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Background  Ticks participate as arthropod vectors in the transmission of pathogenic microorganisms to humans. Several tick-borne infections have reemerged, along with newly described agents of unexplored pathogenicity. In an attempt to expand current information on tick-associated bacteria and protozoans, we performed a cross-sectional screening of ticks, using next-generation sequencing. Ticks seeking hosts and infesting domestic animals were collected in four provinces across the Aegean, Mediterranean and Central Anatolia regions of Turkey and analyzed by commonly used procedures and platforms.    Results  Two hundred and eighty ticks comprising 10 species were evaluated in 40 pools. Contigs from tick-associated microorganisms were detected in 22 (55%) questing and 4 feeding (10%) tick pools, with multiple microorganisms identified in 12 pools.  Rickettsia 16S  ribosomal RNA gene,  gltA ,  sca1  and  ompA  sequences were present in 7 pools (17.5%), comprising feeding  Haemaphysalis parva  and questing/hunting  Rhipicephalus bursa ,  Rhipicephalus sanguineus  ( sensu lato ) and  Hyalomma marginatum  specimens. A near-complete genome and conjugative plasmid of a  Rickettsia hoogstraalii  strain could be characterized in questing  Ha. parva .  Coxiella -like endosymbionts were identified in pools of questing (12/40) as well as feeding (4/40) ticks of the genera  Rhipicephalus ,  Haemaphysalis  and  Hyalomma .  Francisella -like endosymbionts were also detected in 22.5% (9/40) of the pools that comprise hunting  Hyalomma  ticks in 8 pools.  Coxiella -like and  Francisella -like endosymbionts formed phylogenetically distinct clusters associated with their tick hosts.  Borrelia turcica  was characterized in 5% (2/40) of the pools, comprising hunting  Hyalomma aegyptium  ticks. Co-infection of  Coxiella -like endosymbiont and  Babesia  was noted in a questing  R. sanguineus  ( s.l. ) specimen. Furthermore, protozoan  18S  rRNA gene sequences were detected in 4 pools of questing/hunting ticks (10%) and identified as  Babesia ovis ,  Hemolivia mauritanica ,  Babesia  and  Theileria  spp.    Conclusions  Our metagenomic approach enabled identification of diverse pathogenic and non-pathogenic microorganisms in questing and feeding ticks in Anatolia.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-3277-7) contains supplementary material, which is available to authorized users.

parasites and vectors

A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia