Almeida, a researcher at the Department of Veterinary Medicine at the University of Cambridge and lead author of the paper.
He added: “By eating fiber in foods such as vegetables, beans and whole grains, we can provide the raw materials for our gut bacteria to produce short-chain fatty acids, compounds that can protect us from these pathogenic insects.”
Klebsiella pneumonia It can cause pneumonia, meningitis and other infections. The alarming global rise in antibiotic resistance against this bacterial pathogen has led scientists to look for new ways to keep it, and other similar infectious bacteria, under control.
“With higher rates of antibiotic resistance, we have fewer treatment options available. The best approach now is to prevent infections from occurring in the first place, and we can do this by reducing the opportunities for these disease-causing bacteria to thrive in our gut. “Almeida said.
A new understanding of gut microbe interactions
Previous research to understand the interactions between different bacteria in our gut has used mouse models. But some of these new results contradict previous findings.
The new study revealed that 172 species of gut microbes can coexist with disease-causing Enterobacteriaceae. Many of these species are functionally similar to insects: they need the same nutrients to survive. It was previously thought that competition for resources would prevent disease-causing bacteria from establishing themselves in the gut.
This has important implications for treatment: taking probiotics that compete for the same nutrients with the bad bacteria to try to starve them is not going to work. Researchers say it will be more beneficial to change the gut environment, for example through diet, to reduce the risk of Enterobacteriaceae infection.
“This study highlights the importance of studying pathogens not as isolated entities, but in the context of the gut microbiome that surrounds them,” said Dr. Qi Yin, visiting researcher at the Department of Veterinary Medicine at the University of Cambridge and first author. of the report.