Table 1

Overview on the effects of different antibiotics on gut microbiota, according to their classes and excretion

Antibiotic class	Antibiotic excretion	Effects on gut microbiota
Lincosamides Clindamycin	Main biliary excretion	↓Gram-positive aerobes and anaerobes17 ↑Resistance genes18 ↓ Bacteroides diversity18
Macrolides Clarithromycin Erythromycin	Biliary excretion	↓Total bacterial diversity⁰ ↓Actinobacteria (including Bifidobacteria)19 20 ↓Firmicutes (mainly Lactobacilli)20 ↑Bacteroidetes20 ↑Proteobacteria20 ↓Firmicutes26 ↓Actinobacteria26 ↑Proteobacteria26
β-Lactams Penicillin V Amoxicillin Ampicillin/sulbactam Cephalosporins	Main urinary excretion Partial (33–67%) biliary excretion²⁴	No relevant changes20 ↓Firmicutes26 ↓Actinobacteria26 ↑Proteobacteria26 No relevant changes20 21 ↓Total bacterial richness23 ↓Firmicutes23 ↑Bacteroidetes23 ↑Proteobacteria23 ↓Firmicutes26 ↓Actinobacteria26 ↑Proteobacteria26 ↓Total bacterial richness23 ↓Firmicutes23 ↑Bacteroidetes23 ↑Proteobacteria23
Fluoroquinolones Ciprofloxacin Levofloxacin	Partial biliary excretion	↓Bacterial diversity27 ↓Gram-negative facultative anaerobes25 ↑Gram-positive aerobes26 ↓Gram-negative facultative anaerobes25 ↓Gram-positive anaerobes25
Glycopeptides Vancomycin*		↓Total bacterial diversity⁰ ↓Firmicutes20 ↑Proteobacteria20