title: High-level colonisation of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment.
abstract: The gut microbiota is mainly composed of the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria; the Verrucomicrobia phylum is occasionally observed. Antibiotics can change the bacterial diversity of the gut, with limited changes in the proportions of phyla. In this study, the gut repertoire of two patients who received a broad-spectrum antibiotic regimen was studied. As part of a large gut microbiota study, two stool samples were analysed: one sample was collected after broad-spectrum antibiotic therapy in a patient with Coxiella burnetii vascular infection (Patient A); and the other sample was collected from a patient admitted to the Intensive Care Unit (Patient B). Samples were subjected to Gram staining, electron microscopy, 16S rRNA V6 amplicon pyrosequencing and fluorescence in situ hybridisation (FISH). In parallel, the antibiotic susceptibility of Akkermansia muciniphila Muc(T) strain was studied and this strain was observed by electron microscopy. Pyrosequencing revealed that a large proportion of the sequences were associated with Verrucomicrobia (proportions of 44.9% and 84.6% for Patients A and B, respectively). All of the phylotypes were represented by a single species (A. muciniphila), and neither patient presented significant gastrointestinal disorders. Electron microscopy and FISH with specific Verrucomicrobia probes confirmed the presence of the bacterium. The Muc(T) strain was susceptible to imipenem and doxycycline but resistant to vancomycin and metronidazole. Dramatic colonisation of the human gut microbiota by the Verrucomicrobia phylum following a broad-spectrum antibiotic regimen occurred without significant gastrointestinal manifestations, suggesting that influenced by external factors such as antibiotics, the gut repertoire remains partially unknown.
authors.affiliation: Aix-Marseille Université, URMITE, UM 63, CNRS 7278-IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France.
authors.forename: Grégory
authors.initials: G
authors.lastname: Dubourg
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Lagier
authors.forename: Fabrice
authors.initials: F
authors.lastname: Armougom
authors.forename: Catherine
authors.initials: C
authors.lastname: Robert
authors.forename: Gilles
authors.initials: G
authors.lastname: Audoly
authors.forename: Laurent
authors.initials: L
authors.lastname: Papazian
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D000328:Adult; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D054892:Metagenome / Q000187:drug effects*; D008853:Microscopy; D008875:Middle Aged; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D061327:Verrucomicrobia / Q000302:isolation & purification*
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S