A global data set of the microbial community in ticks from a metagenomic study

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data collection

The study was conducted in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) statement20. To obtain a comprehensive review of the published literature on microbiome diversity by NGS in field-collected ticks, a literature search was performed in Chinese and English databases using a range of terms and Boolean operators, mainly via PubMed, Web of Science (WOS). , China National Knowledge Infrastructure (CNKI) and the WanFang databases by April 1, 2022, without language or publication restrictions. In the first step, general search terms such as “tick”, “amblyoma“, “Archaeocroton“, “Bothriocrotone“, “dermacentor“, “hemaphysis“, “Hyaloma“, “Ixodes“, “nosomma“, “Rhipicephalus“, “Ripicentor“, “Robertsicus“, “antricola“, “Argas“, “Carious“, “Nothoaspis“, “Ornithodorus‘, ‘next-generation sequencing’, ‘high-throughput sequencing’, ‘deep sequencing’, ‘Roche 454’, ‘Illumina’, ‘Ion Torrent’, ‘SOLiD’ in English-language literature databases and using the key words (‘tick’, “virome”, “microbiome”, “metagenome”, “high throughput sequencing”, “deep sequencing”, “next generation sequencing”) were used when searching Chinese literature databases. Data on all types of microorganisms including viruses, bacteria and eukaryotes were included. Emerging pathogens were defined as those that were first isolated or discovered after 1980. Ticks can feed on a variety of vertebrates. To highlight the presence of pathogens unique to ticks, we chose to include data obtained from freely collected live ticks, but do not include data from detached ticks, as the latter could represent a complex microbiome shared by both ticks and ticks derived from animal hosts. We excluded the following studies: (i) data obtained from experimentally fed ticks or detached ticks collected from animals; (ii) studies evaluating methods or isolation and propagation of laboratory strains; (iii) review and (iv) studies that tested the specific microorganism only in ticks (Fig. 1a).

Fig. 1

Schematic representation of the literature search. (a) Flow chart of the literature research and screening process; (b) Annual number of literature recording field-collected ticks; (c) Number of references grouped by sequencing platform used. In one literature, the microbiome was assessed using both Roche 454 and Illumina-based metagenomic approaches.

A total of 2797 screening studies were retrieved, 2070 from the English database and 727 from the Chinese database. The title and abstract of the retrieved studies were independently screened by three reviewers (MC L, JTZ, and YZ) to identify studies that were potentially eligible for inclusion, narrowing down to 362 studies. For the third step, the full texts of the remaining studies were retrieved and independently checked for suitability 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 was published in 2011, and the number of publications increased over the years, with a notable increase from 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 are from 46 tick species in 7 genera collected from 24 countries on 6 continents and the geographic distribution of tick genera is shown in Fig. 2a. Viral metagenomic profiling, eukaryotic and bacterial microbiome profiling corresponding to different genera of ticks was displayed across countries (Fig. 2b,c).

Fig. 2
figure 2

The geographic distribution of the tick genus is related to provincial-level microbiome data. (a) viruses, bacteria and eukaryotes; (b) viruses; (c) bacteria and eukaryotes.

The full text of all selected papers was reviewed and the data was extracted into a standardized data set in Microsoft Excel 2019, mainly covering: (i) identification of tested ticks at family, genus and species level, (ii) methods for tick species identification, (iii) life cycle stages of tested ticks, (iv) geographic location of ticks at state and provincial level, (v) taxonomic annotations of microorganisms at family, genus and species level, (vi) platforms used NGS. A recheck by two people (MC L and JT Z) was performed to correct errors and remove duplicates. All disagreements and uncertainties were discussed with a third assessor (JJ C) and resolved amicably. The main variable of interest was the viral/bacterial/eukaryotic component of the microbiome, determined for specific tick species at a specific locus over time. All data were entered into the result by trained co-authors.

geopositioning

Provincial-level tick collection site location information was extracted from the selected literatures. Where no longitude or latitude data was reported or the location information was only given at large scale, e.g. B. a scenic area, a mountainous region, the ArcGIS 10.7 software was used to extract the geographic coordinates of the centers of the corresponding administrative areas from the digital map obtained from GADM (Database of Global Administrative Areas) and Standard Map Service System. If the collection site could not be determined in any of these ways, 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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