Healthy adults, cefprozil antibiotic trial, Canada

The human gut microbiota is affected by antibiotics, but the heterogeneous response between individuals remains unexplored. To specifically address this question and examine the effect of antibiotics on selection of resistance genes, we administered the second-generation cephalosporin cefprozil to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and three months later were analyzed using shotgun metagenomic sequencing. We show that normal antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable fashion. Strikingly, we identified a subgroup of participants that were enriched in opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to the Bacteroides enterotype. Resistance genes that were not detectable before the treatment were observed after a 7-day course of antibiotic. Knowledge of the initial composition of the microbiome could assist in the prevention of the adverse effects of antibiotics.

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

• host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• body site study.title · “of the human gut microbiome determines its”
• body site study.description · “The human gut microbiota is affected”
• life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
• life stage study.description · “cefprozil to healthy volunteers . Stool samples”

1,252 runs over 72 samples · mean 0.78 Gbp per run (median 0.81 Gbp, total 982.56 Gbp; 1,252 runs with a base count) · layout PAIRED 1,252 · platform ILLUMINA 1,252 · models Illumina HiSeq 1000 (1,252) · 90% of runs with a Sandpiper profile · first public 2015-03-05

Raymond F first · Ouameur AA · Déraspe M · Iqbal N · Gingras H · Dridi B · Leprohon P · Plante PL · Giroux R · Bérubé · Bérubé È · Frenette J · Boudreau DK · Simard JL · Chabot I · Domingo MC · Trottier S · Boissinot M · Huletsky A · Roy PH · Ouellette M · Bergeron MG · Corbeil J last · Koo H first · Morrow CD last · Orihara K first · Yahagi K · Saito Y · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · Chen J first · Zhu J · Lu W · Wang H · Pan M · Tian P · Zhao J · Zhang H · Chen W last · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · van Sinderen D · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last · Heidrich V first · Fackelmann G · Ricci L · Spadazzi R · Baldanzi G · Punčochář M · Catassi G · Marchi P · Modesto M · Piccinno G · Porcari S · Rondinella D · Asnicar F · Valles-Colomer M · Mattarelli P · Ianiro G · Segata N last

PRJEB8094.csv.gz (3.8 KB) · parquet (75.9 KB) — all 72 samples, every field with route and confidence · PRJEB8094_determinations.csv.gz (11.3 KB) — 1,076 evidence rows