@article{PAR00012709,
  title = {{T}he rebirth of culture in microbiology through the example of culturomics to study human gut microbiota},
  author = {{L}agier, {J}. {C}. and {H}ugon, {P}. and {K}helaifia, {S}. and {F}ournier, {P}. {E}. and {L}a {S}cola, {B}. and {R}aoult, {D}idier},
  editor = {},
  language = {{ENG}},
  abstract = {{B}acterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. {M}etagenomics 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. {B}y 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. {T}he revolution in bacterial identification also allowed rapid progress. 16{S} r{RNA} bacterial identification allowed the accurate identification of new species. {M}ass spectrometry allowed the high-throughput identification of rare species and the detection of new species. {B}y 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. {F}inally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. {W}e 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.},
  keywords = {},
  booktitle = {},
  journal = {{C}linical {M}icrobiology {R}eviews},
  volume = {28},
  numero = {1},
  pages = {237--264},
  ISSN = {0893-8512},
  year = {2015},
  DOI = {10.1128/cmr.00014-14},
  URL = {https://www.documentation.ird.fr/hor/{PAR}00012709},
}