Frontiers in Microbiology (Oct 2020)
Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut
- Grégory Dubourg,
- Aurélie Morand,
- Aurélie Morand,
- Fatima Mekhalif,
- Fatima Mekhalif,
- Raphael Godefroy,
- Raphael Godefroy,
- Alice Corthier,
- Alice Corthier,
- Abdourahamane Yacouba,
- Abdourahamane Yacouba,
- Ami Diakite,
- Ami Diakite,
- Florent Cornu,
- Marina Cresci,
- Samy Brahimi,
- Samy Brahimi,
- Aurélia Caputo,
- Eric Lechevallier,
- Michel Tsimaratos,
- Valérie Moal,
- Valérie Moal,
- Jean-Christophe Lagier,
- Didier Raoult
Affiliations
- Grégory Dubourg
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Aurélie Morand
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Aurélie Morand
- Pédiatrie Spécialisée et Médecine Infantile, Hôpital de la Timone, AP-HM, Marseille, France
- Fatima Mekhalif
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Fatima Mekhalif
- Fondation Méditerranée Infection, Marseille, France
- Raphael Godefroy
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Raphael Godefroy
- Fondation Méditerranée Infection, Marseille, France
- Alice Corthier
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Alice Corthier
- Fondation Méditerranée Infection, Marseille, France
- Abdourahamane Yacouba
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Abdourahamane Yacouba
- Fondation Méditerranée Infection, Marseille, France
- Ami Diakite
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Ami Diakite
- Fondation Méditerranée Infection, Marseille, France
- Florent Cornu
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Marina Cresci
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Samy Brahimi
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Samy Brahimi
- Fondation Méditerranée Infection, Marseille, France
- Aurélia Caputo
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Eric Lechevallier
- Department of Urology and Renal Transplantation, La Conception University Hospital, AP-HM, Aix-Marseille University, Marseille, France
- Michel Tsimaratos
- Pédiatrie Multidisciplinaire, Hôpital de la Timone, AP-HM, Marseille, France
- Valérie Moal
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Valérie Moal
- Centre de Nephrologie et Transplantation Rénale, Hôpital de la Conception, Aix-Marseille University, Marseille, France
- Jean-Christophe Lagier
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- Didier Raoult
- IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- DOI
- https://doi.org/10.3389/fmicb.2020.513305
- Journal volume & issue
-
Vol. 11
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
