## 2 Overview of the Human Gut Microbiota
### Composition and Functional Organisation of the Human Gut Microbiota  
The GIT is anatomically and functionally divided into the stomach, the small intestine, and the large intestine. The physiological characteristics of each region shape the growth of distinct microbial communities, resulting in variations in both microbiota density and diversity throughout the GIT (Figure 1) [39]. The stomach contains a relatively low number of microorganisms (<10\({}^{3}\) CFU/mL) compared to the distal regions of the GIT, due to its motile activity, gastric acid secretion, and low pH (<4). Gastric lumen harbours bacteria from the phyla _Bacteroidata_, _Actinomycetota_, _Fusobacteria_, and _Pseudomonadota_, while the mucosa is colonised primarily by _Bacilota_ and _Pseudomonad_[40]. Despite the hostile environment, acid-tolerant or transient species belonging to the genera _Neisseria_, _Haemophilus_, _Fusobacterium_, _Precotella_, _Veillonella_, and _Streptococcus_ have been detected in the gastric microbiota of healthy individuals. This microbial presence is likely due to the constant influx of bacteria originating from the oral cavity via swallowing, as well as reflux from the duodenum. Indeed, more than 65% of bacterial phytotypes identified in the stomach correspond to those found in the oral microbiota, suggesting that species, such as _Veillonella_, _Lactobacillus_, and _Clostridium_, detected in gastric samples may largely represent transient populations rather than established residents [41; 42]. The duodenum, the first segment of the small intestine, is characterised by the presence of bile acids, pancreatic secretions, and antimicrobial agents, including bile salts (which can  
Figure 1: Composition and distribution of the microbiota throughout the GIT. The composition of the microbiota differs throughout the GIT, reflecting the distinct environmental conditions and physiological functions of each segment. Anatomically, the GIT is divided into the stomach, small intestine (duodenum, jejunum, and ileum), and large intestine (caecum and colon). Microbial density and diversity increase along the tract, reaching their peak in the colon. reach concentrations up to 11.2 mM postprandially); digestive enzymes, such as proteases and lipases, which can generate antimicrobial compounds; and innate immune molecules like defensins and lysozyme [43]. The rapid transit and the presence of an oxygen gradient along the GIT, with pO\({}_{2}\) levels in the duodenum estimated between 10 and 30 mmHg and progressively decreasing to near-anoxic conditions (<3 mmHg) in the colon, limit both bacterial density (10\({}^{3}\)-10\({}^{4}\) CFU/mL) and biodiversity. The microbial community is mainly composed of facultative anaerobes and transient oral-derived species, mainly from the _Bacilota_ and _Actinomycetota_ phyla, including species such as _Streptococcus salivarius_, _Lactobacillus rhamnus_, _Lactobacillus plantarum_, _Enterococcus faecalis_, and _Enterococcus faecium_[44; 45; 46]. In contrast, the jejunum provides a more suitable environment for the growth of predominantly aerobic Gram-positive and facultative anaerobic and aerotolerant bacteria, with bacterial counts ranging from 10\({}^{3}\) to 10\({}^{7}\) CFU/mL. The most represented genera include _Lactobacillus_, _Enterococcus_, and _Streptococcus_. The most frequently detected species are oral-associated taxa, including _Streptococcus_ spp. (particularly from the _mitis_ and _sanguitis_ groups), _Granulicatella aaticens/para-adicens_, _Gemella haemolysans/taiawanensis_, and _Schaalia odontolytica_ complex, suggesting that the jejun microbiota may largely reflect transient colonisation [44; 47]. In the transition to the ileum, there is a higher population of bacteria, around 10\({}^{9}\) CFU/mL, and the microbiota of this region is dominated by aerobic species, whereas the more distal part shows a distinctive microbial profile that resembles the oral microbiota.