Abstract
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.
Highlights
Culturomics is a high-throughput culture approach that has dramatically contributed to the recent renewal of culture
The 40 additional culture conditions that were added allowed the isolation of 95 additional species compared to the 18 pre-selected conditions, of which 27% (n = 26) are new culturomics taxa
This shows the contribution of the new conditions used, in the isolation of new bacterial species
Summary
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. The culturomics, which is a high scale culture technique was developed to study the human microbiota[1] This approach enabled to drastically expand our knowledge regarding the repertoire of human microbes through the discovery of new taxa and the identification of rare and tedious bacteria[2]. The purpose of this work was to analyse the performances of the 58 conditions used from this work for optimizing the process of culturomics-based strategy
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