Environmental and host-associated determinants of microbiome variation in the brown dog tick Rhipicephalus linnaei in Thailand

Abstract Background The brown dog tick, Rhipicephalus linnaei , is an important vector of veterinary and zoonotic pathogens worldwide. The composition of the tick-associated microbiome may influence tick physiology, adaptation, and vector competence; however, factors shaping the microbiome of R. linnaei in Southeast Asia remain poorly understood. Methods A total of 131 R. linnaei ticks were collected from dogs across five provinces in Thailand, representing different geographical and ecological settings. Full-length bacterial 16S rRNA sequencing was performed using Oxford Nanopore Technology to characterise bacterial community composition. Microbiome diversity and structure were evaluated by geographical region, sampling area (urban versus rural), blood-feeding status, tick sex, and developmental stage using alpha diversity metrics, Bray–Curtis dissimilarities, principal coordinates analysis, PERMANOVA, and ANCOM-BC2 differential abundance analysis. Results The microbiome of R. linnaei was dominated by Candidatus Coxiella mudrowiae, which was detected in all ticks. Significant differences in bacterial community composition were observed between geographical regions, sampling areas, and blood-feeding status. Urban ticks showed lower bacterial diversity than rural ticks, and engorged ticks showed altered microbial diversity compared with feeding ticks. Sex- and developmental stage-associated differences were less pronounced. Differential abundance analysis identified several bacterial taxa associated with ecological and host-related factors. Putative tick-associated bacterial taxa, including Anaplasma and Ehrlichia species, were identified at low frequency. Conclusions This study demonstrates that geography, habitat type, and blood-feeding status are associated with variation in the microbiome of R. linnaei in Thailand. The findings provide new insights into the ecological factors shaping tick-associated bacterial communities in Southeast Asia and highlight the utility of full-length 16S rRNA Nanopore sequencing for vector microbiome investigations.