Data collection
The study was performed according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement20. To attain an exhaustive review of the published literature on the microbiome diversity by NGS in field-collected ticks, a literature search was conducted on Chinese and English databases using a set of terms and Boolean operators, mainly through PubMed, Web of Science (WOS), China National Knowledge Infrastructure (CNKI) and the WanFang databases up to 1 April 2022, without language or publication-type restrictions. At the first step, general search terms were applied that included: “tick”, “Amblyomma”, “Archaeocroton”, “Bothriocroton”, “Dermacentor”, “Haemaphysalis”, “Hyalomma”, “Ixodes”, “Nosomma”, “Rhipicephalus”, “Rhipicentor”, “Robertsicus”, “Antricola”, “Argas”, “Carios”, “Nothoaspis”, “Ornithodoros”, “next-generation sequencing”, “high-throughput sequencing”, “deep sequencing”, “Roche 454”, “Illumina”, “Ion Torrent”, “SOLiD” in English literature databases search, and the keywords (“tick”, “virome”, “microbiome”, “metagenome”, “high throughput sequencing”, “deep sequencing”, “next generation sequencing”) were used in Chinese literature databases search. Data on all types of microorganisms, including viruses, bacteria, and eukaryotes were included. Emerging pathogens were defined as those first isolated or discovered after 1980. Ticks can feed on a wide range of vertebrates, therefore to highlight the presence of pathogens that were unique to ticks, we chose to include data that were performed on field-collected free-living ticks, while not include data from the detached ticks, since the latter might represent a complex microbiome of both tick and animal host derived. We excluded the following studies: (i) data obtained from experimentally fed ticks or detached ticks collected from animals; (ii) studies on the evaluation of the methods or the isolation and propagation of laboratory strains; (iii) review paper and (iv) studies that only tested the specific microorganism in ticks (Fig. 1a).
Schematic diagram of literature search. (a) Flow diagram on the literature search and screening process; (b) Annual number of literature that recorded field-collected ticks; (c) Number of literature grouped by the sequencing platform used. One literature evaluated the microbiome by using both Roche 454- and Illumina-based metagenomic approaches.
A total of 2797 studies were retrieved for screening, comprised of 2070 from the English database and 727 from the Chinese database. The title and abstract of the retrieved studies were screened independently by three reviewers (MC L, JT Z, and Y Z) to identify studies potentially eligible for inclusion, which was narrowed down to 362 studies. For the third step, the full texts of the remaining studies were retrieved and independently assessed for eligibility by two reviewers (ZY H and BK F). Finally, a total of 7 Chinese and 69 English studies were eligible for data extraction (Fig. 1a). The earliest one was published in 2011, and the number of publications increased over the years, with a remarkable increase starting from the year 2017 (Fig. 1b). Of all selected studies, 69 (90.8%) used the Illumina sequencing platform, and 5.3% used the Ion Torrent sequencing platform (Fig. 1c). Data were from 46 species of ticks in 7 genera collected from 24 countries in 6 continents, and the geographical distribution of tick genera was shown in Fig. 2a. The viral metagenomic profiling, eukaryotic and bacterial microbiome profiling that corresponded to various tick genera were displayed across countries (Fig. 2b,c).
Geographical distribution of tick genus in relate to microbiome data at the province level. (a) Viruses, bacteria and eukaryotes; (b) Viruses; (c) Bacteria and eukaryotes.
Full text of all the selected papers were reviewed, and data were extracted into a standardized dataset in Microsoft Excel 2019 that mainly includes: (i) identification of tested ticks at the family, genus, and species levels, (ii) methods for tick species identification, (iii) life cycle stages of the tested ticks, (iv) the geographic location of the ticks at country and province levels, (v) taxonomic annotations of microorganisms at family, genus, species levels, (vi) the platforms used for NGS. A re-check by two persons (MC L and JT Z) was performed to correct errors and remove duplicates. All conflicts of opinion and uncertainties were discussed and resolved by consensus with a third reviewer (JJ C). The main variable of interest was the viral/bacterial/eukaryotic component of the microbiome, determined for specific tick species at a specific site over time. All data were entered into the resultant by trained coauthors.
Geo-positioning
The location information of the tick-collection site was extracted at the province level from the selected literatures. If no data on longitude or latitude were reported, or the location information was only given at a large scale such as a scenic area, mountainous region, ArcGIS 10.7 software was used to extract the geographical coordinates of the center points of the corresponding administrative areas from the digital map, which were obtained from GADM (Database of Global Administrative Areas) and Standard Map Service System. If the collection site could not be determined by any of these means, the authors were contacted for further information. We used R Studio Version 4.1.2 software and ArcGIS 10.7 software to statistically analyze and visualize the obtained geographic data.
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