About 9% of the total variability of the microbiota is associated with pro-inflammatory cytokines IL-6 and IL-8. Gut microbes regulate the balance between pro-inflammatory Th17 cells and anti-inflammatory cells, thus preventing pathological intestinal and systemic inflammation. Certain diets increase pro-inflammatory cytokine production.

Sulphide gas producing bacteria in the gut are a part of hydrogen-producing species. The major species responsible for sulphide gas production are the Sulphate-reducing bacteria (SRB). They utilize a wide range of substrates compared to methanogens in gut. They are mainly involved in production of hydrogen sulphide gas and acetate by acting on sulphur containing amino acids and dietary sources.

Butyrate is a short chain fatty acid and product of degradation of plant fibres and is an energy source for the intestinal cells. Butyrate governs the transepithelial fluid transport, relieves from mucosal inflammation, develops the epithelial defence barrier, and modulates intestinal motility. The role of butyrate in the prevention and inhibition of colorectal cancer has been studied upon in research.

Humans excrete 30% of uric acid and intestinal bacteria participates in its metabolism. There are studies linking the potential effects of intestinal microbiota in the uric acid metabolism. Gut microbiota participates in purine and uric acid metabolism. It is also involved in xanthine oxidase production, which is involved in oxidative metabolism of purine, in turn breaking down to uric acid

Ammonia is produced mostly as a by-product of protein digestion and bacterial metabolism in the gut. Gut bacteria utilize ammonia for protein synthesis, reabsorbed in intestinal blood vessels, pooled in the liver for endogenous detoxification and excreted in the feces. As free ammonia is toxic, it is rapidly converted to non-toxic urea in the liver and excreted in the urine.

Protein fermentation in the gut is an essential function of the gut microbiome and it contributes significantly to amino acids metabolism and host amino acid balance. If dietary protein is not properly digested, gut bacteria ferments it and if in excess, it is converted to harmful by-products. These metabolic by-products increase inflammatory response and colitis severity in the gut.

Vitamin B2 is known as riboflavin and its active forms are flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) that are involved in enzymatic reactions and redox reactions. It plays an important role in cellular metabolism. Humans cannot produce vitamin B2 but is available as dietary source and also produced by gut microbiome. Dietary vitamin B2 is found in the form FAD or FMN which is then converted to free riboflavin in the small intestine, absorbed by the blood, free riboflavin converted back to FAD or FMN and distributed throughout the body. Gut bacteria synthesize vitamin B2 from guanosine triphosphate (GTP) and d-ribulose 5-phosphate and exists as free riboflavin which is directly absorbed in the colon, converted to FAD or FMN and distributed in the body. Some microbes also produce vitamin B2 intermediates.

Vitamin B3 is niacin also known as nicotinic acid and nicotinamide. Vitamin B3 can be generated by mammals, can be obtained in diet and can be produced by intestinal bacteria. Animal based diet contain vitamin B3 as nicotinamide and plant based diet contain it as nicotinic acid. Nicotinic acid is converted to nicotinamide and absorbed in the small intestine. Various gut microbflora belonging to different genera possess vitamin B3 synthesis pathway and synthesizes niacin from tryptophan. Niacin is the precursor for nicotinamide adenine dinucleotide (NAD) involved in aerosbic respiration and a ligand for G-protein coupled receptor in various cells. It inhibits the pro-inflammatory cytokines production and anti-inflammatory properties, playing an important role in the immunological homeostasis.

Vitamin B7 commonly known as biotin has recieved attention for promoting the growth of hair and nails. It is an essential nutrient that is present in some foods naturally, produced by gut microbiome and available as dietary supplements as well. It acts as precursors cofactors for several enzymes that are essential for glucose, amino acid, and fatty acid metabolism. It likely influences immunometabolism by suppressingthe genes involved in the production of several pro-inflammatory cytokines, thus showing anti-inflammatory effects. Dietary biotin exists as biocytin, converted to free biotin in the small intestine by biotinidase which is then absorbed by the colon. Intestinal bacteria possess vitamin B7 synthesis pathway and synthesize free biotin from malonyl CoA which is directly absorbed in the colon.

Vitamin B9 known as folic acid or folate is necessity for humans. It's active form tetrahydrofolate is needed in the biosynthesis of building blocks of nucleotides and in several metabolic reactions. Vitamin B9 contributes in immunologic homeostasis maintenance and is survival factor for Treg cells. It exists as mono- and polyglutamate folate in the diet, polyglutamate folate is deconjugated to monoglutamate form, absorbed in small intestine, is converted to tetrahydrofolate (THF) in the intestinal epithelium and transported to blood. Vitamin B9 is also synthesized by many intestinal bacteria as THF from GTP, directly absorbed in the colon and distributed throughout the body. Folate biosynthesis in gut bacteria are affected by a low-carbohydrate diet, increased protein content, probiotic dietary factors and prebiotic supplementation.

Vitamin B1 is found as thiamine pyrophosphate (TPP) in meats (pork, chicken), eggs, sprouts and beans. Once consumed, dietary TPP are hydrolzyed to free thiamine in the small intestine which is then absorbed by the intestinal epithelium and transported throughout the body. Many intestinal bacteria present in the colon also produces vitamin B1 as free thiamine and TPP. Bacterial thiamine is absorbed in the same manner whereas bacterial TPP is directly aborsbed by the colon and is used for energy generation. Vitamin B1 synthesis pathway is possessed by many intestinal bacteria, including pathways for the synthesis of thiazole and pyrimidine. Some bacteria also needs vitamin B1 for their growth so there is a competition between the host and bacteria for it.

