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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
Doan et al. [57, 58] 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