Table 2.
In vitro studies of the herb–gut microbiome interactions of medicinal plants used for mental health.
| Investigated Plant, Plant Part | Extract, Sample Preparation for Incubation | Preparation of Fecal Samples | Incubation Conditions | Method for Microbiome Analysis | Microbiome Changes | Method for Metabolite Detection | Metabolites | Reference |
|---|---|---|---|---|---|---|---|---|
| Amygdalus communis, semen | blanched finely ground almonds (FG); blanched defatted finely ground almonds (DG) | fecal material from one healthy donor | fecal batch culture after gastric and duodenal digestion (37 °C, pH 6.8, anaerobic; samples were collected over 24 h) | fluorescent in situ hybridization (FISH) with 16S rRNA-targeted probes for Bifidobacterium, Bacteroides, Lactobacillus/Enterococcus spp., Clostridium histolyticum group, Clostridium coccoides-Eubacterium rectale group | increase in Bifidobacterium and E. rectale in FG group; no change in bacterial composition in DG group | SCFA analysis by HPLC with refractive index detector | increase in lactic acid, butyric acid, acetic acid, and propionic acid in FG and DG groups | [65] |
| natural almond skins (NS), blanched almond skins (BS) | fecal material from one healthy donor | fecal batch culture after gastric and duodenal digestion (37 °C, pH 6.8, anaerobic; samples were collected at 0, 4, 8, and 24 h) | FISH with 16S rRNA-targeted probes for Bifidobacterium, Bacteroides, Lactobacillus/Enterococcus spp., Clostridium histolyticum group, Clostridium coccoides-Eubacterium rectale group | increase in Lactobacillus/Enterococcus spp. group, C. coccoides-E. rectale group, and Bifidobacteria in NS and BS group; decrease in C. histolyticum group in NS and BS groups | SCFA analysis by HPLC with refractive index detector | increase in total SCFA, lactic acid, acetic acid, propionic acid, and butyric acid in NS and BS groups | [66] | |
| Centella asiatica, herba | powdered herb | one pooled sample from twelve healthy vegetarian or vegan women and men; 1% herb or 1% glucose | conditions: anaerobic, 37 °C; pH: 7.4 | V3–V4 region of 16S rRNA gene NGS (Illumina); genomic reconstruction of sugar utilization and SCFA pathways |
rel. increase: Enterobacteriaceae and Pseudomonadaceae | [83] | ||
| Citrus aurantium ssp. aurantium, aetheroleum | essential oil | twofold dilutions of essential oil (from 2.0% to 0.004% [v/v]) | conditions: 12 bacterial species representing major intestinal genera on selective agars; 24–72 h cultures | agar dilution method | weak antimicrobial effects on Bacteroides fragilis, Clostridium perfringens; no antimicrobial effects on Bifidobacterium, Lactobacillus | - | - | [88] |
| Curcuma longa, rhizoma | powdered rhizome | one pooled sample from twelve healthy vegetarian or vegan women and men; 1% herb | conditions: anaerobic | V3–V4 region of 16S rRNA gene, NGS (Illumina); genome reconstruction of sugar utilization and SCFA pathways |
rel. increase at family level: Bacteroidaceae, Desulfovibrionaceae, Rikenellaceae, and Lachnospiraceae rel. increase at genus level: Clostridium spp., Bacteroides spp., Blautia, and Enterobacter spp. rel. increase in propionate- and butyrate-producing taxa rel. decrease in Citrobacter freundii, Enterococcus faecalis, Shigella dysenteriae, and Escherichia coli |
[96] | ||
| Ginkgo biloba, folium | extract with ginkgolides, bilobalide, flavonoid glycosides and aglycones (28.1–0.11 µg/mg) | 12 g fresh feces from normal, diabetic, and diabetic nephropathy male Sprague Dawley rats (n = 45) | conditions: anaerobic; 37 °C; reaction mixture taken out at 0.5, 1, 2, 4, 6, 8, 12, 16, 22, 28, 36, and 48 h |
