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Optimization and standardization of the culturomics technique for human microbiome exploration

Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the disco...

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Autores principales: Diakite, Ami, Dubourg, Grégory, Dione, Niokhor, Afouda, Pamela, Bellali, Sara, Ngom, Issa Isaac, Valles, Camille, Tall, Mamadou lamine, Lagier, Jean-Christophe, Raoult, Didier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295790/
https://www.ncbi.nlm.nih.gov/pubmed/32541790
http://dx.doi.org/10.1038/s41598-020-66738-8
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author Diakite, Ami
Dubourg, Grégory
Dione, Niokhor
Afouda, Pamela
Bellali, Sara
Ngom, Issa Isaac
Valles, Camille
Tall, Mamadou lamine
Lagier, Jean-Christophe
Raoult, Didier
author_facet Diakite, Ami
Dubourg, Grégory
Dione, Niokhor
Afouda, Pamela
Bellali, Sara
Ngom, Issa Isaac
Valles, Camille
Tall, Mamadou lamine
Lagier, Jean-Christophe
Raoult, Didier
author_sort Diakite, Ami
collection PubMed
description Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity.
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spelling pubmed-72957902020-06-17 Optimization and standardization of the culturomics technique for human microbiome exploration Diakite, Ami Dubourg, Grégory Dione, Niokhor Afouda, Pamela Bellali, Sara Ngom, Issa Isaac Valles, Camille Tall, Mamadou lamine Lagier, Jean-Christophe Raoult, Didier Sci Rep Article Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture. While metagenomics enabled substantial advances in exploring the microbiota, culturomics significantly expanded our knowledge regarding the bacterial gut repertoire through the discovery and the description of hundreds of new taxa. While this approach relies on the variation of culture conditions and media, we have tested so far more than 300 conditions since the beginning of culturomics studies. In this context, we aimed herein to identify the most profitable conditions for optimizing culturomics approach. For this purpose, we have analysed a set of 58 culturomics conditions that were previously applied to 8 faecal specimens, enabling the isolation of 497 bacterial species. As a result, we were able to reduce the number of conditions used to isolate these 497 of more than a half (i.e. to 25 culture conditions). We have also established a list of the 16 conditions that allowed to capture 98% of the total number of species previously isolated. These data constitute a methodological starting point for culture-based microbiota studies by improving the culturomics workflow without any loss of captured bacterial diversity. Nature Publishing Group UK 2020-06-15 /pmc/articles/PMC7295790/ /pubmed/32541790 http://dx.doi.org/10.1038/s41598-020-66738-8 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Diakite, Ami
Dubourg, Grégory
Dione, Niokhor
Afouda, Pamela
Bellali, Sara
Ngom, Issa Isaac
Valles, Camille
Tall, Mamadou lamine
Lagier, Jean-Christophe
Raoult, Didier
Optimization and standardization of the culturomics technique for human microbiome exploration
title Optimization and standardization of the culturomics technique for human microbiome exploration
title_full Optimization and standardization of the culturomics technique for human microbiome exploration
title_fullStr Optimization and standardization of the culturomics technique for human microbiome exploration
title_full_unstemmed Optimization and standardization of the culturomics technique for human microbiome exploration
title_short Optimization and standardization of the culturomics technique for human microbiome exploration
title_sort optimization and standardization of the culturomics technique for human microbiome exploration
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7295790/
https://www.ncbi.nlm.nih.gov/pubmed/32541790
http://dx.doi.org/10.1038/s41598-020-66738-8
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