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