title: Short-term effect of antibiotics on human gut microbiota.
abstract: From birth onwards, the human gut microbiota rapidly increases in diversity and reaches an adult-like stage at three years of age. After this age, the composition may fluctuate in response to external factors such as antibiotics. Previous studies have shown that resilience is not complete months after cessation of the antibiotic intake. However, little is known about the short-term effects of antibiotic intake on the gut microbial community. Here we examined the load and composition of the fecal microbiota immediately after treatment in 21 patients, who received broad-spectrum antibiotics such as fluoroquinolones and β-lactams. A fecal sample was collected from all participants before treatment and one week after for microbial load and community composition analyses by quantitative PCR and pyrosequencing of the 16S rRNA gene, respectively. Fluoroquinolones and β-lactams significantly decreased microbial diversity by 25% and reduced the core phylogenetic microbiota from 29 to 12 taxa. However, at the phylum level, these antibiotics increased the Bacteroidetes/Firmicutes ratio (p = 0.0007, FDR = 0.002). At the species level, our findings unexpectedly revealed that both antibiotic types increased the proportion of several unknown taxa belonging to the Bacteroides genus, a Gram-negative group of bacteria (p = 0.0003, FDR<0.016). Furthermore, the average microbial load was affected by the treatment. Indeed, the β-lactams increased it significantly by two-fold (p = 0.04). The maintenance of or possible increase detected in microbial load and the selection of Gram-negative over Gram-positive bacteria breaks the idea generally held about the effect of broad-spectrum antibiotics on gut microbiota.
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain.
authors.forename: Suchita
authors.initials: S
authors.lastname: Panda
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain.
authors.forename: Ismail
authors.initials: I
authors.lastname: El khader
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain; Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Casellas
authors.affiliation: Internal Medicine Department, Capio Hospital General de Catalunya, Universitat Internacional de Catalunya, Barcelona, Spain.
authors.forename: Josefa
authors.initials: J
authors.lastname: López Vivancos
authors.affiliation: Internal Medicine Department, Capio Hospital General de Catalunya, Universitat Internacional de Catalunya, Barcelona, Spain.
authors.forename: Montserrat
authors.initials: M
authors.lastname: García Cors
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain.
authors.forename: Alba
authors.initials: A
authors.lastname: Santiago
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain.
authors.forename: Silvia
authors.initials: S
authors.lastname: Cuenca
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain; Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Guarner
authors.affiliation: Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain; Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
authors.forename: Chaysavanh
authors.initials: C
authors.lastname: Manichanh
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001419:Bacteria / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D018533:Biomass; D005243:Feces / Q000382:microbiology; D005260:Female; D041981:Gastrointestinal Tract / Q000187:drug effects* / Q000382:microbiology*; D006801:Humans; D008297:Male; D054892:Metagenome; D064307:Microbiota / Q000187:drug effects*; D008875:Middle Aged; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D012336:RNA, Ribosomal, 16S
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