Objective To investigate the microbiota of the dominant tick species Rhipicephalus microplus in the minority autonomous prefectures of Guizhou province, China, and to provide a scientific basis for the prevention and control of tick-borne disease.Methods Rh. microplus ticks were collected from the body surface of cattle and sheep at 18 sampling sites located in Qiandongnan Miao and Dong Autonomous Prefecture, Qiannan Buyi and Miao Autonomous Prefecture, and Qianxinan Buyi and Miao Autonomous Prefecture in April and July of 2019 and 2020. The ticks were grouped by region, growth stage, and sex, with three parallel samples in each group, followed by metagenomic sequencing. The sequencing results were processed with quality control and assembly procedures before homology alignment with the non-redundant protein database of National Center for Biotechnology Information to obtain taxonomic annotation information. R (v. 3.6.3) and GraPhlAn (v. 1.1.3) were used for visual analysis, including species composition analysis, non-metric multidimensional scaling (NMDS) analysis, and analysis of similarities (ANOSIM).Results The dominant bacterial phylum for Rh. microplus was Firmicutes (60.70%), followed by Proteobacteria (33.76%) and Actinobacteria (4.53%). Staphylococcus aureus (38.29%) was the dominant bacterial species, followed by Klebsiella pneumoniae (7.79%) and Streptococcus pneumoniae (5.26%). Several tick-borne pathogens were detected, including various genotypes of spotted fever group Rickettsia and Anaplasma phagocytophilum (1.38%). R. fournieri (2.91%) was an emerging rickettsiae detected from ticks for the first time in China, and R. japonica (1.76%) and R. monacensis (0.04%) were common tick-borne Rickettsia genotypes in China. R. fournieri and R. japonica were mainly carried by male ticks. The NMDS analysis showed that the microbiota composition of Rh. microplus differed by growth stage and sex. The ANOSIM analysis indicated reasonable grouping, with greater intergroup differences than intragroup differences (R=0.147, P=0.014).Conclusions In the minority autonomous prefectures of Guizhou province, Rh. microplus ticks have a diverse microbiota composition, carrying pathogens that may cause spotted fever and human granulocytic anaplasmosis. Therefore, vector surveillance and pathogen detection should be strengthened, and effective control measures should be taken to reduce the risk of tick-borne diseases.
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