The composition of your gut microbiome can be used to predict how likely you are to succumb to potentially life-threatening infection with Klebsiella pneumoniae, E.coli or other bugs – and your risk can be altered by changing your diet.
University of Cambridge researchers used computational approaches including AI to analyse the gut microbiome composition from more than 12,000 people across 45 countries via their stool samples.
Enterobacteriaceae bacteria are part of the intestinal microbiome and causative agents of various infections
They found a person’s microbiome ‘signature’ can predict whether a person’s gut is likely to be colonised by a group of bacteria called Enterobacteriaceae and the results were consistent across different states of health and geographic locations.
The Enterobacteriaceae group includes Klebsiella pneumoniae, Shigella, E.coli and others. Bacteria in this group are 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 by eating contaminated food – these bugs can cause illness and disease.
Too much Enterobacteriaceae in the gut can be life-threatening in extreme cases.
The researchers identified 135 gut microbe species commonly found in the absence of Enterobacteriaceae, which are probably protecting against infection, including a group of bacteria called Faecalibacterium. These produce beneficial compounds called short-chain fatty acids by breaking down fibre in the foods we eat.
This process seems to protect against infection by a range of disease-causing Enterobacteriaceae bugs.
The study suggests eating more fibre in our diet supports the growth of good bacteria, crowding out the bad ones and significantly reducing the risk of illness.
But they found that taking probiotics, which do not directly change the environment in the gut, is less likely to affect the likelihood of Enterobacteriaceae infection.
“Our results suggest that what we eat is potentially very important in controlling the likelihood of infection with a range of bacteria, including E.coli and Klebsiella pneumoniae, because this changes our gut environment to make it more hostile to invaders,” said Dr Alexandre Almeida, a researcher at the Cambridge’s Department of Veterinary Medicine and senior author of the paper.
“By eating fibre in foods like vegetables, beans and whole grains, we can provide the raw material for our gut bacteria to produce short chain fatty acids – compounds that can protect us from these pathogenic bugs.”
Klebsiella pneumonia can cause pneumonia, meningitis and other infections and there has been an alarming global rise in antibiotic resistance to this bacterial pathogen.
“With higher rates of antibiotic resistance there are fewer treatment options available to us. The best approach now is to prevent infections occurring in the first place, and we can do this by reducing the opportunities for these disease-causing bacteria to thrive in our gut,” said Dr Almeida.
Some of the new findings are at odds with earlier research that relied on mouse models.
The new study found that 172 species of gut microbe can coexist with disease-causing Enterobacteriaceae bugs and many of these species are functionally similar to the bugs, meaning they need the same nutrients to survive.
It had been thought that competition for resources would stop the disease-causing bacteria from getting established in the gut but the new findings reveal that is not the case and means that taking probiotics that compete for the same nutrients with the bad bacteria to starve them out is not going to work.
Instead, we need to change the environment in the gut, for instance through diet, to reduce the risk of infection with Enterobacteriaceae.
“This study highlights the importance of studying pathogens not as isolated entities, but in the context of their surrounding gut microbiome,” said Dr Qi Yin, a visiting researcher at Cambridge’s Department of Veterinary Medicine and first author of the report.
The research, published in the journal Nature Microbiology, was funded by the Medical Research Council.