Gut Microbiome Composition is Independent of Class 1 Integron Presence in Antibiotic-naive Wild Koalas (Phascolarctos cinereus)

Abstract

Antimicrobial resistance (AMR) in wildlife is a One Health concern, yet research has largely focused on anthropogenic contexts and animal species in close contact with humans. How AMR carriage affects wildlife hosts themselves remains poorly understood. The class 1 integron is a clinically important, anthropogenically associated genetic element that captures and disseminates antibiotic resistance genes primarily among Gram-negative bacteria. As the gut microbiome is a key reservoir for antibiotic resistance genes, the relationship between antibiotic resistance carriage and microbiome composition is an important dimension for understanding the integration, persistence, and evolution of antibiotic resistance in bacteria. This study investigated whether carriage of class 1 integrons was associated with gut microbiome composition in wild koalas. Koala faecal samples ( n  = 62) from Belair National Park, South Australia, categorised by presence and absence of class 1 integrons ( intI1 gene), underwent 16S rRNA gene amplicon sequencing. Findings revealed no significant differences in alpha or beta diversity between integron-positive and integron-negative groups. Non-metric multidimensional scaling indicated no association between community composition and integron carriage. Differential abundance analysis revealed no significantly different taxa between groups. These results indicate that class 1 integron presence alone is not related to significant gut microbiome changes in this antibiotic-naïve koala population. These findings contribute to understanding how antibiotic resistance carriage relates to gut microbiome composition in wildlife not exposed to antibiotic selection pressure.