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Microbial culturomics, a new approach to biodiversity applied to human microbes

The iceberg

The last few years have witnessed the triumph of molecular identification techniques to describe microbes living in our environment and those associated to our gut mucosa.

A study carried out by the laboratory of Prof. Raoult (CNRS 7278, INSERM 1095, IRD 198, Aix-Marseilles University) and published in Clinical Microbiology Infection (1) describes a new approach through culture that gives particularly surprising results. The initial objective of this work was to show that if 80% of microbes detected by molecular techniques were not likely to be cultivated by microbiological techniques, we could invent a new strategy called culturomics that would allow growing bacterial species amongst which 80% would not be detected by current molecular techniques. This result was achieved thanks to the association of the use of over 200 culture techniques, the rapid identification using the mass spectrometry tools (MALDI-TOF) recently developed, and the confirmation provided by molecular techniques that a number of species were unknown. This work has led to identify 31 new bacterial species from the gut, which represents 40% of the bacterial species identified in the human gut over the past decade. This culturomics technique led to discover three world records amongst microbes of human origin: the largest giant virus ever isolated in human, Senegalvirus, comparable to a virus already described in Marseillevirus unit, which has a genome of 372Kb; the bacterium having the largest genome ever isolated in human, that we called Microvirga massiliensis with a genome of 9.35 Mb. Finally the development of culture techniques had previously allowed, in association with a team of Luminy, isolating the Archae with the largest genome amongst human samples: Methanomassiliicoccus luminyensis, 2.6 Mb (2). This culture technique is a considerable resource, because only 15% of the 340 cultivated species have been identified at the same time by metagenomic techniques currently used in the analysis of faeces. Finally, obtaining strains through pure culture has allowed sequencing the entire genome of these new species, from which six have already been published. Our conclusion is that the microbial culturomics is a new field that complements molecular techniques and gives another aspect of the composition of microbial populations living in humans and environments, including giant viruses, Archaea, and bacteria.

Reference List

(1) Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection 2012; 18: 1157-1159.

(2) Gorlas A, Robert C, Gimenez G, Drancourt M, Raoult D. Complete Genome Sequence of Methanomassiliicoccus luminyensis, the Largest Genome of a Human-Associated Archaea Species. J Bacteriol 2012 Sep;194(17):4745.

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