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 share 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 profile 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.

It is important to remember that Candida are normal inhabitants of the human gut—many people have Candida albicans, C. glabrata, and sometimes C. tropicalis and C. parapsilosis, and these people can be perfectly healthy. However, when Candida was present and elevated (as often happens after a course of antibiotics, or with immune system problems or gut permeability issues), the subjects tended to have an overgrowth of this fungus.