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The mycobiome, mycobiota, or fungal microbiome, is the fungi community in and on an organism.
The word “mycobiome” comes from the ancient Greek μύκης (mukēs), meaning "fungus" with the suffix “biome” derived from the Greek βίος (bíos), meaning “life.” The term was first coined in the 2009 paper by Gillevet et al.
Most species of fungi are with the ability to break down complex polymers. Fungi are commonly found within plant cells in an Endophyte relationship or as a pathogen. Most plants also form mutualistic relationships with fungi that accelerate nutrient uptake among their root structures. The most common phyla present in the fungal communities that live alongside animals and in aquatic environments are Ascomycota and Basidiomycota. Animals will typically form a Commensalism relationship with fungi with the occasional occurrence of a pathogenic interaction.
Most interactions between microbes in the gut are either competitive or cooperative. This can be seen with multiple fungal microbes as well by observing populations through the treatment of and . Research on microbial populations in animal models has resulted in noticeable fluctuations in microbe populations. Antibiotic treatment has mostly shown increases in parasitic fungal presence, suggesting competitive behaviors between microbes against fungi. Additionally, application of antifungal molecules have resulted in colitis in mice, suggesting that commensal fungi are responsible for balancing bacterial populations that are involved in dysbiosis. Despite limited knowledge on the gut mycobiome, this research suggests that interactions between fungal and bacterial microbes in the mammalian gut are largely competitive.
A prominent example of an entomopathogenic fungus is Ophiocordyceps unilateralis, nicknamed the “zombie-ant” fungus. The fungus infects ants and alters their natural behavioral patterns causing the ant to leave their usual environment in the trees in favor of the forest floor – a more suitable environment for fungal growth. The insects will then attach themselves to the underside of a leaf until it dies. Fungal spores then sprout out of the dead ant's head and are dispersed. (2017). 9781555819576, American Society of Microbiology. ISBN 9781555819576
One of the first descriptions of insect pathogenic fungi was published in 1835 during an infestation of Beauveria bassiana in a silkworm population that upset the silk industry.
The mycobiome is relevant to human physiology as fungi may be important in maintaining microbial community structure, metabolic function, and immune-priming. Mutualism between humans and fungi is not yet well understood, and there is much to be learned about how fungi interact with the nonfungal constituents of the microbiome.
Many human diseases, including hepatitis, cystic fibrosis, obesity, and inflammatory bowel disease have been associated with changes in the human mycobiome, and it has been proposed that any fungal colonization of the GI tract is a sign of disease. Moreover, detecting tumor-associated mycobiomes may be a novel way of cancer screening – it could be used in synergy with other such as of bacteriomes.
Fungal interactions in the human host can be opportunistic, mutualistic, parasitic, commensalistic, and amensalistic. Though there is a small amount of fungi considered to be true pathogens due to causing disease in healthy individuals, the majority of fungi are considered opportunistic, only affecting an immunosuppressed host. In these cases, pathogen-mediated damage is dependent upon the host; disease could only occur if the host has either a hyperactive or weakened immune system. Commensal relationships between human host and pathogen are possible when the fungi are present in a host for long periods of time without causing disease. One example of a fungus that forms a commensal relationship in a human host is Cryptococcus. Candida albicans can also form a long-time commensal relationship with its host.
Some fungi are niche specific symbionts in the human host. Some fungi can be introduced to the host from the environment by skin contact, oral or respiratory routes, while others are acquired vertically through birth.
In the human GI tract, there are about 50 observed genera of fungi. Some are acquired through what the host eats; as such showing that the stability of the fungal population is dependent on the diet of the host and host immune status.
About 20 genera of fungi have been observed in the vaginal niche. Most fungi that colonize the vagina show a commensalistic relationship with the host, but factors like antibiotic uses and pregnancy could influence the vaginal mycobiome.
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