Mycobiome Communities 101: Their Effect On Health & Disease

The microbiome is a collection of microbes that live in—and on—the human body. Our relationship with the microbiome is symbiotic: We depend on them, and they depend on us. One hundred trillion microbes make up the microbiome of the human body—far exceeding the number of human cells. And these different microbial communities are constantly interacting on our skin, mouth, urogenital, respiratory, and digestive tracts (which contain the largest number and diversity of microbes).

For years, the term "microbiome" was synonymous with bacteria, and the vast majority of research investigating the microbiome focused only on the bacterial community (the Bacteriome). However, my research explores the idea that the microbiome encompasses different microbial communities in humans, including fungi (the Mycobiome), parasites, protozoa, amoebae, archaea, and viruses (virome).

To identify the distinct microbiome profiles in healthy people1, my team of researchers analyzed fecal samples from thousands of individuals all across the United States. Each person filled in a questionnaire about dietary habits, lifestyle, sleep, stress, gastrointestinal symptoms, weight, and medical history. Subjects with chronic disease, overweight (BMI > 35 kg/m2), and on medications, etc., were excluded following the guidelines of the Human Microbiome Project.

Our results show that both beneficial (e.g., Faecalibacterium, Lactobacillus, Prevotella) as well as pathogenic (e.g., Serratia, Ruminococcus) microorganisms were detected in fecal samples of healthy subjects. Similarly, the fungal profile has both beneficial (e.g., Galactomyces, Pichia) and pathogenic (e.g., Candida albicans) microorganisms.  

Figure 3 shows that even though subjects included in the study were healthy, their microbiome clustered together into three different groups (Groups 1, 2, and 3). Each group shares a similar microbiome profile: Individuals in Group 1 shared a healthy microbiome profile, while those in Group 2 had elevated levels of harmful bacteria (Proteobacteria2). Finally, Group 3 individuals have elevated levels of Firmicutes (associated with obesity3). 

Analysis of fungal profiles of different groups showed that Ascomycota was the major fungal phyla, representing approximately 95% abundance in all groups. But what about the mycobiome component of these microbiome groups? In our analysis, not surprisingly, Candida species were the key players. The presence of Candida did not appear to be associated more strongly with any of the three groups—some of the microbiomes in each of the groups had high levels of Candida, and some did not.