- | - | HPLC-MS/MS | all compounds were biotransformed by rat intestinal bacteria; notably different time course of all 14 compounds in feces of diseased compared to normal rats | [107] |
| Glycine max, fructus | soybean husk; 0.9 mg/g total flavonoids | feces from toy poodle dogs (6.5 ± 3.5 months in age, 2.9 ± 0.4 kg in body weight) (n = 3) | conditions: intact soybean husk and enzyme-treated soybean husk; incubated at 39 °C for 24 h |
DNA extraction from in vitro cultures; qPCR assay using specific primers |
increase: bifidobacteria no effect on total bacteria, total lactobacilli, and E. coli |
GC-MS for SCFA analysis and D/L-lactic acid assay kit |
increase: total SCFAs, including acetate, propionate, and butyrate acids (p < 0.01) decrease: indole and skatole acids (p < 0.01) no effect on ammonia production |
[110] |
| Humulus lupulus, strobile | supercritical CO2 extract mixed with canola oil (extract/oil 2:1); hop bitter acids (α-acids/β-acids 1.73:1); tested range 1.5 mg–750 mg hop extract | mixed inoculum from 10 healthy volunteers | conditions: anaerobic, pH: 6.8; sampling after 2.5, 5, 10, 16, and 24 h |
qPCR analyses of total bacteria and key bacterial groups; V3–V4 region of 16S rRNA gene NGS (Illumina) |
increase: Proteobacteria, Enterobacteriaceae, Escherichia/Shigella, Enterobacter, Citrobacter, Klebsiella decrease: Lachnospiraceae, Bacteroidetes, Bacteroides, Actinobacteria, Firmicutes, Collinsella, Clostridium, Eubacterium, Desulfovibrio, Bifidobacterium, Lactobacillus, Blautia, Dorea, Veillonella, Coriobacteriaceae; Bacteroides-Prevotella-Porphyromonas group |
analyses of SCFA and other organic acids using HPLC/UV-detection | decrease: total organic acids; butyrate clearly decreased at higher hop concentrations | [123] |
| Lavandula angustifolia, aetheroleum | essential oil | twofold dilutions of essential oil (from 2.0% to 0.004% [v/v]) | conditions: 12 bacterial species representing major intestinal genera on selective agars; 24–72 h cultures | agar dilution method | antimicrobial effects (Bacteroides fragilis, Candida albicans, Clostridium perfringens); no impact on beneficial species | - | - | [88] |
|
Panax quinquefolius, radix |
ethanolic extract (70%) | 6 fecal samples from healthy adult volunteers | conditions: anaerobic, 37 °C; sampling after 24 h incubation | - | - | HPLC/Q-TOF-MS | ginsenoside Rb1 metabolized to compound K and ginsenoside Rg3 | [149] |
| ethanolic extract (70%) | one fresh fecal sample from a healthy Chinese man (28 years old) | conditions: anaerobic, 37 °C; sampling after 24 h incubation |
- | - | HPLC/Q-TOF-MS | 25 identified metabolites: 13 metabolites were undoubtedly assigned, 12 were tentatively assigned; the 3 most abundant metabolites: 20S-ginsenoside Rg3, ginsenoside F2, and compound K; main metabolic pathways: deglycosylation (stepwise cleavage of sugar moieties), dehydration | [153] | |
| Polygala tenuifolia, radix | ethanolic extract (75%) | rat intestinal bacteria with Radix Polygala extract (final concentration of 0.02 g/mL), control, and blank samples | conditions: anaerobic; 37 °C; sampling after 0, 2, 8, 24, 48, 72, or 96 h | V4 region of bacterial 16S rRNA gene, NGS (Illumina); 3 replicates of PCR reactions combined | Bacteroides rel. increase more than 60% | UHPLC-IT-MSn and UHPLC-Q-TOF MS | 44 detected metabolites: 25 triterpene saponin metabolites (formed by deglycosylation, deacetylation); 16 oligosaccharide ester metabolites; 3 xanthone C-glycoside metabolites | [162] |
