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

Abstract

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.

FIG 1

Flow chart of the automated bibliographical request. This figure represents the flow chart of the bacterial species found associated with at least one publication in PubMed database, based on the automatic query and then manual triage of all the publications to keep only prokaryotic species found in the human urinary tract.

FIG 2

Comparison of the percentage of repartition of the most-represented phyla in the human urinary tract bacterial repertoire, the human gut repertoire, and the human global repertoire. This histogram represents the percentage of taxa in the main phyla in the human urinary tract repertoire, compared to those in the human gut and human global repertoires.

FIG 3

Comparison of the percentage of repartition of the most represented genera in the human urinary tract bacterial repertoire, the human gut repertoire, and the human global repertoire. This histogram represents the percentage of taxa in the main genera in the human urinary tract repertoire, compared to those in the human gut and human global repertoires.