title: Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin.
abstract: Gut microbiota play a key role in the host's health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20-22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment- and treatment status-specific indicator operational taxonomic units (OTUs) as well as abundance- and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment- and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.
authors.affiliation: a Institute of Clinical Molecular Biology (ICMB); Christian-Albrechts-University (CAU) Kiel ; Kiel , Germany.
authors.forename: Femke-Anouska
authors.initials: FA
authors.lastname: Heinsen
authors.forename: Henrik
authors.initials: H
authors.lastname: Knecht
authors.forename: Sven C
authors.initials: SC
authors.lastname: Neulinger
authors.forename: Ruth A
authors.initials: RA
authors.lastname: Schmitz
authors.forename: Carolin
authors.initials: C
authors.lastname: Knecht
authors.forename: Tanja
authors.initials: T
authors.lastname: Kühbacher
authors.forename: Philip C
authors.initials: PC
authors.lastname: Rosenstiel
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Anette K
authors.initials: AK
authors.lastname: Friedrichs
authors.forename: Stephan J
authors.initials: SJ
authors.lastname: Ott
mesh_terms: D000328:Adult; D000900:Anti-Bacterial Agents / Q000008:administration & dosage*; D001419:Bacteria / Q000145:classification* / Q000187:drug effects* / Q000235:genetics; D001706:Biopsy; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome / Q000187:drug effects*; D064368:Healthy Volunteers; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology*; D008969:Molecular Sequence Data; D010303:Paromomycin / Q000008:administration & dosage*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010303:Paromomycin
keywords: 16S rRNA gene; antibiotics; lumen; microbiota; mucosa