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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Data availability
The data shown in Fig. 4 are available from the supporting primary research paper previously published by Pérez-Burillo et al.17. The data presented in Figs. 2 and 3 were generated for this protocol. Source data are provided with this paper.
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Acknowledgements
This study was supported by the EU project Stance4Health (contract no. 816303) and by the Plan propio de Investigación y Transferencia of the University of Granada under the program ‘Intensificación de la Investigación, modalidad B’ to J.A.R.-H.
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S.P.-B., S.M., and J.A.R.-H. wrote the manuscript. B.N.-P., A.J.V.-M., D.H.-N., A.L.-M. and S.P. contributed to the writing of the manuscript. S.P.-B., S.M., B.N.-P., A.J.V.-M., D.H.-N. and A.L.-M. contributed to formal analysis and investigation; S.P.-B. developed the methodology. S.P. and J.A.R.-H. supervised the work. J.A.R.-H. obtained funding and coordinates the EU project Stance4Health.
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Peer review information Nature Protocols thanks Francisco Tomás-Barberán and the other, anonymous reviewer(s) for their contribution to the peer review of this work.
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Key references using this protocol
Pérez-Burillo, S. et al. Food Chem. 239, 1253–1262 (2018): https://doi.org/10.1016/j.foodchem.2017.07.024
Pérez-Burillo, S. et al. Food Chem. 279, 252–259 (2019): https://doi.org/10.1016/j.foodchem.2018.11.137
Pérez-Burillo, S., et al. Food Chem. 316, 126309 (2020): https://doi.org/10.1016/j.foodchem.2020.126309
This protocol is an extension to: Nat. Protoc. 14, 991–1014 (2019): https://doi.org/10.1038/s41596-018-0119-1
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Pérez-Burillo, S., Molino, S., Navajas-Porras, B. et al. An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality. Nat Protoc 16, 3186–3209 (2021). https://doi.org/10.1038/s41596-021-00537-x
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DOI: https://doi.org/10.1038/s41596-021-00537-x
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