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...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-06-01
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| Series: | Nutrients |
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| Online Access: | https://www.mdpi.com/2072-6643/13/7/2207 |
| _version_ | 1797411716301062144 |
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| author | Sergio Pérez-Burillo Daniel Hinojosa-Nogueira Beatriz Navajas-Porras Telmo Blasco Francesco Balzerani Alberto Lerma-Aguilera Daniel León Silvia Pastoriza Iñigo Apaolaza Francisco J. Planes Maria Pilar Francino José Ángel Rufián-Henares |
| author_facet | Sergio Pérez-Burillo Daniel Hinojosa-Nogueira Beatriz Navajas-Porras Telmo Blasco Francesco Balzerani Alberto Lerma-Aguilera Daniel León Silvia Pastoriza Iñigo Apaolaza Francisco J. Planes Maria Pilar Francino José Ángel Rufián-Henares |
| author_sort | Sergio Pérez-Burillo |
| collection | DOAJ |
| 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 <i>Bacteroides</i>, 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. |
| first_indexed | 2024-03-09T04:49:07Z |
| format | Article |
| id | doaj.art-b34a46b5519b47d7b282755560149463 |
| institution | Directory Open Access Journal |
| issn | 2072-6643 |
| language | English |
| last_indexed | 2024-03-09T04:49:07Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Nutrients |
| spelling | doaj.art-b34a46b5519b47d7b2827555601494632023-12-03T13:12:06ZengMDPI AGNutrients2072-66432021-06-01137220710.3390/nu13072207Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation ExperimentsSergio Pérez-Burillo0Daniel Hinojosa-Nogueira1Beatriz Navajas-Porras2Telmo Blasco3Francesco Balzerani4Alberto Lerma-Aguilera5Daniel León6Silvia Pastoriza7Iñigo Apaolaza8Francisco J. Planes9Maria Pilar Francino10José Ángel Rufián-Henares11Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, SpainCentro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, SpainCentro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, SpainTecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, SpainTecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, SpainArea de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, SpainArea de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, SpainCentro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, SpainTecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, SpainTecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, SpainArea de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, SpainCentro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, SpainThe 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 <i>Bacteroides</i>, 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.https://www.mdpi.com/2072-6643/13/7/2207gut microbiotafreezingstoragefoodsbioactive compounds |
| spellingShingle | Sergio Pérez-Burillo Daniel Hinojosa-Nogueira Beatriz Navajas-Porras Telmo Blasco Francesco Balzerani Alberto Lerma-Aguilera Daniel León Silvia Pastoriza Iñigo Apaolaza Francisco J. Planes Maria Pilar Francino José Ángel Rufián-Henares Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments Nutrients gut microbiota freezing storage foods bioactive compounds |
| 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 | gut microbiota freezing storage foods bioactive compounds |
| url | https://www.mdpi.com/2072-6643/13/7/2207 |
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