Studies of the microbiome in the human gut focus primarily on bacteria. Other microbes that are also present in the gut – viruses, protists, archaea, and fungi – have largely been overlooked.
New research in mice now suggests an important role for fungi in the gut – the mold and yeast communities known as mycobioma – which are the active interface between the host and its diet.
“We have shown that the intestinal mycobiom of healthy mice is shaped by the environment, including diet, and that it correlates significantly with metabolic outcomes,” said Dr. Kent Willis, Assistant Professor at the University of Alabama at Birmingham and co-author of the study, published in Communications Biology. “Our findings support a role for the gut mycobioma in adapting host metabolism. These findings have important implications for the design of microbiome studies and the reproducibility of experimental host metabolism studies.”
Willis and colleagues studied fungi in the jejunum of the mouse small intestine, the location of the most diverse fungal populations in the mouse intestine. They found that exposure to a processed diet representative of a typical Western diet high in purified carbohydrates resulted in persistent differences in fungal communities compared to mice given a standardized diet. were significantly associated with different body mass deposition in male mice.
The researchers found that fat deposition in the liver, transcriptional adaptation of metabolically active tissues, and metabolic biomarker levels in serum were all linked to changes in the diversity and composition of the fungal community. Variations of mushrooms from two genera – Thermomyces and Saccharomyces – were most strongly associated with metabolic disorders and weight gain.
The study had a brilliant starting point. The researchers received genetically identical mice from four different research animal providers. It is known that intestinal bacterial communities vary widely depending on the provider. Similarly, the researchers found dramatically different variability in jejunum mycobiomas by provider as measured by sequencing the internally transcribed spacer rRNA. At baseline, mice from one supplier had five unique genera of fungi and mice from the other three suppliers had three, two and one unique genus, respectively.
They also examined the make-up of the Interkingdom community – that is, both bacteria and fungi – and found great differences in the basic community of bacterial communities. Based on this initial diversity of fungi and bacteria, they then measured the effects of time and diet differences – standardized feed versus highly processed diet – on the composition of the fungal and bacterial community.
The researchers also addressed a fundamental question: Are the fungal organisms identified by next-generation sequencing obtained from food, or are they real commensal organisms that colonize and multiply in the intestines? They compared the sequencing of the food pellets that contained some mushrooms and the contents of the mouse jejunum to show that the jejunum mushrooms were true commensal colonizers.
So this study was conducted under the direction of Willis and co-author Joseph Pierre, Ph.D., and co-first authors Tahliyah S. Mims and Qusai Al Abdallah, Ph.D., of the University of Tennessee’s Health Science Center, carried out. Memphis, Tennessee – showed that variations in the relative abundance and composition of the gut mycobioma correlate with key features of host metabolism. This provides a basis for understanding the complex interactions between bacteria and fungi and how both together shape and potentially contribute to host homeostasis.
“Our results highlight the potential health implications of the gut mycobioma and have implications for human and experimental metabolism studies,” said Pierre. “The implication for human microbiome studies, which often only look at bacteria and only collect stool, is that the mycobioma may have neglected effects on the results associated with microbiomes.”
Mims, TS et al. The intestinal mycobiom of healthy mice is shaped by the environment and correlates with the metabolic results in response to diet. Commun Biol 4, 281 (2021). https://doi.org/10.1038/s42003-021-01820-z
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