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The human mycobiome is a part of the human microbiome, and it is made up of all species of fungi that inhabit the human body. It is known that the human body is host to many species of microorganisms. The various habitats for these microorganisms in the human body are referred to microbiomes and they play a key role in the health of the human host. It is believed that the mycobiome plays a similar role in host health, though many specifics remain unknown.

Background
The mycobiome makes up a relatively small portion of the human microbiome; the fungal communities are greatly outnumbered by their bacterial counterparts. However, these microorganisms have great significance to the microbiology community.

The human microbiome, and by extension, the mycobiome is known to play a key role in host health. Next generation sequencing technology has allowed scientists to study these microorganisms and investigate their role in human health. Studies have found that these commensal fungi have a hand in the pathology of health and disease in their humans hosts and even play a role in modulation of the host’s immune responses. Research of the human mycobiome is ongoing; a greater understanding will lead to better prediction of how changes in the mycobiome may impact the human host.

There are various mycobiomes throughout the human body. The most well-known of these are located in the oral cavity, the gastrointestinal tract, the skin, the lungs, and the vagina.

Studying the Human Mycobiota
There are two primary types of method study of the human mycobiome: culture dependent and culture independent.

Culture Dependent
Culture dependent study methods incorporate microscopy, biochemical assays, and/or growth on a specific media in order to analyze the fungi of the human mycobiome . Traditionally these methods of study have been the most relied upon by scientists primarily because, until recently, there were no viable alternatives . These methods have also allowed scientists to isolate a specific fungal species of interest . The gastrointestinal mycobiome specifically has been studied through culture dependent methods through the use of specific commercially available growth medias . There are some challenges associated with culture dependent methods of study. Long incubation times make this a time consuming process, and there is a significant bias towards fungal species with faster growth rates .

Culture Independent
There are three main types of culture independent methods of study for fungi: polymerase chain reaction (PCR), sanger sequencing, and next generation sequencing (NGR) . These processes allow researchers to investigate and identify the microbes that are present in a habitat without the need for complex culturomics as the culture dependent processes do . These processes can also facilitate the sequencing and analysis of multiple samples at once, allowing researchers to process large amounts of data in less time .

Oral Mycobiome
The oral cavity is a well-known location for microbial growth in the human body, however very little research has been conducted to assess the fungal members of the oral microbiome. Consequently, there has been no evaluation of the interactions between these microbes and host immune system at present time.

Studies have shown that the oral mycobiome varies amongst individuals. It is known that the oral mycobiome is home to more than 75 types of fungal genera, the most common of which are Candida, Cladosporium, Aureobasidium, Aspergillus, and Fusarium.

The oral cavity is a key point of entry into the body for microorganisms. It is logical to become as familiar with the fungi that enter and inhabit the oral mycobiome as their bacterial counterparts.

Gastrointestinal Mycobiome
The gastrointestinal mycobiome is the most widely studied of the human mycobiota. The inhabitants of the mycobiome and the interactions with the host immune system and microbiome has all been analyzed. Studies have found that the gut specifically is home to more than 50 types of fungal genera, with Candida, Saccharomyces and Cladosporium being the most common.

There are three key interactions that have been studied in the gastrointestinal mycobiome: interactions with amongst the fungi, interactions with the bacterial microbiome, and interactions with the host immune system. The fungal populations in the mycobiome have been found to vary amongst individuals and may be influenced by environmental fungi. Mycobiome interactions with bacteria are likely to play a role in host metabolisms and systemic inflammatory conditions. Relatively little is known about the interactions with the host immune system, although it is known that the host exercises a certain measure of control over the fungi of the gastrointestinal mycobiome.

It is important to become more familiar with the fungi that make up the gastrointestinal mycobiome so that scientists may learn about the role they play in complications in the GI tract such as systemic inflammation conditions.

Skin Mycobiome
As the skin is often the first contact point between microorganisms and the human body, naturally it provides a habitat for billions of microbes, all having developed a commensal relationship with the human host. The skin is a unique mycobiome. Individual mycobiomes vary with the conditions of the skin, and these variations will affect which fungal species inhabit the specific sites. It has been found that the foot has the greatest diversity of fungal species; an estimated 40 to 80 different types of fungal genera have been identified in this mycobiome.

The most common fungal species found in the skin mycobiome are Malassezia, Penicillium, and Aspergillus.

It is important to become more familiar with the fungi that make up the skin mycobiome so that scientists may learn about how they interact with other microbes and their host.

Lung Mycobiome
Despite regular exposure to fungi from the oral mycobiome and the environment, there is actually little evidence of commensal fungal mycobiota in healthy lungs. It is the task of the host’s mucosal immune system to manage the fungi and spores that are regularly inhaled from the environment. This immune system activity could potentially provide insight into how to defend against these fungal species to scientists.

Fungal communities have been found in individuals whose normal lung function has been compromised, the most common being: Aspergillus sp. and Scedosporium sp. .

The lung mycobiome may be lacking in individuals with healthy lung function however there is still value in analyzing the interactions that take place. It is an example of an effective immune system against infection of various fungal species that could provide potential treatment strategies against these fungi.

Vaginal Mycobiome
The vagina is also home to many microbial occupants that must be properly contained in order to maintain the health of the host. Fungal growth in this mycobiome is controlled by other members of the microbiome and the host immune system. The concept that the immune system manages the fungi of the vaginal mycobiome is supported by the association of specific variants of the immune system with recurrent vaginal candidiasis.

There are an estimated 11-20 types of fungal genera in the vaginal mycobiome, the most commonly found being Candida, Saccharomyces, Aspergillus, Alternaria, and Cladosporium.

These fungal species are important because they play a clear role in the host health.