Based on the study of many cell types, biological fluids, and biological tissues, biological metabolic phenotype employs a range of characteristics to broadly characterise the organism in a certain physiological condition. For the first time, Johnson et al. incorporated information on genetics, environment, and gut microbiota into the biological functional phenotype in 2012. This new idea provides a more accurate description of the biological metabolic phenotype. The organism’s genes, gut flora, ecosystem (including stress, food, and lifestyle), and consumption of foreign substances (such as food, cosmetics, medications, and pollutants from the environment) all play a major role in determining the so-called biologically metabolic phenotype. Four typical indicators are used to define them the existence or shortage of metabolites, metabolite concentration, metabolite ratio and the volume of metabolites present, their ratio, and the total information on metabolites.

One of the key elements influencing the natural metabolic phenotype is gut bacteria. Their metabolites and constituents have a direct impact on the host’s development and absorption of nutrients. They also influence the host’s health by stimulating the growth of the immune system and epithelial tissue. In turn, the genetic makeup of the gut microbiome is influenced by the host’s living environment, nutritional status, stage of growth and overall health.

The makeup of gut bacteria affects the kinds, quantities, ratios, and general information of metabolites. As distinct microbial metabolites have distinct metabolic functions, the host exhibits a variety of metabolic phenotypes. For instance, butyrate is produced by Eubacterium rectale and Faecalibacterium prausnitzii; Probiotics like Bifidobacterium and Lactobacillus, as well as 7α-dehydroxybacteria like Clostridium, demonstrate capacity to bile acids due to glycolytic activation; Compared to Gram-negative bacteria, bacterial species classified as Gram-positive are more vulnerable to bile acids. The immediate future exposure to bile acids drastically alters the metabolism of the host by changing the structure of the community of bacteria. Bile acids instantly and swiftly affect the metabolising processes of bacteria, causing harm to the membranes, distortion of amino acid, nucleotide and glucose metabolism, among other effects.

Through the use of outside medications (metformin), some studies have altered the average number of Escherichia, Romboutsia, Intestinibacter and Clostridium bacteria within the gut. This has resulted in changes to the quantities of metabolic products like fatty acids, carbohydrates, and amino acids in the gut. Metformin also inhibits intestinal hypoglycemic-related metabolic pathways by influencing gluconeogenesis, energy metabolism and branched-chain amino acids metabolism. Thus, extensive information on the composition of the gut microbiota and its particular metabolites should receive special attention in order to investigate the effects of gut microorganisms on host metabolic characteristics.

The host’s metabolism, including the metabolism of lipids, carbohydrates, amino acids and nucleic acids is regulated by the gut microbiota. Numerous studies have been conducted on the impact of gut microorganisms on the metabolism of hosts to date, however the majority of them concentrate on the dominating population and its waste products. So, an in-depth comprehension of the molecular phenotype of the microbes in the intestines to the host need to be thoroughly investigated.