## 2 Overview of the Human Gut Microbiota  
The human gut microbiota comprises over 10 trillion microorganisms, including bacteria, archaea, viruses, protozoa, and fungi [10]. These microorganisms form a highly complex ecosystem, engaging in interactions both among themselves, as well as with the host, in a symbiotic relationship that is essential for metabolic and immune system development [11].  
A balanced microbiota is composed mainly of bacteria from four major phyla that adapt to constant changes in lifestyle, _Actinomycetota_, _Pseudomonada_, _Bacilotta_, and _Bacteroidota_, with the latter two representing approximately 90% of the total composition [12].  
While most microbiota studies focus on the bacterial component, the human gut is also colonised by archaea, viruses (including bacteriophages), unicellular eukaryotes, and fungi, which, despite their lower abundance, play important functional roles in maintaining microbial homeostasis [13]. Bacteriophages, in particular, exert a strong influence on bacterial diversity, survival, and activity, and altered virome profiles have been associated with conditions such as inflammatory bowel disease [14; 15]. Furthermore, certain gut viruses, such as _Siphoviidae_ infecting _Streptococcaceae_ and _Enterobacteriaceae_, have been implicated in systemic disorders like atherosclerosis, where viral infections may promote vascular inflammation and plaque formation [16; 17].  
The fungal fraction of the gut microbiota, known as the mycobiota, accounts for approximately 0.1-0.3% of the total microbial community and includes genera such as _Aspergillus_, _Candida_, _Cryptococcus_, _Saccharomyces_, _Malassezia_, and _Penicillium_[18]. Fungal biodiversity appears to be diet-dependent, with _Candida_ spp. being positively associated with carbohydrate intake and _Aspergillus_ spp. being negatively associated with levels of short-chain fatty acids (SCFAs) [19]. Altered fungal profiles have been reported in various disease conditions, including GIT, neurological, and liver diseases, as well as in atherosclerosis [18; 20; 21].  
This delicate and dynamic equilibrium is often referred to as eubiosis, a state in which microbial diversity and function support the host's health. Eubiosis is not defined by a fixed composition, but by the maintenance of beneficial host-microbe interactions and essential physiological functions. Disruption of this balance, known as dysbiosis, may result from antibiotic use, infections, dietary shifts, or chronic inflammation. Dysbiosis is typically associated with reduced microbial diversity, the loss of beneficial species, and the expansion of opportunistic taxa. Functionally, it can impair intestinal barrier integrity and trigger inappropriate immune responses, contributing to gastrointestinal and systemic disorders [22; 23; 24; 25; 26; 27].  
Beyond taxonomic and functional shifts, it is also important to distinguish between the related concepts of the microbiota and the microbiome, sometimes misused as synonyms. While the microbiota refers exclusively to the community of microorganisms, the microbiome encompasses these microorganisms along with their collective genetic material [7]. The human microbiome is estimated to harbour approximately 3.3 million active genes, in contrast to the 22,000 active human genes [28].