| Rhodiola rosea, radix | Methanolic extract (70%) | 1 g of human feces in 10 mL of brain heart infusion medium | static upper GI tract digestion, followed by incubation of intestinal phase non-dialyzed retentate in fecal slurries of healthy donors (anaerobic, 37 °C, 48 h) | HPLC-DAD | main metabolites: cinnamyl alcohol, tyrosol, hydroquinone | [168] | ||
| Vitis vinifera, fructus | red grape polyphenol extract (653 mg gallic acid equivalents (GAE)/g) | fecal samples from two healthy females | dynamic simulator of the GI tract (simgi®); extract with or without probiotic supplementation (Lactobacillus plantarum CLC-17: 2 × 1010 CFU/day); five periods: microbiota stabilization (14 days), extract (800 mg) acute feeding (8 days), probiotic implantation (7 days), extract (800 mg) acute-feeding during probiotic supplementation (8 days), washout (8 days) | 16S rRNA gene, NGS (Illumina); bacteria plate counting and qPCR of Lactobacillus spp. |
increase in Enterobacteriaceae by extract feeding; decrease in Enterobacteriaceae after probiotic implantation; no changes in bacterial diversity after probiotic implantation |
targeted analysis of phenolic compounds by UHPLC-ESI-MS/MS and of ammonium ions by ammonium test | increase in phenolic metabolites (benzoic acids) after probiotic implantation; no change in ammonium production | [193] |
| sun-dried raisins | fecal sample from one healthy volunteer | upper gastrointestinal digestion followed by fecal batch culture fermentation (37 °C, anaerobic, 24 h) | bacteria plate counting; V4 region of 16S rRNA gene, NGS (Illumina) |
sequencing: rel. increase in Proteobacteria, Actinobacteria, and Roseburia ssp. rel. decrease in Bacteroidetes, Ruminococcus, and Faecalibacterium prausnitzii; plate counting: increase in Bifidobacteria and Lactobacilli |
SCFA analysis by HPLC-RID | increase in total SCFAs, lactic acid, acetic acid, propionic acid, and butyric acid | [191] | |
| Vitis vinifera, semen | grape seed polyphenol extract (80% ethanol; 23.5 mg GAE/g) | fecal samples from three healthy volunteers (one female, two males, ages 25–30) | conditions: 37 °C, anaerobic; samples were taken at 0, 12, 24, and 36 h |
FISH targeting specific regions of 16S rRNA for total bacteria, Bifidobacterium spp., Lactobacillus-Enterococcus group, Bacteroides-Prevotella group, Clostridium histolyticum group, Eubacterium-Clostridium group, and Atopobium cluster | increase in Bifidobacterium spp. and Lactobacillus-Enterococcus group; decrease in Bacteroides-Prevotella and Clostridium histolyticum; no change in total bacteria, Eubacterium-Clostridium group, and Atopobium cluster | SCFA analysis by HPLC | increase in acetic acid, propionic acid, and butyric acid | [183] |
| grape seed extract (GSE; 629 mg GAE/g) | in vitro cultured microbiota with a reproducible human microbial community representative of in vivo conditions | in vitro simulator of the gastrointestinal tract SHIME®: ascending colon (AC) and descending colon (DC) compartments; conditions: 37 °C, anaerobic, 48 h; samples were taken at 0, 6, 24, and 48 h |
qPCR, specific primers for total bacteria, Lactobacillus, Bifidobacterium, Bacteroides, Prevotella, Enterobacteriaceae, Blautia coccoides-Eubacterium rectale group, Clostridium leptum, and Ruminococcus | decrease in all analyzed bacterial groups | SCFA and branched-chain fatty acid (BCFA) analysis by GC-FID; phenolic metabolites by UHPLC-ESI-MS/MS |
increase in acetic acid, propionic acid, butyric acid, and total SCFAs and BCFAs in AC; no significant change in SCFAs and BCFAs in DC; steady release of phenylacetic and phenylpropionic acids up to 48 h; formation of flavan-3-ol metabolites |
[182] |