Just passing through: fungi not part of the gut


Fungus species don’t play a role in healthy human microbiomes. Andrew Masterson reports.


Brewers' yeast, very often consumed, but, surprisingly, not a permanent resident of the human gut.
Brewers' yeast, very often consumed, but, surprisingly, not a permanent resident of the human gut.
THOMAS DEERINCK, NCMIR/Getty Images

Fungi found in poo samples are very likely to represent visitors to the body rather than permanent residents, research has shown.

Human beings – indeed, all animals – enjoy a symbiotic relationship with a large community of microbes that live in the gut and play crucial roles in digestion. Changes to this community – known as the microbiome – are known to affect health and wellbeing.

A study published in the journal mSphere reveals that while bacteria and archaea are essential members of this microbiome, fungi are not.

To make this finding, a team led by Thomas Auchtung of the Alkek Centre for Metagenomics and Microbiome Research at Baylor College of Medicine in Houston, Texas, US, set about identifying fungi present in 148 stool samples gathered from 100 healthy volunteers.

DNA sequencing revealed that the only fungi present were those found in the mouth, or in food. There were a greater number of fungi than bacterial species in the samples, but the researchers suspected this was a reflection of food diversity rather than the contents of the stable gut microbial population.

To test this, Auchtung and colleagues recruited four healthy volunteers and asked them to follow a sequence of four specific diets for two days at a time. The diets comprised nuts and dried berries; beans, corn and rice; pasta and marinara sauce; and an egg, sausage and cheese sandwich and peas.

Saliva and stool samples were taken before the diets began, to serve as controls, and then after each set of foods. The results showed only fungi present in saliva or in the foods consumed.

One species of fungus, Candida albicans, which can cause a range of unpleasant infections, was placed in bioreactors that simulate the inside of the gut. In conditions combining oxygen and low bacterial diversity, it flourished, but when the bioreactors were ramped up to replicate healthy gut values, it failed to thrive.

The presence of the fungus in stool samples dropped 100-fold after volunteers were asked to brush their teeth using a fluoride toothpaste after every meal – a strong indication that it travels from the mouth straight through to the exit without pausing to set up house.

Finally, the scientists tested the persistence of one of the most commonly ingested fungus species, Saccharomyces cerevisiae, which is the catalyst for beer and bread fermentation, and also widely used in food processing. Volunteers were put on a diet devoid of the species, and levels in poo dropped to undetectable levels in just two days.

“A lot of fungi don't grow well at body temperature, and the gut can be a very inhospitable place,” says Auchtung, adding that fungi may have dropped out of the human microbiome as a result of evolutionary pressures.

  1. http://msphere.asm.org/
  2. http://msphere.asm.org/
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