Human Bacterial Repertoire of the Urinary Tract: a Potential Paradigm Shift

J Clin Microbiol. 2019 Feb 27;57(3):e00675-18. doi: 10.1128/JCM.00675-18. Print 2019 Mar.


The aim of this article is to review the human repertoire of bacteria in urine already described by culture and metagenomic techniques and published in the literature. Our study led us to compare this repertoire with other available human repertoires. We followed automatic and manual bibliographical methods and found 562 bacterial species reported in the literature as part of the human urinary microbiota. Of the 562 species, 322 were described only by culture, 101 by both culture and metagenomics, and 139 only by metagenomics. A total of 352 species (62.6%) have been associated with at least one case report of human infection, of which 225 (40.0%) have been described as causative agents of urinary tract infection. The urinary tract bacterial repertoire contains 21.4% of the known prokaryotic diversity associated with human beings (464 species in common), and it shares 23.6% species with the human gut microbiota (350 species in common, 62.3% of the urine species). The urinary repertoire shares a significant difference in aerointolerant species compared with those of the gut microbiota (100/562 [17.8%] and 505/1,484 [34.0%], respectively; P < 0.001; odds ratio [OR] = 9.0 [7.0 to 11.4]). Studies using high-throughput sequencing show a higher proportion of aerointolerant bacteria in urine (74/240 [30.8%]) than studies using culture techniques (40/423 [9.5%]). Most pathogenic bacteria are part of the commensal human urinary tract bacteria, and their pathogenicity may occur following any imbalance of this microbiota. The restoration of urinary tract health can occur following a fecal transplantation. The potential gut origin of the human bacterial microbiota has to be explored.

Keywords: bacteria; culture; human; microbiota; repertoire; urine.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / growth & development
  • Bacteria / pathogenicity
  • Bacterial Physiological Phenomena
  • Biodiversity*
  • Dysbiosis
  • Gastrointestinal Microbiome
  • Humans
  • Microbiota
  • Urinary Tract / microbiology*
  • Urinary Tract Infections / microbiology
  • Urine / microbiology*