The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Abstract

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

FIG 1

A MALDI-TOF incrementation database in a 4,000-bed university hospital in Marseille, France. The number of spectra has tripled in 3 years because we added the spectra of all the bacterial species identified by molecular tools that were cultured from routine laboratory samples and in culturomics studies.

FIG 2

Contribution of environmental microbiologists to improving bacterial culture due to diffusion chambers, allowing the number of colonies cultured to increase 300 times by mimicking the natural environment (8).

FIG 3

Brief history of Akkermansia muciniphila (2004 to 2014) from its first culture to its relationships with humans, including its suggested role in obesity (157, 158, 160, 161).

FIG 4

Challenges for culturomics and specific answers, including the techniques used to limit the overgrowth of common bacteria and to increase the growth of fastidious bacteria.

FIG 5

Overall vision of the strategy from clinical sample to genomic applications. All the bacteria identified by MALDI-TOF MS and by molecular tools were compared with our database of species from humans. We determined the genomes of all the bacteria first isolated in humans (microbiogenomics), and all the new bacterial species were described by using taxonogenomics. All these bacteria were deposited in our collection of bacterial strains (CSUR). GenBank accession numbers are shown in parentheses.