Table 3.

Influence of phenolic compounds in gut microbiota composition.

Polyphenol Type	Tested Bacteria	Growth (+)/Inhibitory (−) Effect	Type of Study	Methods Used	Duration	Doses	References
IN VITRO CELL CULTURE STUDIES
Flavonols
Quercetin
	Bacteroides galacturonicus	(−)	In vitro	Counting on culture medium	24 h	4, 20 or 50 μg/mL	[166]
	Lactobacillus sp.	(−)
	Enterococcus caccae	(−)
	Bifidobacterium catenulatum	(−)
	Ruminococcus gauvreauii	(−)
	Escherichia coli	(−)
Rutin						20, 100 or 250 μg/mL
	Bacteroides galacturonicus,	NS
	Lactobacillus sp.	(+)
	Enterococcus caccae	NS
	Bifidobacterium catenulatum	(−)
	Ruminococcus gauvreauii	NS
	Escherichia coli	(−)
Flavonols	Bifidobacterium adolescentis		In vitro	Counting on culture medium	24 h	flavonol (galangin,kaempferol, quercetin, myricetin, or fisetin dissolved in dimethylsulphoxide (DMSO); final 25 µM; final 0.1% DMSO	[168]
Galangin		(−)
Kaempferol		NS
Quercetin		NS
Myricetin		NS
Fisetin		NS
Isoflavones		MIC (μg/mL)	In vitro	Minimum Inhibitory Concentration Assay (MIC)	1 h	Concentrations ranging from 62.5 to 1000 μg/mL	[170]
Daidzein	Eschericia coli	1000
	Staphylococcus aureus	125
	Salmonella typhimirum	1000
	Lactobacillus rhamnosus	1000
Genistein	Eschericia coli	1000
	Staphylococcus aureus	125
	Salmonella typhimirum	1000
	Lactobacillus rhamnosus	1000
Flavanones		MIC (μg/mL)	In vitro	Minimum Inhibitory Concentration Assay (MIC)	1 h	Concentrations ranging from 62.5 to 1000 μg/mL	[169]
Naringenin	Eschericia coli	125
	Staphylococcus aureus	62.5
	Salmonella typhimirum	125
	Lactobacillus rhamnosus	125
Phenolic acids		MIC (μg/mL)	In vitro	Minimum Inhibitory Concentration Assay (MIC)	1 h	Concentrations ranging from 62.5 to 1000 μg/mL	[169]
caffeic acid	Eschericia coli	500
	Staphylococcus aureus	125
	Salmonella typhimirum	500
	Lactobacillus rhamnosus	≤250
chlorogenic acid	Eschericia coli	1000
	Staphylococcus aureus	125
	Salmonella typhimirum	1000
	Lactobacillus rhamnosus	≤250
o-coumaric acid	Eschericia coli	250
	Staphylococcus aureus	125
	Salmonella typhimirum	250
	Lactobacillus rhamnosus	250
p-coumaric acid	Eschericia coli	500
	Staphylococcus aureus	125
	Salmonella typhimirum	500
	Lactobacillus rhamnosus	500
Ellagitannins	POMx		In vitro	Liquid culturing method	POMx (100 mL)	comercial extract of pomegranate at 0.01% as well as the effect of its main constituents (0.05%)	[175]
Extract of pomegranate (POMx) and its main constituents (punicalagins, punicalins, elagic acid, gallic acid)	L. acidophilus	(+)
	L. casei ssp. casei	NS
	L. paracasei ssp.	NS
	L. pentosus	(+)
	L. rhamnosus	(+)
	B. breve	(+)
	B. infantis	(+)
	B. longum	NS
	B. bifidum	(+)
	B. animalis ssp. lactis	NS
	Bacteroides fragilis	NS
	C. perfringens	(−)
	Clostridium clostriidoforme	NS
	C. ramosum	(−)
	S. aureus	(−)
	Punicalagin
	L. acidophilus	NS
	L. casei ssp. casei	NS
	L. paracasei ssp.	NS
	L. pentosus	NS
	L. rhamnosus	NS
	B. breve	(+)
	B. infantis	NS
	B. longum	NS
	B. bifidum	NS
	B. animalis ssp. lactis	(+)
	Bacteroides fragilis	NS
	C. perfringens	(−)
	Clostridium clostriidoforme	(−)
	C. ramosum	(−)
	S. aureus	(−)
	Punicalin
