title: Partial recovery of microbiomes after antibiotic treatment.
abstract: Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted.
authors: a Centre de Recherche en Infectiologie, CHU de Québec-Université Laval , Québec , Canada.|b Big Data Research Center, Université Laval , Québec , Canada.
authors: Frédéric
authors: F
authors: Raymond
authors: a Centre de Recherche en Infectiologie, CHU de Québec-Université Laval , Québec , Canada.|b Big Data Research Center, Université Laval , Québec , Canada.
authors: Maxime
authors: M
authors: Déraspe
authors: a Centre de Recherche en Infectiologie, CHU de Québec-Université Laval , Québec , Canada.
authors: Maurice
authors: M
authors: Boissinot
authors: a Centre de Recherche en Infectiologie, CHU de Québec-Université Laval , Québec , Canada.|d Département de microbiologie-infectiologie et d'immunologie , Université Laval , Québec , Canada.
authors: Michel G
authors: MG
authors: Bergeron
authors: a Centre de Recherche en Infectiologie, CHU de Québec-Université Laval , Québec , Canada.|b Big Data Research Center, Université Laval , Québec , Canada.|c Département de médecine moléculaire , Université Laval , Québec , Canada.
authors: Jacques
authors: J
authors: Corbeil
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D001419:Bacteria / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D001424:Bacterial Infections / Q000188:drug therapy* / Q000382:microbiology; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002511:Cephalosporins / Q000627:therapeutic use*; D000069196:Gastrointestinal Microbiome / Q000187:drug effects*; D041981:Gastrointestinal Tract / Q000187:drug effects / Q000382:microbiology; D006801:Humans; D000097670:Cefprozil
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D002511:Cephalosporins; D000097670:Cefprozil
keywords: Microbiome; antibiotic resistance; bioinformatics; metagenome comparison; metagenomics