Gut bugs’ diet may impact intestinal permeability: Study

By Tim Cutcliffe

- Last updated on GMT

© iStock
© iStock
The food preferences of different bacteria in our guts may have major implications for our own digestive health, say researchers.

According to research published in Nature Microbiology, a much larger numbers of bacterial species than previously thought were found to thrive in the presence of mucin - a complex protein that is critical to the maintenance of the gut mucous membrane.

It was previously thought that mucin was degraded by relatively few bacterial species, say the research team from the European Molecular Biology Laboratory.

The finding could have implications for gut permeability, say the team who suggest the previously unrecognised capability of a larger number of gut bacteria to utilise mucin as a food source may mean they are linked to the breakdown of gut barrier integrity which can lead to inflammation and poor gut barrier functions.

“We were surprised to find new bacteria with the capability to utilise mucin, the protein that makes up mucus,”​ commented study co-leader Professor Kiran Patil. “These bacteria can contribute to inflammation and infection by weakening the protective mucus barrier lining the gut.”

Unexpected findings

The research team examined 96 strains from 72 bacterial species, including  the most abundant species in the human microbiome.  They also analysed species associated with infectious or other types of gut diseases, such as colorectal cancer and inflammatory bowel disease (IBD).

Nineteen different growth media (15 single ‘defined’ media and 4 ‘rich’ mixtures) were used to identify nutritional preferences of the bacterial strains. The researchers were surprised to find that the ‘rich’ multi-nutrient media sometimes were harmful, rather than beneficial to some species.

“It turns out that rich media with many nutrients can be toxic for these species, whereas we used to think: the more food, the better,”​ said Patil

The team made another unexpected discovery that some species of gut bacteria were actually inhibited by amino acids and short-chain fatty acids (SCFA’s). Acetate, propionate, and butyrate, the three most common SCFAs in the gut were previously thought to promote bacterial growth.

“Another surprise came from bacteria that proved to be inhibited by amino acids and short-chain fatty acids, common ingredients in most growth media,”​ Patil added.

Finally, the scientists found that even closely related bacteria had very different nutritional preferences.


The study findings provide new insights into the preferred food of various bacteria, and into how different species metabolise nutrients. These factors have an important impact of our microbiome composition and how its inhabitants interact with their human hosts, the researchers explained.

They also found that the growth media they used for the in vitro ​experiments provided a good model for how bacteria grow inside the gut, leading to more accurate modelling of in vivo ​conditions.

“Our analysis also uncovers media for in vitro studies wherein growth capacity correlates well with in vivo abundance,” ​wrote first authors Dr. Melanie Tramontano and Sergej Andrejev

“Our resource provides scientists with tools to experimentally investigate the gut microbiome ecology, going beyond correlations and identifying causes and effects,”​ concluded study co-leader Dr. Nassos Typas.

Source: Nature Microbiology
Published online 19 March 2018, doi: 
“Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies”
Authors: Melanie Tramontano, Sergej Andrejev, Georg Zeller, ​Peer Bork, Athanasios Typas, Kiran Raosaheb Patil et al

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