	L. acidophilus	NS
	L. casei ssp. casei	NS
	L. paracasei ssp.	NS
	L. pentosus	NS
	L. rhamnosus	NS
	B. breve	NS
	B. infantis	NS
	B. longum	NS
	B. bifidum	NS
	B. animalis ssp. lactis	(+)
	Bacteroides fragilis	NS
	C. perfringens	NS
	Clostridium clostriidoforme	NS
	C. ramosum	NS
	S. aureus	NS
IN VITRO FAECAL MICROBIOTA STUDIES
Flavonols	Erysipelotrichaceae	(−)	In vitro	16S rDNA reads	6 weeks	30 mg/kg BW/day	[167]
Quercetin	Ruminococcaceae	NS
	Clostridiaceae	NS
	Bacteroidaceae	NS
	Lachnospiraceae	NS
	Acidaminococcaceae	NS
	Eubacteriaceae	NS
	Prevotellaceae	NS
	Acholeplasmataceae	NS
	Lactobacillaceae	NS
	Graciibacteraceae	NS
	Clostridium aldenense	NS
	Clostridium hathewayi	NS
	Bacteroides vulgatus	(+)
	Clostridium clariflavum	(+)
	Clostridium methylpentosum	NS
	Clostridium sp. C9	NS
	Clostridium sp. XB90	NS
	Clostridium sp. MLG661	(+)
	Blautia stercoris	NS
	Gracilibacter thermotolerans	NS
	Parabacteroides distansonis	NS
	Eubacterium cylindroides	(−)
	Akkermansia muciniphila	NS
	Bilophila wadsworthia	NS
	Bacteroides sp. dnLKV7	NS
	Barnesiella intestinihominis	NS
	Bacteroides sp. S-18	NS
	Bacteroides chinchillae	NS
	Candidatus Prevotella conceptionensis	NS
Flavanols					10 h (150 mg/L)	150 mg/L and 1000 mg/L	[171]
(+)-catechin	Bifidobacterium spp.	(+)			17 h (1000 mg/L)	150 mg/L and 1000 mg/L
	Bacteroides spp.	NS
	Lactobacillus/Enterococcus spp.	NS
	Clostridium coccoides–Eubacterium rectale group	(+)
	C. histolyticum group	(−)	In vitro	Fluorescent in situ hybridization (FISH)
	Escherichia coli	(+)
(−)-epicatechin
	Bifidobacterium spp.	NS
	Bacteroides spp.	NS
	Lactobacillus/Enterococcus spp.	NS
	Clostridium coccoides–Eubacterium rectale group	(+)
	C. histolyticum group	NS
	Escherichia coli	NS
Flavan-3-ols	Lactobacillus/Enterococcus	(+)	In vitro	Fluorescent in situ hybridization (FISH)	Samples were collected at 0, 5, 10, 24, 30 and 48 h of fermentation	600 mg/L	[172]
2 fractions of grape seed	Clostridium histolyticum	(−)	Human fecal microbiota
Anthocyanins			In vitro	Fluorescent in situ hybridization (FISH)	0, 1, 2, 4, 5, 10, and 24 h	20 mg/L and 200 mg/L	[174]
Malvidin-3-glucoside	Total bacteria count	(+)
	Atopobium spp.	(+)
	Bif idobacterium spp.	(+)
	C. cocoides−Eubacterium rectale	(+)
	Bacteroides spp.	(−)
	Lactobacillus spp.	(+)
	Clostridium histolyticum	(−)
Stilbenes	Erysipelotrichaceae	NS	In vitro	16S rDNA reads	6 weeks	15 mg/kg BW/day	[167]
Trans-resveratrol	Ruminococcaceae	NS
	Clostridiaceae	NS
	Bacteroidaceae	NS
	Lachnospiraceae	NS
	Acidaminococcaceae	NS
	Eubacteriaceae	NS
	Prevotellaceae	NS
	Acholeplasmataceae	NS
	Lactobacillaceae	NS
	Graciibacteraceae	(−)
	Clostridium aldenense	(−)
	Clostridium hathewayi	(−)
	Bacteroides vulgatus	NS
	Clostridium clariflavum	NS
	Clostridium methylpentosum	NS
	Clostridium sp. C9	(−)
	Clostridium sp. XB90	(+)
	Clostridium sp. MLG661	(−)
	Blautia stercoris	NS
	Gracilibacter thermotolerans	(−)
	Parabacteroides distansonis	(−)
	Eubacterium cylindroides	NS
	Akkermansia muciniphila	NS
	Bilophila wadsworthia	NS
	Bacteroides sp. dnLKV7	NS
	Barnesiella intestinihominis	NS
	Bacteroides sp. S-18	NS
