Journal
GUT MICROBES
Volume 7, Issue 5, Pages 428-434Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/19490976.2016.1216747
Keywords
antibiotic resistance; bioinformatics; metagenome comparison; metagenomics; Microbiome
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Funding
- Quebec Consortium for Drug Discovery (CQDM)
- Canada Research Chair Program
- Mitacs post-doctoral fellowship
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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 similar to 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.
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