ArticleNature protocols2021
An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- Article
- Grain proteins ameliorate glucose metabolism disorders by activating intestinal AhR and the hepatic NLK/FOXO1 pathway via gut microbiota-derived indole metabolites.Journal of advanced research · 2026Article
- Metabolic Profile and Dynamic Characteristics of Ziziphi Spinosae Semen Flavonoids During Biotransformation and Their Effect on Human Gut Microbiota In Vitro.Foods (Basel, Switzerland) · 2026Article
- Article
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Digestibility and microbiota modulation by nuts and sunflower seeds in cystic fibrosis: an in vitro approach.European journal of nutrition · 2026Article
- Healthy Nutrition and Fermented Animal-Sourced Foods as a Complementary One Health Strategy: Effects on Foodborne Pathogens and Intestinal Host Defense.Journal of clinical practice and research · 2026Review
- Metabolomic Characterization of Baby Spinach Phenolics Transformation During Gastrointestinal Digestion and Microbiome-Mediated Metabolism.Foods (Basel, Switzerland) · 2026Article
- The effects of bacteriophage cocktail treatment on healthy gut microbiota: anMicrobial genomics · 2026Article
- Towards a Standard Protocol for Fecal Microbiota Transplantation in Irritable Bowel Syndrome.Journal of neurogastroenterology and motility · 2026Review
- Comparative metabolomic assessment of bioconverted traditional and black wheat via the in vitro piglet digestion model.Scientific reports · 2026Article
- Pooled feces reduce the inter-sample variation of microbiota in pig models.BMC microbiology · 2026Article
- Article
- Feeding Type Shapes Infant Gut Microbiota and Metabolite Profiles in a Simulated Colonic Model.Microorganisms · 2026Article
- Dual-pathway detoxification byFood chemistry: X · 2026Article
- In Vitro Assessment of Gut Microbiota Modulation Through Functional Biscuits Enriched with Almond By-Products.Foods (Basel, Switzerland) · 2026Article
- Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models.FEMS microbiology reviews · 2026Review
- Article
- Carrot flour-enriched pasta withFrontiers in nutrition · 2026Article
- Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Knowledge of the effect of foods on gut microbiota composition and functionality is expanding. To isolate the effect of single foods and/or single nutrients (i.e., fiber, polyphenols), this protocol describes an in vitro batch fermentation procedure to be carried out after an in vitro gastrointestinal digestion. Therefore, this is an extension of the previous protocol described by Brodkorb et al. (2019) for studying in vitro digestion. The current protocol uses an oligotrophic fermentation medium with peptone and a high concentration of fecal inoculum from human fecal samples both to provide the microbiota and as the main source of nutrients for the bacteria. This protocol is recommended for screening work to be performed when many food samples are to be studied. It has been used successfully to study gut microbiota fermentation of different foodstuffs, giving insights into their functionality, community structure or ability to degrade particular substances, which can contribute to the development of personalized nutrition strategies. The procedure does not require a specific level of expertise. The protocol takes 4-6 h for preparation of fermentation tubes and 20 h for incubation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.