Table 2.

Major microbiota-mediated mechanisms that influence host circadian and metabolic pathways *.

Microorganisms	Microbial Function	Interactions with Host Pathway
Firmicutes (Lachnospiraceae, Clostridiaceae, Erysepelotrichaceae, Ruminococcaceae, Lactobacillus), Bacteroidetes (Bacteroides), and Bifidobacterium [72,73].	Microbial bile salt hydrolases deconjugate bile deoxycholic acid and lithocholic acid [76].	Microbial bile salt hydrolase associated with modulation of canonical clock genes, genes related to lipid metabolism and immune homeostasis [76].
Desulfovibrio, Desulfotobacter, Desulfobulbus, Bilophila wadsworthia [13].	Act on sulfated compounds to generate hydrogen sulfide in the colon.	Hydrogen sulfide phase-delays hepatic Bmal1 expression, which is also associated with suppressed substrate oxidation and elevated systemic glucose [65].
Lachnospiraceae (Roseburia), Eubacteriaceae (Eubacterium rectale), and Ruminococcaceae (Ruminococcus bromii, Faecalibacterium prausnitzii) [11,12]	Break down dietary fiber to generate butyrate in the colon [58].	Butyrate is a key metabolic fuel for colonic epithelial cells [11,12]; regulates plasma glucose by multiple mechanisms including activation of receptors that signal the secretion of satiety hormones, stimulation of insulin secretion and suppression of pancreatic glucagon [6,80]; modulates canonical clock genes in peripheral tissue [65]; acts as a histone deacetylase inhibitor [82,83].
Clostridum sporogenes and Ruminococcus gnavus [87].	Generate precursors of biogenic amines such as serotonin [87].	Bioamines such as serotonin play a role in intestinal motility and secretory activity [88].

* Microorganisms related to synthesis of vitamins elaborated in Table 3.