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Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments

The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen...

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Autores principales: Pérez-Burillo, Sergio, Hinojosa-Nogueira, Daniel, Navajas-Porras, Beatriz, Blasco, Telmo, Balzerani, Francesco, Lerma-Aguilera, Alberto, León, Daniel, Pastoriza, Silvia, Apaolaza, Iñigo, Planes, Francisco J., Francino, Maria Pilar, Rufián-Henares, José Ángel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8308218/
https://www.ncbi.nlm.nih.gov/pubmed/34199047
http://dx.doi.org/10.3390/nu13072207
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author Pérez-Burillo, Sergio
Hinojosa-Nogueira, Daniel
Navajas-Porras, Beatriz
Blasco, Telmo
Balzerani, Francesco
Lerma-Aguilera, Alberto
León, Daniel
Pastoriza, Silvia
Apaolaza, Iñigo
Planes, Francisco J.
Francino, Maria Pilar
Rufián-Henares, José Ángel
author_facet Pérez-Burillo, Sergio
Hinojosa-Nogueira, Daniel
Navajas-Porras, Beatriz
Blasco, Telmo
Balzerani, Francesco
Lerma-Aguilera, Alberto
León, Daniel
Pastoriza, Silvia
Apaolaza, Iñigo
Planes, Francisco J.
Francino, Maria Pilar
Rufián-Henares, José Ángel
author_sort Pérez-Burillo, Sergio
collection PubMed
description The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow’s milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization.
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spelling pubmed-83082182021-07-25 Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments Pérez-Burillo, Sergio Hinojosa-Nogueira, Daniel Navajas-Porras, Beatriz Blasco, Telmo Balzerani, Francesco Lerma-Aguilera, Alberto León, Daniel Pastoriza, Silvia Apaolaza, Iñigo Planes, Francisco J. Francino, Maria Pilar Rufián-Henares, José Ángel Nutrients Article The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow’s milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization. MDPI 2021-06-27 /pmc/articles/PMC8308218/ /pubmed/34199047 http://dx.doi.org/10.3390/nu13072207 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pérez-Burillo, Sergio
Hinojosa-Nogueira, Daniel
Navajas-Porras, Beatriz
Blasco, Telmo
Balzerani, Francesco
Lerma-Aguilera, Alberto
León, Daniel
Pastoriza, Silvia
Apaolaza, Iñigo
Planes, Francisco J.
Francino, Maria Pilar
Rufián-Henares, José Ángel
Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments
title Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments
title_full Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments
title_fullStr Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments
title_full_unstemmed Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments
title_short Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments
title_sort effect of freezing on gut microbiota composition and functionality for in vitro fermentation experiments
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8308218/
https://www.ncbi.nlm.nih.gov/pubmed/34199047
http://dx.doi.org/10.3390/nu13072207
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