Gut Microbiota: Culturomics: Illuminating Microbial Dark Matter

RESEARCH HIGHLIGHTS

Nature Reviews Gastroenterology & Hepatology | Published online 23 Nov 2016; doi:10.1038/nrgastro.2016.189

were isolated, including GUT MICROBIOTA 197 potentially new species. By genome sequencing the new species and Culturomics: illuminating comparing the data with metagenomic studies from the Human microbial dark matter Microbiome Project, ‘Culturomics’ uses multiple high- human microbiome. Lagier and the researchers throughput culture conditions with colleagues have now reduced confirmed that mass spectroscopy or 16S ribosomal and optimized the culturomics culturomics enables RNA sequencing for the identification workload and addressed the the culture of of previously unculturable bacterial weaknesses of previous studies. microorganisms that species (often termed ‘dark matter’). “Our aim in this work was to extend correspond to previously L au Now, the culturomics process has the human gut bacteria repertoire as ra M unassigned sequences. arsha been further refined and used to much as possible,” explains author ll/NPG “We demonstrated that double the number of bacterial Didier Raoult. culturomics is able to fill a part of species isolated from the human gut. First, the investigators deduced the [microbial] dark matter,” reports Metagenomics has revolutionized the 18 best culture conditions Raoult. “These efforts, by increasing the study of the human microbiome, and implemented new protocols knowledge of the [gut microbiota] but obtaining DNA sequences that (fresh-sample inoculation and repertoire, will allow detection of cannot be attributed to known microcolony detection) with a focus potential probiotics for therapeutic bacterial species remains a problem. on the culture of Proteobacteria approaches.” The investigators also Pure cultures of microorganisms and halophilic or microaerophilic plan to apply culturomics to other are also required for extensive bacteria. Using the refined conditions human samples beyond the gut. microbiology research but many with a range of stool, small bowel Iain Dickson species are resistant to classic culture- and colonic samples from healthy ORIGINAL ARTICLE Lagier, J.-C. et al. Culture of based techniques. Culturomics aims individuals and patients with various previously uncultured members of the human gut to overcome these problems and to diseases from different geographical microbiota by culturomics. Nat. Microbiol. http:// fill in gaps in our knowledge of the origins, 1,057 prokaryotic species dx.doi.org/10.1038/nmicrobiol.2016.203 (2016)