1. Introduction

Humans have been interested in the microbial flora found on and in our bodies since the advent of microbiology. In 1681, Antony van Leeuwenhoek, one of the pioneers in the field observed “great numbers of small animals” in his stool. He also looked at the difference in the stool samples when he was well and when he had diarrhoea (reviewed in [ 1 ]). Fast forward to modern times, the use of stool samples for gut microbiota studies remains unchanged, and the quest to understand more about the “small animals” with new analysis methods has unveiled many more questions that need to be answered.

The microbiome, also known as the microflora or microbiota, is usually assumed to be the bacterial microbiota. Though bacterial flora on the skin, oral tract, vagina, etc., have been sequenced, the gut flora is the most studied by far [ 2 ]. The gut microbiome has been the major topic of interest, due to the large amounts of bacteria found in our gastrointestinal (GI) tract. The National Institutes of Health (NIH) human microbiome project (HMP) and Metagenomics of the Human Intestinal Tract (MetaHIT) projects were initiated to characterize the microbial, namely bacterial microbiota, communities in humans and their impact on human health [ 3 4 ]. However, there are other inhabitants of the microbiome too, namely the commensal fungi and archaea. The term “mycobiome”, used to differentiate the mycology aspect of the microbiome, has been gaining momentum—from being first coined in 2009 [ 5 ], to 10 results using a Pubmed search in 2013 [ 6 ], to at least 70 results as of July 2016.

Candida albicans , which causes systemic candidiasis in immunocompromised patients, is a normal part of the gut microflora [ Commensal fungi that normally inhabit our bodies have been much less studied, as fungi form the minority of the total commensal organisms in humans [ 7 ]. A large portion of these fungi are also unculturable [ 7 ]. The fungal mycobiome studies, therefore, are important in characterizing these fungi and pave a way for the “good fungi” to be studied. Also, many pathogenic fungi are “pathobionts”—commensals in our bodies that cause no harm in normal conditions, but have pathogenic potential. For example,, which causes systemic candidiasis in immunocompromised patients, is a normal part of the gut microflora [ 8 ]. What makes these fungi, which are non-pathogenic in normal conditions, turn pathogenic is still a hot topic of debate. The burden of fungal disease forms a substantial amount of the total infectious diseases spectrum. A large proportion consists of fungal infections in immunocompromised patients with an estimated mortality between 35% to 45% (reviewed in [ 9 ]).

11, Candida species was mostly isolated from human stool and colonic samples [ Currently, the gut microbiome has been linked to many gut-linked conditions, such as inflammatory bowel disease (IBD) and obesity, as well as many seemingly unrelated conditions, such as maturation of the immune system and even cardiac size [ 2 ]. However, the role of the mycobiome is still unclear for many of them. Mycobiome studies pose similar, if not more, challenges as microbiome studies. As the microbiome changes in accordance to a person’s age, diet, use of antibiotics, etc., [ 10 12 ] we can assume the mycobiome changes accordingly too. Researchers are now increasingly aware of the role of the mycobiota in health and disease. Before the development of genomic-based, culture-independent techniques, the gut microflora was mostly studied qualitatively by microscopy and quantitively by anaerobic culture techniques [ 13 14 ]. Current methods for microbiome and mycobiome studies are mainly focused on targeted or metagenomic sequencing. The falling costs of sequencing due to next generation sequencing technologies has allowed a much larger set of the microbiome to be sequenced, including the unculturable bacteria, fungi, and archaea [ 15 ]. While culture-based techniques have helped identify hundreds of bacterial species in the gut [ 13 14 ], next generation sequencing technologies have ballooned the bacterial diversity to over 1000 species [ 4 ]. Using classical culture methods before the advent of sequencing, fungalspecies was mostly isolated from human stool and colonic samples [ 16 ]. Current state-of-the-art technologies, such as next generation sequencing, pyrosequencing, and targeted sequencing, could remove the culturing-bias and reveal many more unculturable fungi in the gut [ 16 ].