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The aim of this study is to screen the important tick-borne pathogens (TBPs) carried by hard ticks in Inner Mongolia using metagenomic next-generation sequencing (mNGS) and to estimate the risk of human infection imposed by tick bites.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>The adult <jats:italic>Dermacentor nuttalli<\/jats:italic> (<jats:italic>n<\/jats:italic>\u2009=\u2009203) and <jats:italic>Ixodes persulcatus<\/jats:italic> (<jats:italic>n<\/jats:italic>\u2009=\u200936) ticks feeding on cattle were collected. The pooled DNA samples prepared from these ticks were sequenced as the templates for mNGS to survey the presence of TBPs at the genus level. Individual tick DNA samples were detected by genus--specific or group-specific nested polymerase chain reaction (PCR) of these TBPs and combined with DNA sequencing assay to confirm the results of mNGS.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p><jats:italic>R. raoultii<\/jats:italic> (45.32%, 92\/203), <jats:italic>Candidatus R. tarasevichiae<\/jats:italic> (5.42%, 11\/203), <jats:italic>Anaplasma<\/jats:italic> sp. Mongolia (26.60%, 54\/203), <jats:italic>Coxiella-<\/jats:italic>like endosymbiont (CLE) (53.69%, 109\/203), and <jats:italic>Babesia venatorum<\/jats:italic> (7.88%, 16\/203) were detected in <jats:italic>D. nuttalli<\/jats:italic>, while <jats:italic>R. raoultii<\/jats:italic> (30.56%, 11\/36), <jats:italic>Anaplasma<\/jats:italic> sp. Mongolia (27.80%, 10\/36), and CLE (27.80%, 10\/36) were detected in <jats:italic>I. persulcatus<\/jats:italic>. The double- and triple-pathogen\/endosymbiont co-infections were detected in 40.39% of <jats:italic>D. nuttalli<\/jats:italic> and 13.89% of <jats:italic>I. persulcatus<\/jats:italic>, respectively. The dual co-infection with <jats:italic>R. raoultii<\/jats:italic> and CLE (14.29%, 29\/203) and triple co-infection with <jats:italic>R. raoultii<\/jats:italic>, <jats:italic>Anaplasma<\/jats:italic> sp. Mongolia, and CLE (13.79%, 28\/203) were most frequent in <jats:italic>D. nuttalli<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study provides insight into the microbial diversity of <jats:italic>D. nuttalli<\/jats:italic> and <jats:italic>I. persulcatus<\/jats:italic> in Inner Mongolia, China, reporting for the first time that <jats:italic>Candidatus R. tarasevichiae<\/jats:italic> had been found in <jats:italic>D. nuttalli<\/jats:italic> in China, and for the first time in the world that <jats:italic>Anaplasma<\/jats:italic> sp. Mongolia has been detected in <jats:italic>I. persulcatus<\/jats:italic>. This study proves that various vertically transmitted pathogens co-inhabit <jats:italic>D. nuttalli<\/jats:italic> and <jats:italic>I. persulcatus<\/jats:italic>, and indicates that cattle in Inner Mongolia are exposed to several TBPs.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-021-04740-3","type":"journal-article","created":{"date-parts":[[2021,5,27]],"date-time":"2021-05-27T19:02:52Z","timestamp":1622142172000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Identification of tick-borne pathogens by metagenomic next-generation sequencing in Dermacentor nuttalli and Ixodes persulcatus in Inner Mongolia, China"],"prefix":"10.1186","volume":"14","author":[{"given":"Jun","family":"Jiao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyu","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonghui","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangxuan","family":"Ou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengjiao","family":"Fu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuee","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nier","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingliang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bohai","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongsheng","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghong","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaolu","family":"Xiong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,27]]},"reference":[{"issue":"1","key":"4740_CR1","doi-asserted-by":"publisher","first-page":"e2566","DOI":"10.1371\/journal.pntd.0002566","volume":"8","author":"XY Liu","year":"2014","unstructured":"Liu XY, Bonnet SI. 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