## 2 Overview of the Human Gut Microbiota
### Factors Influencing the Gut Microbiota
#### 2.3.2 Diet  
The composition and diversity of the gut microbiota, as well as the relative abundance of microbial metabolites, are profoundly shaped by diet, as specific nutrients exert selective pressures that favour bacterial species capable of metabolise them. As a result, changes in eating habits, as well as food scarcity or excess, can lead to transient alterations of the microbiota [85].  
A diet rich in animal proteins and amino acids, such as Western diets, has pronounced effects at the level of microbial metabolism, leading to the increased production of branched-chain fatty acids and potentially toxic substances such as sulphides, ammonia, and N-nitroso compounds [86]. This type of diet also increases luminal bile acid content, favouring bile-tolerant anaerobic bacteria such as _Bacteroides_ spp., _Alistiques_ spp., and _Bilophila_ spp., leading to an increase in TMAO. Additionally, this intake stimulates the synthesis of nitric oxide (\(\bullet\)NO), a free radical with antimicrobial properties that can influence gut microbiota composition [87]. Gut bacteria, such as _Lactobacillus_ and _Bifidobacterium_ species, are generally susceptible to the antimicrobial effects of \(\bullet\)NO, resulting in their decreased abundance under high-\(\bullet\)NO conditions. Conversely, certain facultative anaerbes and nitrate-reducing bacteria, including _Enterobacteriaceae_ family members like _E. coli_, are more resistant to \(\bullet\)NO and can survive or even flourish, potentially contributing to dysbiosis [87; 88; 89]. Moreover, \(\bullet\)NO in excessive concentrations may induce oxidative stress and inflammation, further impacting the gut microbial balance [90].  
In contrast, the intake of plant-based proteins has been associated with an increase in beneficial bacteria such as _Bifidobacterium_ spp. and _Lactobacillus_ spp., along with a decrease in potentially pathogenic species such as _Bacteroides fragilis_ and _Clostridium perfringens_[91].  
Similarly, microbial composition and diversity are significantly affected by increased fat intake, which alters the _Bacilota/Bacteroidota_ ratio by increasing the relative abundance of the former while reducing the latter [92]. It should also be noted that a high-fat diet indirectly influences microbiota composition by promoting an increase in bile acid secretion [93; 94]. In the distal small intestine, luminal pH rises progressively from approximately 6.5 in the proximal segments to around 7.5 near the ileum. Upon reaching the large intestine, pH temporarily drops to approximately 6.0 near the caecum and then increases again toward the rectum, approaching pH 7.0 [95]. These pH shifts, along with the antimicrobial properties of unabsorbed bile acids, contribute to an inhospitable environment for acid-sensitive commensals such as _Bifidobacterium_ spp. and _Lactobacillus_ spp. Conversely, they favour the expansion of bile- and acid-resistant taxa, including _Bilophila vadsworthia_, _Bacteroides_ spp., and _Alistipes_ spp., which are frequently associated with pro-inflammatory profiles and metabolic dysregulation [96; 97].  
Conversely, a fibre-rich diet, particularly one high in plant polysaccharides, promotes the growth of _Bacteroidota_ at the expense of _Bacillota_[98; 99]. _Bacteroidota_, especially _Bacteroides_ spp., are known for producing a variety of carbohydrate-active enzymes (CAZymes), including xylanases and pectinases, which degrade complex plant fibres. In contrast, members of the _Bacillota_ phylum, such as _Clostidium_ spp. and _Ruminococcus_ spp., produce enzymes like cellulases and amylases, which also contribute to polysaccharide breakdown [100]. A higher prevalence of _Bacillota_ compared to _Bacteroidota_ ensures a the presence of a greater number of enzymes capable of breaking down dietary polysaccharides, leading to increased monosaccharide absorption and, consequently, greater energy extraction from the diet [87].