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. 2020 Oct 16:11:513305.
doi: 10.3389/fmicb.2020.513305. eCollection 2020.

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

Grégory Dubourg  1 , Aurélie Morand  1   2 , Fatima Mekhalif  1   3 , Raphael Godefroy  1   3 , Alice Corthier  1   3 , Abdourahamane Yacouba  1   3 , Ami Diakite  1   3 , Florent Cornu  1 , Marina Cresci  1 , Samy Brahimi  1   3 , Aurélia Caputo  1 , Eric Lechevallier  4 , Michel Tsimaratos  5 , Valérie Moal  1   6 , Jean-Christophe Lagier  1 , Didier Raoult  1
Affiliations

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut

Grégory Dubourg et al. Front Microbiol. .

Retraction in

Abstract

Human urine was considered sterile for a long time. However, 416 species have been previously cultured, including only 40 anaerobic species. Here, we used culturomics, particularly those targeting anaerobes, to better understand the urinary microbiota. By testing 435 urine samples, we isolated 450 different bacterial species, including 256 never described in urine of which 18 were new species. Among the bacterial species identified, 161 were anaerobes (35%). This study increased the known urine repertoire by 39%. Among the 672 bacterial species isolated now at least once from urine microbiota, 431 (64.1%) were previously isolated from gut microbiota, while only 213 (31.7%) were previously isolated from vagina. These results suggest that many members of the microbiota in the urinary tract are in fact derived from the gut, and a paradigm shift is thus needed in our understanding.

Keywords: bladder; culture; culturomics; microbiota; urine.

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Figures

FIGURE 1
FIGURE 1
Evolution over time of the urinary repertoire according to culturomics studies. The bacterial species are represented in five categories: Known in urines, prokaryotes isolated by other laboratories but not by culturomics; identified in urines by culturomics, taxa recovered by culturomics studies and already known to belong to the bacterial urinary repertoire; new species culturomics, new taxa discovered as a part of other culturomics studies; unknown in humans, prokaryotes first isolated in humans; and new species culturomics urines, species isolated from urinary tract as a part of this study.
FIGURE 2
FIGURE 2
Number of specimens for which at least one uropathogen (A) and E. coli (C) were recovered by culture in this study, respectively, among male and female patients. (B) highlights the median number of uropathogens cultured per sample among men and women. *p < 0.05.
FIGURE 3
FIGURE 3
Venn diagram showing the shared cultured species between the human urinary tract (this study and Morand et al., 2019), the human gut (Lagier et al., 2016), the human respiratory tract/oral cavity (Fonkou et al., 2018), and the human vagina (Diop et al., 2019).
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