@article{fdi:010058171,
  title = {{M}icrobial culturomics : paradigm shift in the human gut microbiome study},
  author = {{L}agier, {J}. {C}. and {A}rmougom, {F}abrice and {M}illion, {M}. and {H}ugon, {P}. and {P}agnier, {I}. and {R}obert, {C}. and {B}ittar, {F}. and {F}ournous, {G}. and {G}imenez, {G}. and {M}araninchi, {M}. and {T}rape, {J}ean-{F}ran{\c{c}}ois and {K}oonin, {E}. {V}. and {L}a {S}cola, {B}. and {R}aoult, {D}.},
  editor = {},
  language = {{ENG}},
  abstract = {{C}omprehensive determination of the microbial composition of the gut microbiota and the relationships with health and disease are major challenges in the 21st century. {M}etagenomic analysis of the human gut microbiota detects mostly uncultured bacteria. {W}e studied stools from two lean {A}fricans and one obese {E}uropean, using 212 different culture conditions (microbial culturomics), and tested the colonies by using mass spectrometry and 16{S} r{RNA} amplification and sequencing. {I}n parallel, we analysed the same three samples by pyrosequencing 16{S} r{RNA} amplicons targeting the {V}6 region. {T}he 32 500 colonies obtained by culturomics have yielded 340 species of bacteria from seven phyla and 117 genera, including two species from rare phyla ({D}einococcus-{T}hermus and {S}ynergistetes, five fungi, and a giant virus ({S}enegalvirus). {T}he microbiome identified by culturomics included 174 species never described previously in the human gut, including 31 new species and genera for which the genomes were sequenced, generating c. 10 000 new unknown genes ({ORF}ans), which will help in future molecular studies. {A}mong these, the new species {M}icrovirga massiliensis has the largest bacterial genome so far obtained from a human, and {S}enegalvirus is the largest virus reported in the human gut. {C}oncurrent metagenomic analysis of the same samples produced 698 phylotypes, including 282 known species, 51 of which overlapped with the microbiome identified by culturomics. {T}hus, culturomics complements metagenomics by overcoming the depth bias inherent in metagenomic approaches.},
  keywords = {{C}ulturomics ; gut microbiota ; {MALDI}-{TOF} {MS} ; metagenomic analysis ; uncultured bacteria},
  booktitle = {},
  journal = {{C}linical {M}icrobiology and {I}nfection},
  volume = {18},
  numero = {12},
  pages = {1185--1193},
  ISSN = {1198-743{X}},
  year = {2012},
  DOI = {10.1111/1469-0691.12023},
  URL = {https://www.documentation.ird.fr/hor/fdi:010058171},
}