BackgroundAntibiotic-induced disruption of the gut microbiota is known to influence host metabolism; however, whether its metabolic effects depend on the duration of exposure remains unclear, particularly in relation to adipose thermogenesis under high-fat diet (HFD) conditions.MethodsC57BL/6 mice fed an HFD were treated with a broad-spectrum antibiotic cocktail for either short-term (2 weeks) or long-term (10 weeks). Body weight, adiposity, metabolic parameters, and energy expenditure were assessed. Thermogenic capacity was evaluated by histology and gene expression analysis in brown and white adipose tissues, following stimulation with the β3-adrenergic receptor agonist CL316243. Gut microbiota composition was analyzed using 16S rRNA sequencing.ResultsShort-term antibiotic treatment attenuated HFD-induced weight gain, reduced fat accumulation, and increased weight-adjusted CL316243-stimulated metabolic rate, accompanied by upregulation of thermogenic genes (Ppargc1a, Pparg, Ucp1). In contrast, long-term treatment exacerbated obesity, decreased metabolic rate and rectal temperature, and suppressed thermogenic gene expression. Microbiota analysis revealed partial recovery of α-diversity after short-term intervention, whereas long-term treatment led to persistent dysbiosis with reduced diversity and altered community structure.ConclusionThe metabolic consequences of antibiotic-induced microbiota disruption are strongly duration-dependent. Transient perturbation is associated with enhanced adipose thermogenesis and energy expenditure, whereas prolonged disruption correlates with impaired thermogenic capacity and worsened metabolic outcomes. However, causal relationships remain to be established. These findings highlight the importance of temporal dynamics in host–microbiota interactions and provide insight into microbiota-targeted strategies for metabolic disorders.