Vitamin B5 known as pantothenic acid, is a precursor of coenzyme A (CoA) and plays an essential role in the TCA cycle and fatty acid oxidation. Vitamin B5 is involved in energy generation and in the host community control. It is also shown to involved in the promotion of keratinocyte proliferation and differentiation into fibroblasts that was facilitated by facial acne improvement. It enhances protection to host defense by promoting innate and adaptive immunity thus acting as a natural adjuvant. Dietary vitamin B5 is found as CoA or phosphopantetheine that are converted to free pantothenic acid and absorbed by small intestine. Free pantothenic acid is converted back to CoA before distribution in the body. Microbial vitamin B5 already exists as free pathothenic acid, absorbed by the colon and distributed in same manner as dietary vitamin. Many intestinal commensal bacteria possess a vitamin B5 biosynthesis pathwayand produce vitamin B5.

Oxalate are a part of many natural foods and it conjugates with calcium during digestion process. It is usually excreted as a by-product in the urine or through faeces. In the gut, commensal bacteria with oxalate degrading ability have the potential to regulate oxalate levels.

Gut microbes are involved in production of various metabolites which regulates biochemical processes in the host. One metabolites is bile acids synthesized from cholesterol and metabolized by gut microbes. Bile Acids emulsifies dietary fats and absorbs fat-soluble vitamins. Bile acids also acts as signalling molecules and activates genes involved in carbohydrate, lipid metabolism. Bile acids show antimicrobial and anti-inflammatory activity.

The metabolism of choline containing compounds such as betaine or l-carnitine by gut microbiota forms trimethylamine (TMA). TMA is converted into TMAO by FMO.TMA is a biomarker of kidney function. TMAO is either transported to the tissues or excreted through the urine. Certain rare mutations in FMO3 gene causes a reduced or absent TMAO formation, leading to accumulation of TMA

Gut microbiota produces Short Chain Fatty Acids (SCFAs) which releases anti-inflammatory cytokines. Butyrate a type of SCFA, produced by gut microbes has anti-inflammatory properties. It is known fact that certain gut microbes inhibit inflammatory processes by reducing expression of pro-inflammatory cytokines and stimulating production of anti-inflammatory cytokines. Tryptophan metabolites by gut microbes stimulates anti-inflammation and maintains intestinal barrier integrity.

Vitamin B12 also known as cobalamin, is the most intricate and cobalt-containing vitamin. Its active forms are methylcobalamin and adenosylcobalamin that catalyzes methionine synthesis. Vitamin B12 along with other vitamins plays an important role in red blood cell formation and nucleic acid synthesis in neurons specially. It also acts as an immunomodulator to promote cellular immunity. Humans cannot synthesize vitamin B12 but are obtained from diets and gut microbiome. Vitamin B12 in foods exists in complex with dietary proteins which is converted to free vitamin B12 in the stomach, absorbed by the small intestine and converted to its active form in the colon before distributing throughout the body. Some gut bacteria can synthesize vitamin B12 as they possess vitamin B12 synthesis pathway, that is directly absorbed by the colon and distributed to the body.

Vitamin K occurs in two forms based on the sources: vitamin K1 or phylloquinone found in green leafy vegetables and vitamin K2 or menaquinone synthesized by certain intestinal bacteria. in Humans, Vitamin K serves as cofactor for the production of clotting factors and for the enzyme that converts specific glutamyl residues in a few proteins to g?carboxyglutamyl (Gla) residues. It is also found to be an essential factor for many other proteins in the body. Gut bacteria provides half of the daily Vitamin K requirement. Several protein are vitamin K dependent that are involved in coagulation, bone development, and cardiovascular health.

Vitamin B6 exists as as pyridoxine, pyridoxal, and pyridoxamine that are precursors involved in a variety of cellular metabolic processes such as amino acid, lipid, and carbohydrate metabolism. It contributes to the regulation of intestinal immune system. It is important to maintain vitamin B6 synthesis for homeostatic processes and host immune response. It can be obtained from diet and gut microbiome synthesis. Dietary vitamin B5 exists as pyridoxal phosphate (PLP) or pyridoxamine phosphate (PMP) that is converted to free vitamin B6 and absorbed by small intestine which then enters the blood and is converted back to PLP or PMP. Microbial vitamin B6 is synthesized as PLP, converted to free vitamin B6 in the large intestine, transported to the blood, and distributed throughout the body.

The excess sodium in the system has been linked with Hypertension and Cardiovascular complications. It also affects the gut health. Salt consumption has been linked to considerable changes in the probiotic bacterial community. Due to excess sodium, beneficial or the probiotic microbes are unable to thrive in the gut leading to inflammatory environment in the gut.

Putrescine is a polyamine derived from amino acids that play an important role in cell metabolism. Putrescine is produced by intestinal bacteria, a major source of polyamines in the lower intestinal tract. Polyamines helps in protein fermentation. Putrescines inhibit the production of pro-inflammatory cytokines, like IL-1, IL-6, and TNF-?. However, increased putrescine intake causes serious toxicological consequences

Lipopolysaccharide (LPS) is a potent endotoxin that induces inflammatory responses. LPS is present in Gram-negative bacteria and the release of LPS from these bacteria in blood stream causes toxicity. Gut bacteria produce LPS and also triggers innate immune response upon entry of pathogenic bacteria. Although, it is thought to involve in proinflammation but studies suggest it to be immunoinhibitory.

Methanogenic bacteria a part of hydrogen producing species which play a key role in many microbial pathways in the gut. These microbe groups convert the carbon dioxide and hydrogen into methane. The methanogens often rely on by-products of carbohydrate digestion in gut. Increased levels of hydrogen related gases such as methane have been linked to pro-inflammatory state of the gut.