title: A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks.
abstract: Ticks transmit a variety of viral, bacterial and protozoal pathogens, which are often zoonotic. The aim of this study was to identify diverse tick microbiomes, which may contain as-yet unidentified pathogens, using a metagenomic approach. DNA prepared from bacteria/archaea-enriched fractions obtained from seven tick species, namely Amblyomma testudinarium, Amblyomma variegatum, Haemaphysalis formosensis, Haemaphysalis longicornis, Ixodes ovatus, Ixodes persulcatus and Ixodes ricinus, was subjected to pyrosequencing after whole-genome amplification. The resulting sequence reads were phylotyped using a Batch Learning Self-Organizing Map (BLSOM) program, which allowed phylogenetic estimation based on similarity of oligonucleotide frequencies, and functional annotation by BLASTX similarity searches. In addition to bacteria previously associated with human/animal diseases, such as Anaplasma, Bartonella, Borrelia, Ehrlichia, Francisella and Rickettsia, BLSOM analysis detected microorganisms belonging to the phylum Chlamydiae in some tick species. This was confirmed by pan-Chlamydia PCR and sequencing analysis. Gene sequences associated with bacterial pathogenesis were also identified, some of which were suspected to originate from horizontal gene transfer. These efforts to construct a database of tick microbes may lead to the ability to predict emerging tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding tick biology, including vector competency and interactions with pathogens and symbionts.
authors.affiliation: Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Nakao
authors.forename: Takashi
authors.initials: T
authors.lastname: Abe
authors.forename: Ard M
authors.initials: AM
authors.lastname: Nijhof
authors.forename: Seigo
authors.initials: S
authors.lastname: Yamamoto
authors.forename: Frans
authors.initials: F
authors.lastname: Jongejan
authors.forename: Toshimichi
authors.initials: T
authors.lastname: Ikemura
authors.forename: Chihiro
authors.initials: C
authors.lastname: Sugimoto
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D056890:Eukaryota / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota; D010802:Phylogeny; D017282:Tick-Borne Diseases / Q000382:microbiology / Q000469:parasitology / Q000821:virology; D013987:Ticks / Q000145:classification / Q000382:microbiology* / Q000469:parasitology* / Q000821:virology; D014780:Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification