In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools
Abstract
:1. Introduction
2. Materials and Methods
3. The Colonic Fermentation Process
4. Available Colonic In Vitro Fermentation Models
4.1. Static Colonic Fermentation Models
4.2. Dynamic Colonic Fermentation Models
5. Addressing Colonic In Vitro Digestion Studies
5.1. Faecal Inoculum Collection and Preparation
5.2. Changes in the Microbiota Populations and Their Metabolic Response
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Main Objective | Study Subject | References |
---|---|---|
To assay the prebiotic effect of polysaccharides and oligosaccharides on gut microbiota and their metabolites | Polysaccharides and oligosaccharides from: -Fruits: Mulberry fruit. -Fungi: Craterellus cornucopioides. -Algae: Saccharina japonica, and Corallina pilulifera. -Plants: flowers of Camellia sinensis and A. tequilana Weber var. -Grains: Tibetan hull-less barley. -Bacteria: Weissella cibaria and Bifidobacteria. -Beans: Red kidney bean. -Tea: Fuzhuan brick tea. | [30,31,32,36,37,38,39,40,41,42] |
To assay the prebiotic effect of some polyphenols on gut microbiota and their metabolites. | Different polyphenols from: -Foods: cereal, meat, and dairy. -Drinks: coffee, tea, wine, and different juices. -New snacks: Pineapple snack bars. -Industrial residues: Persimmon and blueberry residues. -Pomaces: Blueberry pomace. | [28,29,34,43,44,45,46] |
To assay the effect of sample processing on gastrointestinal digestion and fermentation, gut microbiota, and their metabolites. | -Dairy, egg, fish, and meat products after boiling, frying, grilling, and roasting. -Plant food products (alcoholic drinks, cereals, cocoa, coffee, fruits, legumes, nuts, oils, tubers, and vegetables) after boiling, frying, grilling, roasting, and toasting. -Enzymatic modification of the cell wall integrity: cotyledon cells from pinto bean seeds. -Extrusion: whole grain oats and wheat bran. -Particle size manipulation: maize bran, cellulose, and whole grain oat flakes. | [27,33,47,48,49,50,51,52,53] |
To assay the effect of whole foods or additives on gut microbiota and their metabolites. | -Cheonggukjang: a Korean traditional fermented soybean soup. -Edible insects: black field cricket nymphs, grass grub larvae, and wax moth larvae. -Moringa oleifera Lam. Leaves -Probiotic salami. -Tibetan hull-less barley and refined Tibetan hull-less barley. -Spent coffee grounds. -Sun-dried raisins. Additives such as: -Dietary emulsifiers: sodium CMC, P80, soy lecithin, sophorolipids, and rhamnolipids. | [34,50,54,55,56,57,58,59] |
To assay the gut microbiota metabolism in response to food components. | Biotransformation of polyphenols by human gut microbiota: -Catechin. -Flavonoid O- and C-glycosides. -[6]-Shogaol from ginger. | [35,60] |
Dynamic Model | Main Objective and Examples | References |
---|---|---|
SHIME | Assessing the probiotic effect of some bacteria: -Bacteria (e.g., Lactobacillus, Bifidobacterium, or Enterococcus) carried in cheese, chocolate, cereals, sausages, and drinks. -Probiotic formulations (e.g., Lactobacillus, Bifidobacterium, or Bacillus) | [63,68,78,79,79,80,81,82,83,84] |
Assessing the prebiotic effect of some compounds: -Polyphenols (e.g., black tea or red wine grape extract, t-resveratrol, and ε-viniferin extract). -Polysaccharides (e.g., branched fructans, arabinogalactan, fructooligosaccharides, commercially available plant polysaccharide) | [85,86,87,88,89] | |
Assessing the symbiotic effect (probiotic + prebiotic): -Milks and beverages fermented by different microorganisms (e.g., Lactobacillus) and supplemented with different compounds (e.g., passion fruit, grape pomace) -Probiotic and prebiotic formulations (e.g., Bifidobacterium + 3′-sialyllactose, Lactobacillus + red win polyphenolic extract, Lactobacillus + fructooligosaccharides, Bifidobacterium + pectins -Repressing Escherichia coli colonization of the gut mucus. | [65,67,70,71,90,91,92] | |
Other applications assessing the effect of: -Food ingredients (e.g., Mexican “taco” from corn tortilla and black beans). -Dietary emulsifiers (e.g., polysorbate 80 and carboxymethylcellulose). -Antibiotics (e.g., amoxicillin, ciprofloxacin, and tetracycline). -Processing (e.g., fresh and pasteurized orange juice). | [75,93,94] | |
TIM-2 | Assessing the prebiotic effect of some compounds: -Polyphenols (e.g., polyphenols in pre-digested mango peel, pre-digested Hibiscus sabdariffa calyces) -Polysaccharides: (e.g., High- and low-acetylated galactoglucomannooligosaccharides, agave fructans, xylo-oligosaccharides, pectins, chicory root pulp polysaccharides) | [62,73,95,96,97,98] |
Other applications assessing the effect of: -Supplementation with minerals (e.g., iron). -Food ingredients (e.g., two types of Mexican sauces) -Symbiotic effect (e.g., functional pasta with Bacillus and β-glucans). | [99,100,101] | |
SIMGI | Assessing the probiotic effect of some bacteria -Lactobacillus. | [66] |
Assessing the prebiotic effect of some compounds: -Polysaccharides: (e.g., apple, potato, oat and psyllium fibres, hydroxypropyl methylcellulose, and microcrystalline cellulose). -Polyphenols: (e.g., grape pomace extracts). | [69,102] | |
Other applications assessing the effect of: -Food (e.g., red wine). | [103] | |
PolyFermS | Assessing the prebiotic effect of some compounds: -Polysaccharides: (e.g., fructo-oligosaccharides, β-glucan, α-galactooligosaccharide, xylo-oligosaccharide | [64] |
Other uses assessing the effect of: -Supplementation with minerals (e.g., iron). | [104] |
Main Objective | Analytical Determinations | References |
---|---|---|
To assay the prebiotic effect of different polysaccharides or oligosaccharides on gut microbiota and their metabolites. | -Microbiota analysis: 16S rDNA Sequencing, qPCR, plate counting with selective media or PCR-DGGE gel. -SCFA analysis: GC-FID. -SCFA and BCFA analysis: ion-chromatography. -Metabolite analysis in fermentation broth: GC-MS or HPLC. -pH measurement: pH meter. -Ammonia: anion measurer connected to a selective-ion electrode. -Volume gas production: graduated syringe displacement method. -Other analysis: Reducing sugar (DNS method), viscosity measurements (rheometer), or particle size measurements (laser diffraction particle size analyser). | [26,30,31,36,37,38,42,54,64,69,79,80,97,109] |
To assay the prebiotic effect of different polyphenols on gut microbiota and their metabolites. | -Microbiota analysis: 16S rDNA Sequencing, plate counting with selective media, qPCR or PCR-DGGE gel. -SCFA and metabolite analysis: GC-FID, HPLC or GC-MS. -Phenolic compounds analysis: HPLC-MS, UPLC-MS, UHPLC-MS, or UPLC-ESI–MS/MS. -Ammonium: pH/ion meter coupled to an ammonium selective-ion electrode. | [29,43,44,46,85,86,95,99,102] |
To assay the effect of sample processing on antioxidant capacity during gastrointestinal digestion and fermentation. | -Antioxidant tests: TEACDPPH assay, TEACFRAP assay, Folin–Ciocalteu assay and TEACABTS assay. -Determination of phenolic acids: LC-MS or HPLC. -Microbiota analysis: 16S rDNA Sequencing. | [33,45,47,110] |
To assay the effect of dietary emulsifiers on gut microbiota and its pro-inflammatory contributions. | -SCFA analysis: GC-FID. -Microbiota analysis: 16S rDNA Sequencing and metatranscriptomic analysis. -Other analysis: Cell culture for flagellin detection (flagellin is a virulence factor). | [56,75] |
To assay sample processing (extrusion, and diverse thermal treatments) on gut microbiota | -Gut microbiota contents: 16S rDNA Sequencing, qPCR, or FISH. -SCFA analysis: HPLC or GC. | [50,51,53] |
To assay functional foods effect on gut microbiota. | -Antioxidant assays: TEACABTS assay, TEACFRAP assay, TEACOH method, TEACAAPH method, GEACRED method, solid residue antioxidant capacity, Folin–Ciocalteu colorimetric method. -Analysis of phenolic acids: HPLC. -SCFA analysis: HPLC or GC-FID. -Microbiota analysis: 16S rDNA sequencing or plate counting with selective media. | [34,59,111] |
To assay the probiotic effect of some bacteria on gut microbiota. | -SCFA analysis: GC-FID. -pH measurement: pH meter. -Ammonium: Using a selective ion meter coupled to a selective-ion electrode or realising ammonium as ammonia and titrating it with HCl. -Microbiota analysis: qPCR, plate counting, PCR-DGGE, or 16S rRNA sequencing. | [68,79,81,83] |
To assay the symbiotic (prebiotic + probiotic) on gut microbiota | -Microbiota analysis: 16S rDNA sequencing, plate counts, PCR-DGGE, or qPCR. -SCFA analysis: GC-FID. -Ammonium analysis: Using an anion measurer connected to a selective-ion electrode or realising ammonium as ammonia and titrating it with HCl. -Lactic acid: spectrophotometrically with an enzymatic D-/L-lactic acid Kit. -Phenolic metabolites analysis: UPLC-MS/MS. | [65,67,71,84,92] |
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Veintimilla-Gozalbo, E.; Asensio-Grau, A.; Calvo-Lerma, J.; Heredia, A.; Andrés, A. In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools. Appl. Sci. 2021, 11, 8135. https://doi.org/10.3390/app11178135
Veintimilla-Gozalbo E, Asensio-Grau A, Calvo-Lerma J, Heredia A, Andrés A. In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools. Applied Sciences. 2021; 11(17):8135. https://doi.org/10.3390/app11178135
Chicago/Turabian StyleVeintimilla-Gozalbo, Elena, Andrea Asensio-Grau, Joaquim Calvo-Lerma, Ana Heredia, and Ana Andrés. 2021. "In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools" Applied Sciences 11, no. 17: 8135. https://doi.org/10.3390/app11178135