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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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8308218 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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