Table 2.

Metabolites associated with microbial metabolism or microbial–host cometabolism.

Metabolites	Bacteria	Biological functions	References
BACTERIAL METABOLISM
SCFAs: acetate, propionate, butyrate; branched CFAs: iso-butyrate, valerate and iso-valerate	Clostridial clusters IV and XIVa Lactobacillus, Eubacterium, Roseburia, Faecalibacterium, Coprococcus	Increasing cholesterol synthesis (acetate); gluconeogenesis (propionate); energy source for colonocytes (butyrate); cholesterol synthesis inhibition; linked to: cardiovascular disease, ulcerative colitis, Crohn's disease, antibiotic-associated diarrhea, obesity, metabolic syndrome, bowel disorders and cancer	Harig et al., 1989; Scheppach et al., 1991; Scheppach, 1994; Sabatino et al., 2005; Binder, 2010; Donohoe et al., 2011; Fukuda et al., 2011; Nicholson et al., 2012; Chambers et al., 2015
Organic acids: benzoate, hippurate, phenylacetate, phenylpropionate, hydroxybenzoate, hydroxyphenylacetate, hydroxyphenylpropionate 3,4-dihydroxyphenylpropionat and D-lactate	Clostridium difficile, Faecalibacterium prausnitzii, Bifidobacterium, Subdoligranulum, Lactobacillus	Related to hypertension and obesity, colorectal cancer, autism in children in humans and diabetes in a rat model	Lord and Bralley, 2008; Calvani et al., 2010; Qiu et al., 2010; Zhao et al., 2010; Zheng et al., 2011; Nicholson et al., 2012
Vitamins: vitamin B9, vitamin B2, vitamin B12, niacin, pyridoxine, vitamin K, vitamin B1, vitamin B5, vitamin B8	Bifidobacterium bifidum, Bifidobacterium longum subsp. infantis, Bifidobacterium breve, B. longum subsp. longum Bifidobacterium adolescentis, commensal Lactobacilli, Bacillus subtilis Escherichia coli and anaerobes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria	Cellular metabolism	Deguchi et al., 1985; Noda et al., 1994; Roth et al., 1996; Bacher et al., 2000; Perkins and Pero, 2002; Stanton et al., 2005; Pompei et al., 2007; Smith et al., 2007; Rossi and Amaretti, 2010; Magnúúsdóóttir, et al., 2015
BACTERIAL TRANSFORMED COMPOUNDS
Bile salts: cholate, hyocholate, deoxycholate, chenodeoxycholate, α-muricholate, β-muricholate, ω-muricholate, taurocholate, glycocholate, taurochenoxycholate, glycochenodeoxycholate, taurocholate, tauro–α–muricholate, tauro–β–muricholate, lithocholate, ursodeoxycholate, hyodeoxycholate, glycodeoxylcholate, taurohyocholate, taurodeoxylcholate	Bacteroides, Clostridium, Lactobacillus, Bifidobacterium, Enterobacter, Eubacterium, Escherichia	Absorption of dietary fats and lipid-soluble vitamins, facilitate lipid assimilation, maintain gut barrier function, regulate triglycerides, cholesterol and glucose by endocrine functions and energy homeostasis. Secondary bile salts linked to colon cancer.	Lis et al., 1976; Russell and Setchell, 1992; Groh et al., 1993; Ridlon et al., 2006; Dawson et al., 2009; Suhre et al., 2010; Nicholson et al., 2012
Polyphenol: Hydroxycinnamic acids and flavonoids	Lactobacillus, Bifidobacterium	Secondary metabolites production	Couteau et al., 2001; Clifford, 2004; Manach et al., 2004; Taverniti and Guglielmetti, 2012; Amaretti et al., 2015; Marín et al., 2015; Raimondi et al., 2015
Lipids: glycerol	Bifidobacterium, Roseburia, Lactobacillus, Klebsiella, Enterobacter, Citrobacter, Clostridium	Intestinal permeability, glucose homeostasis, promotion of chronic systemic inflammation by LPS; hyperinsulinemia improvement by conjugated FAs, immune system enhancement and lipoprotein profiles alteration.	Holmes et al., 2011; Nicholson et al., 2012
Amino Acids	Colonic bacteria, Clostridium, Peptostreptococcus anaerobius	ammonia production by deamination, amines production by decarboxylation	Moss et al., 1970; Clinton et al., 1988; Macfarlane and Macfarlane, 1995