Optimization and standardization of the culturomics technique for human microbiome exploration.

Autor: Diakite A; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Dubourg G; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Dione N; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Afouda P; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Bellali S; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Ngom II; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Valles C; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Tall ML; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Lagier JC; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.; IHU Méditerranée Infection, Marseille, France., Raoult D; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France. didier.raoult@gmail.com.; IHU Méditerranée Infection, Marseille, France. didier.raoult@gmail.com.
Jazyk: angličtina
Zdroj: Scientific reports [Sci Rep] 2020 Jun 15; Vol. 10 (1), pp. 9674. Date of Electronic Publication: 2020 Jun 15.
DOI: 10.1038/s41598-020-66738-8
Abstrakt: 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.
Databáze: MEDLINE
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