Abstract
Ticks can transmit numerous pathogens and harbor diverse microbial communities. Considerable progress has been made in the characterization of the bacterial profiles of ticks, whereas other members of tick microbiota (such as fungi and viruses) and the functional characteristics of ticks warrant further exploration. To investigate the taxonomic and functional profiles and explore potential pathogens they were carrying, samples of different developmental stages and of both sexes of Haemaphysalis longicornis were collected in the present study and the metagenomic deep sequencing method was applied. Metagenomic deep sequencing results revealed that bacteria were predominant, followed by fungi, viruses, archaea and metazoans. Proteobacteria was the dominant phylum in the microbiota of H. longicornis. The abundance of microbial species varied significantly among groups, the bacteria of nymphs and female adults demonstrated unique characteristics, and the microbial community of males overlapped with those of nymphs and females. Functional annotation results demonstrated that the metagenomic sequences of the three groups were classified under metabolism, genetic information processing, environmental information processing and cellular processes. Differences in functional characteristics were observed in both the pathways composition and abundance of carbohydrate-active enzymes. Furthermore, whole metagenome sequencing helped to elucidate the diversity of pathogens carried by H. longicornis, which may facilitate further research attempting to prevent and control tick-borne diseases.
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Data availability
All metagenomics datasets were deposited in NCBI Sequence Read Archive (SRA) database with accession number: PRJNA659144.
References
Abraham NM, Liu L, Jutras BL, Yadav AK, Narasimhan S, Gopalakrishnan V, Ansari JM, Jefferson KK, Cava F, Jacobs-Wagner C, Fikrig E (2017) Pathogen-mediated manipulation of arthropod microbiota to promote infection. Proc Nat Acad Sci USA 114:E781–E90. https://doi.org/10.1073/pnas.1613422114
Bicalho MLS, Machado VS, Higgins CH, Lima FS, Bicalho RC (2017) Genetic and functional analysis of the bovine uterine microbiota. Part I: metritis versus healthy cows. J Dairy Sci 100:3850–3862
Bonnet SI, Binetruy F, Hernández-Jarguín AM, Duron O (2017) The tick microbiome: why non-pathogenic microorganisms matter in tick biology and pathogen transmission. Front Cell Infect Microbiol 7:236. https://doi.org/10.3389/fcimb.2017.00236
Brinkmann A, Dinçer E, Polat C, Hekimoğlu O, Hacıoğlu S, Földes K, Özkul A, ÖktemİMA Nitsche A, Ergünay K (2018) A metagenomic survey identifies Tamdy orthonairovirus as well as divergent phlebo-, rhabdo-, chu- and flavi-like viruses in Anatolia, Turkey. Ticks Tick Borne Dis 9(5):1173–1183. https://doi.org/10.1016/j.ttbdis.2018.04.017
Chen Z, Liu Q, Liu JQ, Xu BL, Lv S, Xia S, Zhou XN (2014) Tick-borne pathogens and associated co-infections in ticks collected from domestic animals in central China. Parasit Vectors 7:237–244. https://doi.org/10.1186/1756-3305-7-237
Chen L, Zheng D, Liu B, Yang J, Jin Q (2016) VFDB 2016: hierarchical and refined dataset for big data analysis−10 years on. Nucleic Acids Res 44:D694–D697. https://doi.org/10.1093/nar/gkv1239
Clay K, Klyachko O, Grindle N, Civitello D, Oleske D, Fuqua C (2008) Microbial communities and interactions in the lone star tick, Amblyomma americanum. Mol Ecol 17:4371–4381. https://doi.org/10.1111/j.1365-294x.2008.03914.x
de la Fuente J, Estrada-Pena A, Venzal JM, Kocan KM, Sonenshine DE (2008) Overview: ticks as vectors of pathogens that cause disease in humans and animals. Front Biosci 13:6938–6946. https://doi.org/10.2741/3200
de la Fuente J, Antunes S, Bonnet S, Cabezas-Cruz A, Domingos AG, Estrada-Peña A, Johnson N, Kocan KM, Mansfield KL, Nijhof AM, Papa A, Rudenko N, Villar M, Alberdi P, Torina A, Ayllón N, Vancova M, Golovchenko M, Grubhoffer L, Caracappa S, Fooks AR, Gortazar C, Rego ROM (2017) Tick-Pathogen interactions and vector competence: identification of molecular drivers for Tick-Borne diseases. Front Cell Infect Microbiol 7:114. https://doi.org/10.3389/fcimb.2017.00114
Denic S, Janbeih J, Nair S, Conca W, Tariq WU, Al-Salam S (2011) Acute thrombocytopenia, leucopenia, and multiorgan dysfunction: the first case of SFTS bunyavirus outside China? Case Rep Infect Dis 2011:204056. https://doi.org/10.1155/2011/204056
