Recent developments in Next Generation Sequencing (NGS) technologies have allowed culture-independent and deep molecular analysis of the microbial diversity in faecal samples, and have provided new insights into the bacterial composition of the distal gut microbiota. Studies of the microbiome in different patient groups using metagenomics or 16S rRNA gene sequencing are increasing our knowledge of how the microbiota influences health and disease. The majority of recent advances in our understanding of human microbiota structure and dynamic changes in disease were made through phylogenetic interrogation of small subunit (SSU) rRNA (Paliy and Agans 2012). However, until recently such studies have generally failed to include data on common eukaryotic, endobiotic organisms such as single-celled parasites and yeasts (‘micro-eukaryotes’). This deficiency may strongly bias the interpretation of results and ignoring an entire kingdom of organisms is a major limitation of human microbiome studies.

It has been known for many decades that yeasts constitute part of the intestinal flora. Recently, overgrowth of Candida spp. was found to be negatively associated to Clostridium difficile infection (Manian and Bryant, 2012). Iliev et al. (2012) reported on the eukaryotic fungal community in the gut (the ‘mycobiome’) that coexists with bacteria, and emphasized the substantial expansion of the repertoire of organisms interacting with the intestinal immune system to influence health and disease. Recent data from our lab show that up to 50% of individuals in some Danish cohorts may be colonized by other micro-eukaryotes, such as the protists Blastocystis and Dientamoeba (unpublished observations). By contrast these parasites are practically absent in patients with active inflammatory bowel disease, including ulcerative colitis and Crohn’s Disease (unpublished observations). Although efforts continue to identify relevant genetic markers for phylogenetic interrogation studies, the very role and impact of these micro-eukaryotes on the host and surrounding microbiota remain an enigma.

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