Table 1.

Overview of metabolites, bacterial species currently known to produce these metabolites, and experimental models used to assess anti-IBD effects.

Microbial Metabolite	Parental Compound	Phylum	Species	Experimental Model	Ref.
Indole-3-aldehyde (I3Al)	Tryptophan	Firmicutes	Lactobacillus reuteri Lactobacillus murinus	in vitro, in vivo	[10,11,12]
Indole-3-propionic acid (I3Pr)	Tryptophan	Firmicutes	Peptostreptococcus russellii Peptostreptococcus anaerobius Peptostreptococcus asaccharolyticus Clostridium sporogenes Clostridium botulinum Clostridium caloritolerans Clostridium paraputrificum Clostridium cadaveris	in vitro, in vivo	[13,14,15,16,17,18]
Indole-3-pyruvic acid (I3Py)	Tryptophan	Firmicutes	Clostridium sporogenes	in vitro, in vivo	[15,19]
Indole-3-acrylic acid (I3Acr)	Tryptophan	Firmicutes	Peptostreptococcus russellii Peptostreptococcus anaerobius Clostridium sporogenes	in vitro	[15,20]
Urolithin A (UrA)	Ellagic acid	Actinobacteria	Bifidobacterium pseudocatenulatum	in vitro, in vivo	[21,22,23,24,25,26]
Isouroithin A (iUrA)	Ellagic acid	Actinobacteria	Ellagibacter isourolithinifaciens	in vitro	[25,27,28]
Urolithin B (UrB)	Ellagic acid	Actinobacteria	Bifidobacterium pseudocatenulatum	in vitro	[21,24,25]
Urolithin C (UrC)	Ellagic acid	Actinobacteria	Gordonibacter urolithinfaciens Gordonibacter pamelaeae	in vitro	[24,29,30]
Enterolactone (EL) Enterodiol (ED)	Lignans	Firmicutes	Lactobacillus gasseri Lactobacillus salivarius Clostridium scindens Lactonifactor longoviformis Peptostreptococcus productus	in vitro	[31,32,33,34,35,36,37,38,39,40]
		Actinobacteria	Bifidobacterium bifidum Bifidobacterium catenulatum Bifidobacterium pseudolongum Bifidobacterium adolescentis Eggerthella lenta
Quercetin	Quercitrin	Fusobacteria	Fusobacterium K-60	in vitro, in vivo	[41,42,43,44]
	Rutin	Firmicutes	Enterococcus avium Lactobacillus acidophilus Lactobacillus plantarum Lachnoclostridium spp. Eisenbergiella spp. Blautia sp.	in vitro, in vivo	[45,46,47,48,49,50,51,52,53]
		Actinobacteria	Bifidobacterium dentium
		Bacteroidetes	Bacteroides uniformis Bacteroides ovatus Parabacteroides distasonis
Protocatechuic acid (PCA)/3,4-dihydroxybenzoic acid 3,4-dihydroxyphenylacetic acid (DHPA) 3,4-dihydroxyphenylpropionic acid (DHPP)	Flavonols Flavan-3-ols Flavones Anthocyanins	Firmicutes	Eubacterium oxidoreducens Eubacterium ramulus Enterococcus casseliflavus Flavonifractor plautii Catenibacillus scindens Butyrivibrio spp.	in vitro, in vivo	[54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69]
Gallic acid (GA)/3,4,5-trihydroxybenzoic acid	Anthocyanins	Firmicutes	Lactobacillus plantarum Lactobacillus casei	in vitro, in vivo	[70,71,72,73,74,75,76,77]
		Actinobacteria	Bifidobacterium lactis
3,4-dihydroxyphenyl-γ-valeric lactone (DHPVL)	Flavan-3-ols Proanthocyanins	Firmicutes	Lactobacillus plantarum Clostridium coccoides Flavonifractor plautii	in vitro	[54,55,58,59,60,63,78,79,80]
		Actinobacteria	Eggerthella lenta Eggerthella sp.
Dihydroberberine	Berberine	Firmicutes	Enterococcus faecium Enterococcus faecalis Staphylococcus aureus Staphylococcus epidermis	in vitro a, in vivo	[81,82,83,84,85,86,87]
		Proteobacteria	Escherichia coli Enterobacter cloacae Klebsiella pneumoniae
Oxyberberine	Berberine	Firmicutes	Lactobacillus acidophilus Streptococcus aureus	in vivo	[88]
		Actinobacteria	Bifidobacterium longum
		Proteobacteria	Escherichia coli Pseudomonas aeruginosa
Compound K (CK)	Ginsenoside Rb1	Firmicutes	Eubacterium	in vitro, in vivo	[89,90,91,92,93,94]
		Actinobacteria	Bifidobacterium
		Bacteroidetes	Bacteroides
		Fusobacteria	Fusobacterium

^a in vitro experiments are performed with berberine, as dihydroberberine is known to be re-oxidized to berberine after absorption.