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Extensive culturomics of 8 healthy samples enhances metagenomics efficiency

Abstract : Molecular approaches have long led to the assumption that the human gut microbiota is dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and in particular that of culturomics have demonstrated that these prokaryotes can in fact be cultured. This is increasing in a dramatic manner the repertoire of commensal microbes inhabiting the human gut. Following eight years of culturomics approach applied on more than 900 samples, we propose herein a remake of the pioneering study applying a dual approach including culturomics and metagenomics on a cohort of 8 healthy specimen. Here we show that culturomics enable a 20% higher richness when compared to molecular approaches by culturing 1 archaeal species and 494 bacterial species of which 19 were new taxa. Species discovered as a part of previous culturomics studies represent 30% of the cultivated isolates, while sequences derived from these new taxa enabled to increase by 22% the bacterial richness retrieved by metagenomics. Overall, 67% of the total reads generated were covered by cultured isolates, significantly reducing the hidden content of sequencing methods compared to the pioneering study. By redefining culture conditions to recover microbes previously considered fastidious, there are greater opportunities than ever to eradicate metagenomics dark matter.
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Ami Diakite, Gregory Dubourg, Niokhor Dione, Pamela Afouda, Sara Bellali, et al.. Extensive culturomics of 8 healthy samples enhances metagenomics efficiency. PLoS ONE, Public Library of Science, 2019, 14 (10), pp.e0223543. ⟨10.1371/journal.pone.0223543⟩. ⟨hal-02467010⟩

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