Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

Elizabeth A Rettedal; Heidi Gumpert; Morten O A Sommer

doi:10.1038/ncomms5714

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

Nat Commun. 2014 Aug 28:5:4714. doi: 10.1038/ncomms5714.

Authors

Elizabeth A Rettedal¹, Heidi Gumpert¹, Morten O A Sommer²

Affiliations

¹ Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
² 1] Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, DK-2900 Hørsholm, Denmark.

PMID: 25163406
DOI: 10.1038/ncomms5714

Abstract

The human gut microbiota is linked to a variety of human health issues and implicated in antibiotic resistance gene dissemination. Most of these associations rely on culture-independent methods, since it is commonly believed that gut microbiota cannot be easily or sufficiently cultured. Here, we show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. We use this approach to determine the phylogenetic distribution of antibiotic tolerance phenotypes for 16 antibiotics in the human gut microbiota. Based on the phenotypic mapping, we tailor antibiotic combinations to specifically select for previously uncultivated bacteria. Utilizing this method we cultivate and sequence the genomes of four isolates, one of which apparently belongs to the genus Oscillibacter; uncultivated Oscillibacter strains have been previously found to be anti-correlated with Crohn's disease.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Bacteria / classification
Bacteria / genetics
Bacteria / isolation & purification*
Bacteriological Techniques
Crohn Disease / microbiology
Drug Resistance, Bacterial
Gastrointestinal Microbiome / drug effects
Gastrointestinal Microbiome / physiology*
Humans
Molecular Sequence Data
Phenotype
Phylogeny*
RNA, Ribosomal, 16S

Substances

Anti-Bacterial Agents
RNA, Ribosomal, 16S

Associated data

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