A new study has found that the composition of your gut
microbiome helps predict how likely you are to succumb to potentially
life-threatening infection with Klebsiella
pneumoniae, E.coli and other bugs – and it may be altered by changing
your diet.
Our results suggest that what we eat is potentially very important in
controlling the likelihood of infection with a range of bacteria.Alexandre
Almeida
The group of
bacteria called Enterobacteriaceae, including 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 by eating contaminated
food – these bugs can cause illness and disease. In extreme cases, too much
Enterobacteriaceae in the gut can be life-threatening.
Researchers have used computational approaches including AI to analyse the
gut microbiome composition of over 12,000 people across 45 countries from their
stool samples. They found that a person’s microbiome ‘signature’ can predict
whether a person’s gut is likely to be colonised by Enterobacteriaceae. The
results are consistent across different states of health and geographic
locations.
The researchers identified 135 gut microbe species that are commonly found
in the absence of Enterobacteriaceae, likely protecting against infection.
Notable amongst the protective gut species are a group of bacteria called
Faecalibacterium, which produce beneficial compounds called short-chain fatty
acids by breaking down fibre in the foods we eat. This seems to protect against
infection by a range of disease-causing Enterobacteriaceae bugs.
The researchers suggest that eating more fibre in our diet will support the
growth of good bacteria – and crowd out the bad ones to significantly reduce
the risk of illness.
In contrast, taking probiotics – which don’t directly change the
environment in the gut – is less likely to affect the likelihood of
Enterobacteriaceae infection.
The results
are published today in the
journal Nature
Microbiology.
“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 University of
Cambridge’s Department of Veterinary Medicine and senior author of the paper.
He added: “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. The alarming
global rise in antibiotic resistance to this bacterial pathogen has led
scientists to look for new ways of keeping it, and other similar infectious
bacteria, under control.
“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 Almeida.
A new
understanding of gut microbe interactions
Earlier research to understand interactions between the different bacteria
in our gut has used mouse models. But some of these new results are at odds
with previous findings.
The new study revealed that 172 species of gut microbe can coexist with
disease-causing Enterobacteriaceae bugs. Many of these species are functionally
similar to the bugs: they need the same nutrients to survive. Previously it was
thought that competition for resources would stop the disease-causing bacteria
from getting established in the gut.
This has important implications for treatment: taking probiotics that
compete for the same nutrients with the bad bacteria to try and starve them out
isn’t going to work. The researchers say that it will be more beneficial 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 the University of Cambridge’s Department of
Veterinary Medicine and first author of the report.
Journal article: https://www.nature.com/articles/s41564-024-01912-6
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