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Table 2 Key findings of summarized work

From: Understanding the impact of antibiotic perturbation on the human microbiome



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