Many More Microbes in Humans: Enlarging the Microbiome Repertoire

Clin Infect Dis. 2017 Aug 15;65(suppl_1):S20-S29. doi: 10.1093/cid/cix404.


The proportion of cultured microorganisms is dramatically lower than those predicted to be involved in colonization, acute, or chronic infections. We report our laboratory's contribution to promoting culture methods. As a result of using culturomics in our clinical microbiology laboratories (including amoeba co-culture and shell-vial culture) and through the use of matrix-assisted laser desorption/ionization-time-of-flight and the 16S rRNA gene for identification, we cultured 329 new bacterial species. This is also the first time that 327 of species have been isolated from humans, increasing the known human bacterial repertoire by 29%. We isolated 4 archaeal species for the first time from human, including 2 new species. Of the 100 isolates of giant viruses, we demonstrated the human pathogenicity of Mimivirus in pneumonia and Marseillevirus in diverse clinical situations. From sand flies, we isolated most of the known Phlebovirus strains that potentially cause human infections. Increasing the repertoire of human-associated microorganisms through culture will allow us to test pathogenicity models with viable microorganisms.

Keywords: 16S rRNA amplification and sequencing; MALDI-TOF; culturomics; giant viruses; human microbiota.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Bacteria / pathogenicity
  • Bacterial Typing Techniques
  • DNA, Bacterial
  • DNA, Viral
  • Giant Viruses / classification
  • Giant Viruses / genetics
  • Giant Viruses / isolation & purification*
  • Giant Viruses / pathogenicity
  • Humans
  • Microbiota* / genetics
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods


  • DNA, Bacterial
  • DNA, Viral
  • RNA, Ribosomal, 16S