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Table 1 Main antibiotics used for pediatric or adult infections that modify the microbiome

From: The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

Antibiotic Molecular target Class Resistance mechanism Effect on gut microbiota Effect on gut transcriptome Effect on gut proteome Effect on gut metabolome
Amoxicillin Transpeptidase β-lactam Altered target, β-lactamase Reduced abundance enterobacteria [167] NA NA NA
Ampicillin Transpeptidase β-lactam Altered target, β-lactamase Decreased bacterial diversity, greater prevalence of Enterobacter spp. [42] Increased expression of genes involved in tRNA biosynthesis, translation, vitamin biosynthesis, phosphate transport, stress response, proton motive force, antibiotic resistance and phage [72]; reduced immune cell and mitochondrial gene expression [19] Increased bacterial glycosidase and mucinase activity [168] NA
Cefotaxime Transpeptidase β-lactam (third generation cephalosporin) Altered target Decreased bacterial cell count [169]; decreased abundance of anaerobes and enterobacteria [170] NA NA NA
Chloramphenicol NA NA NA NA Increased expression of genes involved in tRNA biosynthesis, translation, vitamin biosynthesis, phosphate transport, stress response, proton motive force, antibiotic resistance and phage [72] NA NA
Ciprofloxacin DNA gyrase Fluoroquinolone Altered target, efflux Decreased abundance of enterobacteria [171]. Lower bacterial diversity [68, 69], decrease in short-chain fatty acid (SCFA) producers [71] Increased expression of genes involved in tRNA biosynthesis, translation, vitamin biosynthesis, phosphate transport, stress response, proton motive force, antibiotic resistance and phage [72] NA NA
Clarithromycin plus metronidazole Bacterial 50S rRNA/DNA synthesis Macrolide (clarithromycin) and nitroimidazole (metronidazole) Altered target/drug inactivation (clarithromycin) and efflux (metronidazole) Reduction in abundance of Actinobacteria, partial recovery of pretreatment state [70] NA NA NA
Clindamycin Bacterial 50S rRNA Lincosamide Altered target Initial decreased abundance of enterococci, streptococci, and anaerobic bacteria, subsequent recovery of abundance of streptococci and anaerobic bacteria [172]; reduced diversity of Bacteroides spp. [74]; decrease in abundance of bacteria producing short-chain fatty acids [71] NA Increased production of immunoglobulin proteins, transthyretin and chymotrypsin-like elastase family proteins; decreased production of proteins involved in T-cell activation, chymotrypsinogen B, phospholipase A2, myosin-1a and cytochrome C [20] Increased creatine and creatinine, and levels of primary bile acids, N-acetylated amino acids, proline-hydroxyproline, pyroglutamylglutamine, myo-inositol, chiroinositol, methyl-chiro-inositol and γ-glutamyl amino acids, and increased host tryptophan metabolism; decreased levels of secondary bile acids, enterolactone, equol, N-acetyl-aspartate, short-chain fatty acids and sugar alcohols, and decreased bacterial tryptophan metabolism [84]
Erythromycin Translation Macrolide Efflux Decreases in abundance of Streptococci, enterococci, and enterobacteria; increases in abundance of staphylococci; alteration in abundance of anaerobes [173] Increased expression of genes involved in tRNA biosynthesis, translation, vitamin biosynthesis, phosphate transport, stress response, proton motive force, antibiotic resistance, and phage [72] NA NA
Gentamicin Bacterial 30S ribosome Aminoglycoside Decreased uptake, drug modification Decreased bacterial diversity, greater prevalence of Enterobacter spp. [42] NA NA Increased levels ofoligosaccharides and secondary bile acids; decreased levels of short-chain fatty acids, phenolic acids, uracil, primary bile acids, branched-chain amino acids and aromatic amino acids [85]
Meropenem Transpeptidase Carbapenem Altered target, β-lactamase Reduced abundance of enterobacteria, streptococci, Clostridia, Bacteroides spp., and Gram-negative cocci [174] NA NA NA
Streptomycin Bacterial 30S ribosome Aminoglycoside Decreased uptake, drug modification Overall diversity decreases; abundance of Ruminococcaceae and Bacteroidaceae increases [20] NA Increased production of peptidases, proteins involved in actin polymerization, transthyretin, chymotrypsin-like elastase family proteins, myosin-1a, and cytochrome C; decreased production of chymotrypsinogen B and phospholipase A2 [20] Bile acid metabolism, steroid metabolism, and eicosanoid synthesis affected; levels of leukotriene B4 decrease [88]
Ticarcillin Transpeptidase β-lactam Altered target, β-lactamase Decreased abundance of enterococci [175] NA NA NA
Tigecycline Bacterial 30S ribosome Tetracycline Altered target, efflux Reduction in abundance of enterococci, E. coli, lactobacilli, and bifidobacteria and increases in other enterobacteria and yeasts [176]; reduction in abundance of Bacteroidetes and increases in Proteobacteria [81] NA NA NA
Vancomycin Peptidoglycan Glycopeptide Altered peptidoglycan target Decreased bacterial diversity [177] Increased expression of genes involved in tRNA biosynthesis, translation, vitamin biosynthesis, phosphate transport, stress response, proton motive force, antibiotic resistance, and phage [72]; reduced immune cell and mitochondrial gene expression [19] NA Leukotriene B4 affected [88]; increased levels of oligosaccharides and decreased levels of short-chain fatty acids and uracil [86]; low doses increase levels of short-chain fatty acids [53]
  1. NA data not available
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Genome Medicine

ISSN: 1756-994X

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