@article{fdi:010060809,
  title = {{T}he gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics},
  author = {{D}ubourg, {G}. and {L}agier, {J}. {C}. and {A}rmougom, {F}abrice and {R}obert, {C}. and {H}amad, {I}. and {B}rouqui, {P}. and {R}aoult, {D}idier},
  editor = {},
  language = {{ENG}},
  abstract = {{G}ut microbiota consists of 10(10) bacteria per gram of stool. {M}any antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. {W}e analyzed one stool sample collected from a patient treated for drug-resistant {M}ycobacterium tuberculosis and who ultimately died from pneumonia due to a {S}treptococcus pneumoniae 10 months later. {W}e performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry ({MALDI}-{TOF}) and 16{S} r{RNA} amplification and sequencing, pyrosequencing, and 18{S} r{RNA} amplification and clone sequencing. {E}lectron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. {B}y culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. {T}he pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. {O}nly two phylotypes overlapped with culturomics. {I}n contrast, an amount of chloroplasts was found. {A}dditionally, specific molecular eukaryote detection found three fungal species. {W}e recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. {W}e propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of {S}. pneumoniae. {T}his finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.},
  keywords = {},
  booktitle = {},
  journal = {{E}uropean {J}ournal of {C}linical {M}icrobiology and {I}nfectious {D}iseases},
  volume = {32},
  numero = {5},
  pages = {637--645},
  ISSN = {0934-9723},
  year = {2013},
  DOI = {10.1007/s10096-012-1787-3},
  URL = {https://www.documentation.ird.fr/hor/fdi:010060809},
}