Table 1.

Impact of antibiotics on gut microbiota, metabolism, and systemic homeostasis.

Antibiotic	Gut Microbiota Composition	Effect on gut metabolite	Effect on Homeostasis	Inflammation makers	Withdrawal Impact	References
Ceftriaxone (β-lactam)	Increase in conditionally pathogenic bacteria (E. coli, Clostridium, Staphylococcus spp.)	Decreased SCFA levels, impaired receptor (FFA2, FFA3) function, altered transporter activity (SMCT1, MCT1, MCT4)	Disrupted oxidant-antioxidant balance, increased epithelial permeability, tissue remodelling	Elevated TNF-α, IL-10	Long-term dysbiosis, lasting changes in SCFAs, increased susceptibility to colitis even 56 days after withdrawal.	[101]
Cefoperazone/Sulbactam, Ceftazidime/Avibactam, Cefepime/Enmetazobactam (β-lactam/β-lactamase inhibitors)	Significant reduction in resistance rates when combined with SCFAs	MIC of SCFAs was 3750 μg/mL (60 mM) against E. coli; SCFAs decreased MIC values for β-lactams	Colonic SCFA concentrations (65–123 mM) significantly suppressed E. coli growth and virulence	Reduction in expression of virulence genes (fliC, ipaH, FimH, BssS) at colonic SCFA concentrations	Withdrawal not discussed; study focused on in vitro effects and immediate bacterial response to SCFAs along with β-lactam	[102]
Meropenem (β-lactam)	Significant disruption; increased opportunistic Enterococcaceae	Decrease in SCFA-producing bacteria (e.g., Roseburia, Lachnospiraceae, Ruminococcaceae)	Disruption of gut homeostasis; impaired colonization resistance	Increased IL-1β, IL-6, IL-12, IL-17, TNF-α	Microbial composition returned to pretreatment levels within 60 days; persistent elevated cytokines	[103]
Cefoperazone/Sulbactam (β-lactam)	Significant disruption; depletion of beneficial taxa, increased pathogens	Decrease in SCFA production; reduced butyrate-producing taxa	Disruption of gut homeostasis; increased carbohydrate availability	Increased IL-1β, IL-6, IL-12, IL-17, TNF-α	Similar to Meropenem; microbial composition tended to return but cytokine levels elevated	[103]
Aztreonam (β-lactam)	Probiotic strains resistant; significant disruption in gut microbiota	No specific effects on SCFA reported	Disruption of gut homeostasis; potential long-term effects	Increased IL-1β, IL-6, IL-12, IL-17, TNF-α	Microbial composition changes persisted long after treatment	[103]
Levofloxacin (Fluoroquinolone)	Transient increase in Firmicutes; decrease in Bacteroidetes	No significant effect reported	Return to baseline levels on Day 8 and Day 60	Similar to control group	Microbial composition returned to baseline levels on Day 8 and Day 60	[103]
Neomycin, Gentamicin (Aminoglycoside)	Significant disruption; reduced beneficial taxa; loss of diversity	17 metabolites decreased; notably, indole-3-propionic acid and hippuric acid remarkably decreased	Disruption observed; energy metabolism changes	Increased IL-1β, IL-6, IL-12, IL-17, TNF-α	Changes persisted long after treatment	[104]
Moxifloxacin, Levofloxacin (Fluoroquinolone)	Increased opportunistic taxa; decreased Firmicutes	15 metabolites decreased; increased complex lipids; decreased hippuric acid and indole-3-acetic acid	Noted disruption; complex lipids increased	Increased IL-1β, IL-6, IL-12, IL-17, TNF-α	Microbial changes seen; some metabolites elevated post-treatment	[104]
Doxycycline, Tetracycline (Tetracycline)	Significant disruption; loss of beneficial taxa	13 metabolites decreased; 9 increased; decreased hippuric acid and indole-3-acetic acid noted	Disruption observed; changes in energy metabolism	Increased IL-1β, IL-6, IL-12, IL-17, TNF-α	Microbial composition changes persisted	[104]
Erythromycin, Azithromycin (Macrolide)	Reduced microbial capacity for carbohydrate metabolism and SCFA biosynthesis	Depletion of keystone bacteria; reduced SCFA biosynthesis; alterations in serotonin (5-HT) and C-peptide	Disruption in metabolic homeostasis; changes in gastrointestinal motility	Reduction in MCP-1, IL-5, and IL-10 (significant with azithromycin); trends for IL-4, IL-6, IL-7, TNF-α, IFN-γ (not significant)	Long-term changes in gut microbiota composition, impacting systemic homeostasis	[105]