title: Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics.
abstract: The human gut flora is currently widely characterised using molecular techniques. Microbial culturomics (large-scale culture conditions with identification of colonies using MALDI-TOF or 16S rRNA) is part of the rebirth of bacterial culture that was initiated by environmental microbiologists for the design of axenic culture for intracellular bacteria in clinical microbiology. Culturomics was performed on four stool samples from patients treated with large-scale antibiotics to assess the diversity of their gut flora in comparison with other culture-dependent studies. Pyrosequencing of the V6 region was also performed and was compared with a control group. Gut richness was also estimated by bacterial counting after microscopic observation. In total, 77 culture conditions were tested and 32,000 different colonies were generated; 190 bacterial species were identified, with 9 species that had not been isolated from the human gut before this study, 7 newly described in humans and 8 completely new species. A dramatic reduction in diversity was observed for two of the four stool samples for which antibiotic treatment was prolonged and uninterrupted. The total number of bacteria was generally preserved, suggesting that the original population was replaced but was sustained in size. Discordances between culture and pyrosequencing biodiversity biomarkers highlight the depth of bias of molecular studies. Stool samples studied showed a dramatic reduction in bacterial diversity. Considering the variable antibiotic concentration in the gut, this reduction in the number of species is possibly linked to the production of bacteriocin in the upper digestive tract by specific bacteria, such as Lactobacillus spp.
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
authors: Grégory
authors: G
authors: Dubourg
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
authors: Jean Christophe
authors: JC
authors: Lagier
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France.
authors: Catherine
authors: C
authors: Robert
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France.
authors: Fabrice
authors: F
authors: Armougom
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
authors: Perrine
authors: P
authors: Hugon
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France.
authors: Sarah
authors: S
authors: Metidji
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France.
authors: Niokhor
authors: N
authors: Dione
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France.
authors: Nicole Prisca Makaya
authors: NP
authors: Dangui
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France.
authors: Anne
authors: A
authors: Pfleiderer
authors: Departamento de Microbiologia, Laboratório de Vírus, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors: Joñatas
authors: J
authors: Abrahao
authors: Institut Louis Malardé, Pape'ete, Tahiti, French Polynesia.
authors: Didier
authors: D
authors: Musso
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France; Service de Réanimation Médicale-Détresse Respiratoires et Infections Sévères-Hôpital Nord, Chemin des Bourrely, 13015 Marseille, France.
authors: Laurent
authors: L
authors: Papazian
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France.
authors: Philippe
authors: P
authors: Brouqui
authors: Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors: Fehmida
authors: F
authors: Bibi
authors: Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors: Muhammad
authors: M
authors: Yasir
authors: Service de Nutrition, Hôpital Timone, 13005 Marseille, France.
authors: Bernard
authors: B
authors: Vialettes
authors: Aix-Marseille University, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE; Research Unit on Infectious and Tropical Emerging Diseases) UM 63 CNRS 7278 IRD 198 INSERM U1095, Faculties of Medicine and Pharmacy, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: Didier.raoult@gmail.com.
authors: Didier
authors: D
authors: Raoult
mesh_terms: D000293:Adolescent; D000328:Adult; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D001419:Bacteria / Q000737:chemistry / Q000145:classification* / Q000187:drug effects* / Q000254:growth & development; D058491:Bacterial Load; D058448:Biota / Q000187:drug effects*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: Antibiotics; Culturomics; Diversity; Microbiota; Pyrosequencing