	Bacteroides chinchillae	NS
	Candidatus Prevotella conceptionensis	NS
Phenolic acids	Total bacteria count	(+)	In vitro	Fluorescent in situ hybridization (FISH)	0, 1, 2, 4, 5, 10, and 24 h	150 mg/L and 1000 mg/L	[174]
Gallic acid	Atopobium spp.	(+)
	Bif idobacterium spp.	(+)
	C. cocoides−Eubacterium rectale	(+)
	Bacteroides spp.	(−)
	Lactobacillus spp.	(+)
	Clostridium histolyticum	(−)
Ellagitannins	Total bacteria	(+)	In vitro	batch-culture fermentation system inoculated with fecal samples from healthy individuals, FISH	Samples collected at 0, 5, 10, 24 and 48 h	POMx (1.5 mL) and punicalagins (250 mg) were inoculated in stirring batch-culture vessels (one per treatment) containing faecal slurry (1:10, w/v).	[175]
pomegranate by-product (POMx)	Bifidobacterium spp.	(+)
	Lactobacillus spp.	(+)
	Clostridium coccoides–Eubacterium rectale group C. histolyticum group	(+)
		NS
Lignans	Lactobacillus rhamnosus VTT E-97800	(+)	In vitro colon model	Counting on culture medium	0, 2, 4, 6, 8, and 24 h	8 mL of fecal suspension, and a 16.7% (w/v) final concentration of fresh fecal matter	[179]
Lignins	L. rhamnosus VTT E-97948	(+)
	Lactobacillus paracasei VTT E-97949	(+)
	Lactobacillus salivarius VTT E-981006	(+)
	Bifidobacterium adolescentis VTT E-981074, Bifidobacterium breve VTT E-981075, Bifidobacterium longum VTT E-96664	(+)
	Lactobacillus rhamnosus VTT E-97800,	(+)
	L. rhamnosus VTT E-97948	(+)
IN VIVO STUDIES
Isoflavones	Clostridium coccoides-Eubacterium rectale cluster	(+)	In vivo	FISH and flow cytometry analyses	2 months (Fecal samples were collected on day 0, 30, and 60)	100 mg/day of isoflavones aglycon equivalents	[170]
	Lactobacillus-Enterococcus group,	(+)
	Faecalibacterium prausnitzii subgroup, Bifidobacterium genus	(+)
	Clostridium coccoides-Eubacterium rectale cluster	(+)
Condensed Tannins	Lachnospiraceae	(+)	In vivo	culture-independent barcoded next generation sequencing	3 days normal diet	1% w/w Grape Seed Extract	[173]
Proanthocyanidins	Clostridiales	(+)			6 days treatment diet
	Lactobacillus	(+)			3 days post treatment control-feeding
	Ruminococcaceae	(+)			fecessamples taken daily
Stilbenes			In vivo	Agar dilution method	25 days	1 mg/kg/day	[179]
Resveratrol	Lactobacillus	(+)
	Bifidobacterium	(+)
	Enterobacteria	Diminished the increase
Stilbenes	Bacteroidetes-to-Firmicutes ratio,	(+)	In vivo	FISH and flow cytometry	12 weeks	200 mg/kg/day	[180]
Resveratrol	Enterococcus faecalis	(−)
	Lactobacillus	(+)
	Bifidobacterium	(+)
Ellagitannins	Lactobacilli	(+)	In vivo	Agar dilution method with fecal microbiota of rats	Samples collected at days 0, 10, 20	250 mg/kg/day	[177]
Pomegranate ellagitannins and their microbiota-derived metabolite urolithin A	Bifidobacterium	(+)
Ellagitannins	Actinobacteria	(+)	In vivo	FISH and flow cytometry	4 weeks	1000 mg POM extract	[178]
Pomegranate (POM) ellagitannins	Firmicutes	(−)
	Verrucomicrobia (Akkermansia muciniphila)	(+)
	Butyrivibrio	(+)
	Enterobacter	(+)
	Eschericia	(+)
	Lactobacillus	(+)
	Prevotella	(+)
	Serratia	(+)
	Veillonella	(+)
	Collinsella	(−)

NS: no significant difference, (+): increase, (−): decrease.