A recent study has revealed that the makeup of your gut microbiome can indicate your susceptibility to serious infections caused by bacteria such as Klebsiella pneumoniae and E. coli. Additionally, your diet might be able to change this microbiome composition.
The group of bacteria known as Enterobacteriaceae, which includes Klebsiella pneumoniae, Shigella, E.coli, and others, typically exists in small quantities in a healthy gut microbiome. However, when these bacteria multiply due to factors like bodily inflammation or consuming contaminated food, they can lead to illness. In severe instances, an overabundance of Enterobacteriaceae can be life-threatening.
Researchers employed AI-driven computational methods to analyze stool samples from more than 12,000 individuals across 45 countries. They discovered that a person’s unique microbiome ‘signature’ can predict whether Enterobacteriaceae will inhabit their gut. Notably, these findings were consistent regardless of a person’s health state or geographic location.
The study pinpointed 135 different gut microbial species that seem to be present in individuals lacking Enterobacteriaceae, likely providing a defensive barrier against infections.
Among these protective microbe species is Faecalibacterium, a group of bacteria that generate beneficial substances called short-chain fatty acids by digesting fiber from our diet. This process appears to help guard against infections from various harmful Enterobacteriaceae.
The researchers recommend increasing fiber intake, as it fosters the growth of beneficial bacteria and helps limit the populations of harmful ones, thereby significantly lowering disease risk.
Conversely, using probiotics—products that do not directly alter the gut environment—is less effective in preventing Enterobacteriaceae infections.
The findings are published today in the journal Nature Microbiology.
“Our findings indicate that dietary choices play a crucial role in influencing the likelihood of infections from various bacteria, such as E.coli and Klebsiella pneumoniae, by modifying our gut environment to become less welcoming to harmful invaders,” commented Dr. Alexandre Almeida, a researcher at the University of Cambridge’s Department of Veterinary Medicine and the study’s senior author.
He further stated: “Consuming fiber from vegetables, legumes, and whole grains provides essential materials for our gut bacteria to produce short-chain fatty acids, which help shield us from pathogenic bacteria.”
Klebsiella pneumonia can lead to pneumonia, meningitis, and various other infections. The disturbing rise in antibiotic-resistant strains of this bacterium has spurred scientists to explore new strategies for managing it and similar infectious agents.
“With rising antibiotic resistance, treatment options are dwindling. Preventing infections from occurring initially is now the best strategy. We can accomplish this by minimizing conditions that allow disease-causing bacteria to flourish in our gut,” explained Almeida.
Enhancing our understanding of gut microbe interactions
Previous studies on the interactions between different gut bacteria have been conducted using mouse models, but some recent discoveries contradict earlier conclusions.
The new research found that 172 gut microbial species can coexist with harmful Enterobacteriaceae bacteria, many of which share similar functional characteristics. They require the same nutrients to thrive, which challenges the previous belief that competition for resources would inhibit the establishment of harmful bacteria in the gut.
This has significant implications for treatments: taking probiotics that compete for the same nutrients as harmful bacteria is unlikely to be effective in eliminating them. The researchers argue that adjusting the gut environment—primarily through dietary changes—will be more effective in minimizing the risk of Enterobacteriaceae infections.
“This research underscores the importance of studying pathogens not as isolated organisms but in relation to the surrounding gut microbiome,” stated Dr. Qi Yin, a visiting researcher at the University of Cambridge’s Department of Veterinary Medicine and the study’s lead author.
