Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut
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 d...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-10-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.513305/full |
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doaj-8e889584e1134285819d59872d89effc |
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Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
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 |
| spellingShingle |
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 Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut Frontiers in Microbiology urine microbiota culturomics bladder culture |
| author_facet |
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 |
| author_sort |
Grégory Dubourg |
| title |
Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut |
| title_short |
Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut |
| title_full |
Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut |
| title_fullStr |
Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut |
| title_full_unstemmed |
Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut |
| title_sort |
deciphering the urinary microbiota repertoire by culturomics reveals mostly anaerobic bacteria from the gut |
| publisher |
Frontiers Media S.A. |
| series |
Frontiers in Microbiology |
| issn |
1664-302X |
| publishDate |
2020-10-01 |
| description |
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. |
| topic |
urine microbiota culturomics bladder culture |
| url |
https://www.frontiersin.org/article/10.3389/fmicb.2020.513305/full |
| work_keys_str_mv |
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doaj-8e889584e1134285819d59872d89effc2020-11-25T03:41:14ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-10-011110.3389/fmicb.2020.513305513305Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the GutGrégory Dubourg0Aurélie Morand1Aurélie Morand2Fatima Mekhalif3Fatima Mekhalif4Raphael Godefroy5Raphael Godefroy6Alice Corthier7Alice Corthier8Abdourahamane Yacouba9Abdourahamane Yacouba10Ami Diakite11Ami Diakite12Florent Cornu13Marina Cresci14Samy Brahimi15Samy Brahimi16Aurélia Caputo17Eric Lechevallier18Michel Tsimaratos19Valérie Moal20Valérie Moal21Jean-Christophe Lagier22Didier Raoult23IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FrancePédiatrie Spécialisée et Médecine Infantile, Hôpital de la Timone, AP-HM, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceFondation Méditerranée Infection, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceFondation Méditerranée Infection, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceFondation Méditerranée Infection, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceFondation Méditerranée Infection, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceFondation Méditerranée Infection, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceFondation Méditerranée Infection, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceDepartment of Urology and Renal Transplantation, La Conception University Hospital, AP-HM, Aix-Marseille University, Marseille, FrancePédiatrie Multidisciplinaire, Hôpital de la Timone, AP-HM, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceCentre de Nephrologie et Transplantation Rénale, Hôpital de la Conception, Aix-Marseille University, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceIRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix-Marseille University, Marseille, FranceHuman 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.https://www.frontiersin.org/article/10.3389/fmicb.2020.513305/fullurinemicrobiotaculturomicsbladderculture |