Abstract
With the advent of high-throughput sequencing techniques, the astonishing extent and complexity of the microbial communities that reside within and upon us has begun to become clear. Moreover, with advances in computing and modelling methods, we are now beginning to grasp just how dynamic our interactions with these communities are. The diversity of both these communities and their interactions—both within the community and with us—are dependent on a multitude of factors, both microbial- and host-mediated. Importantly, it is becoming clear that shifts in the makeup of these communities, or their responses, are linked to different disease states. Although much of the work to define these interactions and links has been investigating bacterial communities, recently there has been significant growth in the body of knowledge, indicating that shifts in the host fungal communities (mycobiome) are also intimately linked to disease status. In this review, we will explore these associations, along with the interactions between fungal communities and their human and microbial habitat, and discuss the future applications of systems biology in determining their role in disease status.
Highlights
With the global burden of fungal diseases rising, researchers have begun to turn to next-generation sequencing (NGS) technology to investigate the role fungi play in the spectrum of human health and disease
Similar to what has been seen with the 16S ribosomal RNA gene cluster (rRNA) gene in amplicon-based bacterial microbiome studies [20], there is currently a lack of consensus between authors regarding which genetic target offers the best level of taxonomical and phylogenetic resolution [13], and as such several alternative primer sets exists that target different regions of these fungal genes (Cui et al [19] gives a good overview of the different fungal rDNA primers used in mycobiome studies to date)
INteractive Optimization), and the use of GEMs for predominant bacteria in human gut, the alteration in the amino acid profile of both feces and serum in response to diet interventions can be simulated and validated [73]. These successful examples of metabolic modeling of human tissue/cell-lines, fungi, and microbiome communities pave the way for the application of these methods on mycobiome research, enabling us to better understand the interactions between fungi and bacteria, other fungi and their host habitat; this allows us to elucidate their role in different diseases, alongside their overall contributions in human host-microbial metabolism
Summary
With the global burden of fungal diseases rising, researchers have begun to turn to next-generation sequencing (NGS) technology to investigate the role fungi play in the spectrum of human health and disease. At the forefront of this advancement is the “Superorganism” hypothesis, where humans are considered to be complex organisms made up of numerous mutually independent smaller organisms (i.e., bacteria, fungi, virus, archaea) and their genomes. This group of microbial cells and their genomes are collectively referred to as the human microbiota and microbiome, respectively. The ability to discriminate between fungal taxa is influenced by sequencing primer choice and, curated databases for taxonomic assignment and/or the annotation of fungal genomes are lacking or are incomplete [13,14] It is against this backdrop that a number of authors have begun to unravel the mystery of the human mycobiome. This review aims to explore the current status of human mucosal mycobiome research, focusing on the gastrointestinal tract
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