Extensive culturomics of 8 healthy samples enhances metagenomics efficiency

Autoři: Ami Diakite aff001;  Grégory Dubourg aff001;  Niokhor Dione aff001;  Pamela Afouda aff001;  Sara Bellali aff001;  Issa Isaac Ngom aff001;  Camille Valles aff001;  Matthieu Million aff001;  Anthony Levasseur aff001;  Frédéric Cadoret aff003;  Jean-Christophe Lagier aff001;  Didier Raoult aff001
Působiště autorů: Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France aff001;  IHU Méditerranée Infection, Marseille, France aff002;  Assistance Publique-Hôpitaux de Marseille, Marseille, France aff003
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0223543


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.

Klíčová slova:

Anaerobic bacteria – Bacteria – Matrix-assisted laser desorption ionization time-of-flight mass spectrometry – Metagenomics – Microbiome – New species reports – Sequence databases – Species delimitation


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2019 Číslo 10
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