Human holobiomes are networks of mutualistic interactions between human cells and complex communities of bacteria and fungi that colonize the human body. The immune system must tolerate colonization with commensal bacteria and fungi but defend against invasion by either organism. Molecular ecological surveys of the human prokaryotic microbiota performed to date have revealed a remarkable degree of bacterial diversity and functionality. However, there is a dearth of information regarding the eukaryotic composition of the microbiota. In this review, we describe the ecology and the human niches of our fungal "fellow travelers" in both health and disease, discriminating between passengers, colonizers, and pathogens based on the interaction of these fungi with the human immune system. We conclude by highlighting the need to reconsider the etiology of many fungal and immune-related diseases in the context of the crosstalk between the human system and its resident microbial communities.Keywords: Dysbiosis r Fungal metagenomics r Host-microbe interaction r Mycobiota
IntroductionHumans live in close association with a complex community of bacteria, viruses, fungi, and archaea [1][2][3], which inhabit their bodies. Many groups have surveyed these microbial populations using the so-called "next generation" or "deep" sequencing approaches, revealing that the human microbiota differs radically at various body sites and among individuals [2][3][4]. The differences in the human microbiota are influenced by the availability of nutrients, environmental exposure to microorganisms, and other sitespecific features, such as the immunological makeup of a given location. The origin of differences in the microbiota between individuals potentially reflects different patterns of colonization early in life (reviewed in [5]), different dietary regimens [6,7], and different environmental exposures, such as antibiotic use [8,9]. Recently, the application of deep sequencing approaches have genCorrespondence: Dr. Duccio Cavalieri e-mail: duccio.cavalieri@fmach.it erated novel hypotheses about the microbial determinants underlying human disorders of immune origin (reviewed in [10]). Several metabolites of the interaction between diet and host microbiota, such as short-chain fatty acids, have been shown to play a fundamental role in shaping immune responses (reviewed in [11]). The application of microbial ecology concepts is ultimately leading to the conclusion that health and disease can be understood only through an understanding of the ways in which the symbiotic interactions between microbes and human organs harmonically integrate in the context of the hologenome [12].Human microbial diversity is not limited to bacteria; microorganisms such as fungi also play major roles in the stability of microbial communities in human health and disease (reviewed in [13]). Yeasts were detected in human stool samples as far back as 1917, and by the mid-20th century the presence of yeasts in the human intestine was proposed to have a saprotrophic role [14]....