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

Figure 3 shows that even though the study participants were healthy, their microbiomes clustered into three distinct groups (groups 1, 2, and 3). Each group has a similar microbiome profile: individuals in Group 1 shared a healthy microbiome profile, while individuals in Group 2 had elevated levels of harmful bacteria (Proteobacteria2). Finally, group 3 individuals have elevated levels Firmicutes (associated with obesity3).

Analysis of the profile of fungi of different groups showed that Ascomycota was the main type of fungi, accounting for approximately 95% in all groups. But what about the mycobiome component of these microbiome groups? In our analysis, surprisingly, Candida species were the key players. Availability Candida did not appear to be more strongly associated with any of the three groups—some microbiomes in each group had high candida, and some don’t.

It is important to remember this Candida are normal inhabitants of the human intestine – in many people Candida albicans, C. glabrata, and sometimes C. tropicalis and C. parapsilosis, and these people can be completely healthy. But when Candida was present and elevated (as is often the case after a course of antibiotics or with problems with the immune system or intestinal permeability), the subjects tended to have an overgrowth of this fungus.