Human beings are surrounded and inhabited by microbial communities, including bacteria, fungi, viruses, and protozoa, with distinct ensembles of microorganisms residing in specific body niches (such as mouth, nose, gastrointestinal tract, and vagina). In particular, the gut microbiome is recognized as the most densely populated microbial ecosystem on Earth, which has co-evolved with its host in a largely mutualistic relationship over millions of years, helping to shape our phenotypes across human evolutionary history. By producing a large and diverse repertoire of small bioactive molecules, through the metabolism of dietary or host-derived compounds, the intestinal microbiome has the potential to exert a strong influence on multiple aspects of our physiology, from energy balance and metabolic regulation to the development and functioning of the immune, endocrine, and nervous systems. The great deal of plasticity exhibited by microbial communities allows them to adapt quickly to endogenous and exogenous challenges (including changes in age, diet, lifestyle, or, more generally, environment), while persisting in eubiotic states, a condition instrumental to the maintenance of the host health. Though the key drivers of variation of the human microbiome are most probably still to be discovered, it is known that exposure to certain stressors may significantly disrupt or unbalance microbial communities towards a dysbiotic profile, with impairment of mutualism and triggering or consolidation of a disease state. To date, multiple disorders, at both the enteric and systemic level (including metabolic, autoimmune, cardiovascular, hepatic, respiratory, neurological, and oncologic diseases, often referred to as non-communicable or civilization diseases), have been associated with altered microbial layouts and, particularly, with an overall reduction of biodiversity, the loss of typically beneficial microbes, the bloom of pathobionts, or a broad ecosystem restructuring. Notwithstanding intriguing data, even on possible causal relationships, the actual role of human microbiomes in the pathological context and the underlying mechanisms remains mostly elusive. Similarly, the long-term effectiveness of microbiome-tailored intervention strategies in preventing or treating disorders and alleviating drug side effects must still be proven.

This Special Issue aims to provide a greater understanding of host–microbiome interactions and the role of human-related microbial communities in health and disease, through multiple approaches, also targeting in silico, in vitro, and in vivo functionality of microbes. We invite submissions of reviews, research articles, or short-communications reporting omics and mechanistic studies on microbiomes and their hosts.

Prof. Silvia Turroni
Guest Editor

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• Microbiome
• microbial ecology
• microbiome–host interaction
• co-evolution
• dysbiosis
• intervention strategies