Table 2 Key findings of summarized work
From: Understanding the impact of antibiotic perturbation on the human microbiome
Authors | Population | General findings | Species and ARGs implicated |
|---|---|---|---|
Parnanen et al. 2018 [52] | Fecal samples of 16 mother-infant pairs shotgun metagenomic sequenced over the first 6 months of life | Intrapartum antibiotics increased fetal ARGs and decreased diversity at 1 month | Efflux pumps and other ARGs mapping to E. coli and Klebsiella spp. enriched in antibiotic-exposed subjects |
Gibson et al. 2016 [54] | 84 NICU-hospitalized preterm neonates with stool samples flanking antibiotic treatment sequenced | Meropenem, cefotaxime, and ticarcillin-clavulanate decreased microbiome diversity whereas gentamicin and vancomycin had variable effects | Abundance of E. coli and S. aureus and the two-component regulator system, cpxR/cpxA predicted gut microbiome response to vancomycin and gentamicin |
Bokulich et al. 2016 [55] | 43 infants followed over the first 2 years of life | Antibiotics delayed microbiome maturation with fewer species and lower diversity that resolved after 1 year of life | Relative abundance of Clostridiales and Ruminococcus decreased from 3 to 9 months in the antibiotic-exposed group |
Palleja et al. 2018 [56] | 12 healthy adults treated with 4 days of meropenem, gentamicin, and vancomycin with fecal shotgun metagenomic sequencing for 6 months after | Gut microbiome diversity recovered after 6 months, but richness did not; no persistent enrichment of ARGs | Multi-drug efflux pumps most enriched immediately after treatment; complete absence at 6 months of baseline species belonging to Bifidobacterium, Coprococcus, and Methanobrevibacter within individuals |
Lloyd-Price et al. 2019 [7] | Multi-omic analysis of 132 children and adults with IBD or controls contributing 2965 specimens | Increased inter-individual variation during IBD flare; multi-omic signatures differentiate dysbiosis from baseline | Prevotella copri maintained high relative abundance in Crohn’s disease patients but fluctuated in its abundance in controls; dysbiosis marked by decreased Faecalibacterium prausnitzii and Roseburia hominis and increased E. coli |
Gasparrini et al. 2019 [32] | 41 NICU-hospitalized preterm infants variably exposed to antibiotics and 17 antibiotic-naive near-term infants followed through 21 months of life | Preterm infant microbiome exhibited delayed development with recovery by 15 months | Persistent MDRO Enterobacteriales colonization in several infants; model including Prevotella copri, Eubacterium rectale, Ruminococcus spp., and ARGs 96% predictive of whether a fecal sample originated from a preterm, antibiotic-exposed or near-term antibiotic-naive infant |
Yassour et al. 2016 [28] | 39 Finnish children aged 2 to 36 months contributing monthly stool samples | Frequent antibiotic courses diminished gut microbiome species and strain diversity and enriched for ARGs | Antibiotic treatment more drastically affected the strain-level diversity of Bacteroides fragilis than Bacteroides vulgatus; relative abundance of many ARGs decreased after cessation; others (CfxA6 beta-lactamase) remained high |
30 children in Niger randomized to placebo or bi-annual azithromycin for 2 years | No dramatic effect on microbiome diversity or relative abundance | Decreased relative abundance of Campylobacter spp.; increased macrolide resistance overall and in S. pneumoniae at 24 months | |
Suez et al. 2018 [59] | 21 healthy adults treated with 7 days of ciprofloxacin and metronidazole then randomized to probiotics, autologous FMT, and spontaneous recovery | FMT accelerated and probiotics inhibited microbiome structural and functional recovery | Relative abundance of Enterococcus casseliflavus and Blatia producta inversely correlated with overall microbiome richness |