Dillon RJ, Dillon VM (2004) The gut bacteria of insects: nonpathogenic interactions. Annu Rev Entomol 49:71–92. https://doi.org/10.1146/annurev.ento.49.061802.123416
Dong Y, Manfredini F, Dimopoulos G (2009) Implication of the mosquito midgut microbiota in the defense against malaria parasites. PLoS Pathog 5:e1000423. https://doi.org/10.1371/journal.ppat.1000423
Engel P, Moran NA (2013) The gut microbiota of insects - diversity in structure and function. FEMS Microbiol Rev 37:699–735. https://doi.org/10.1111/1574-6976.12025
Gall CA, Reif KE, Scoles GA, Mason KL, Mousel M, Noh SM, Brayton KA (2016) The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility. ISME J 10:1846–55. https://doi.org/10.1038/ismej.2015.266
Gray JS, Dautel H, Estrada-Pena A, Kahl O, Lindgren E (2009) Effects of climate change on ticks and tick-borne diseases in europe. Interdiscip Perspect Infect Dis 2009:593232. https://doi.org/10.1155/2009/593232
Guan G, Moreau E, Liu J, Hao X, Ma M, Luo J, Chauvin A, Yin H (2010) Babesia sp. BQ1 (Lintan): molecular evidence of experimental transmission to sheep by Haemaphysalis qinghaiensis and Haemaphysalis longicornis. Parasitol Int 59:265–267
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JHF, Nelson DR, Unger MF, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA (2016) Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun 7:10507. https://doi.org/10.1038/ncomms10507
Hoogstraal H, Roberts FH, Kohls GM, Tipton VJ (1968) Review of Haemaphysalis (Kaiseriana) longicornis, Neumann (Resurrected) of Australia, New Zealand, New Caledonia, Fiji, Japan, Korea, and northeastern China and U.S.S.R. and its parthenogenetic and bisexual populations (Ixodoidea, Ixodidae). J Parasitol 54:1197–1213
Hughes GL, Dodson BL, Johnson RM, Murdock CC, Tsujimoto H, Suzuki Y, Patt AA, Cui L, Nossa CW, Barry RM, Sakamoto JM, Hornett EA, Rasgon JL (2014) Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes. Proc Natl Acad Sci U S A 111:12498–503. https://doi.org/10.1073/pnas.1408888111
Hunter DJ, Torkelson JL, Bodnar J, Mortazavi B, Laurent T, Deason J, Thephavongsa K, Zhong J (2015) The Rickettsia endosymbiont of Ixodes pacificus contains all the genes of de novo folate biosynthesis. PLoS One 10:e0144552. https://doi.org/10.1371/journal.pone.0144552
Jongejan F, Uilenberg G (2004) The global importance of ticks. Parasitology 129(Suppl):S3-14. https://doi.org/10.1017/s0031182004005967
Kaushal G, Kumar J, Sangwan RS, Singh SP (2018) Metagenomic analysis of geothermal water reservoir sites exploring carbohydrate-related thermozymes. Int J Biol Macromol 119:882–895. https://doi.org/10.1016/j.ijbiomac.2018.07.196
Ko SJ, Kang JG, Kim SY, Kim HC, Klein TA, Chong ST, Sames WJ, Yun SM, Ju YR, Chae JS (2010) Prevalence of tick-borne encephalitis virus in ticks from southern Korea. J Vet Med Sci 11:197–203. https://doi.org/10.4142/jvs.2010.11.3.197
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923
Lee MJ, Chae JS (2010) Molecular detection of Ehrlichia chaffeensis and Anaplasma bovis in the salivary glands from Haemaphysalis longicornis ticks. Vector Borne Zoonotic Dis 10:411–413. https://doi.org/10.1089/vbz.2008.0215
Lee JH, Park HS, Jung KD, Jang WJ, Koh SE, Kang SS, Lee IY, Lee WJ, Kim BJ, Kook YH, Park KH, Lee SH (2003) Identification of the spotted fever group rickettsiae detected from Haemaphysalis longicornis ticks in Korea. Microbiol Immunol 47:301–304
Lee JH, Park HS, Jang WJ, Koh SE, Park TK, Kang SS, Kim BJ, Kook YH, Park KH, Lee SH (2004) Identification of the Coxiella sp. detected from Haemaphysalis longicornis ticks in Korea. Microbiol Immunol 48:125–130
Li W, Godzik A (2006) Cd-Hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659. https://doi.org/10.1093/bioinformatics/btl158
Li D, Liu CM, Luo R, Sadakane K, Lam TW (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676. https://doi.org/10.1093/bioinformatics/btv033
Liu LM, Liu JN, Liu Z, Yu ZJ, Xu SQ, Yang XH, Li T, Li SS, Guo LD, Liu JZ (2013) Microbial communities and symbionts in the hard tick Haemaphysalis longicornis (Acari: Ixodidae) from north China. Parasit Vectors 6(1):310. https://doi.org/10.1186/1756-3305-6-310
Lockwood S, Brayton KA, Broschat SL (2016) Comparative genomics reveals multiple pathways to mutualism for tick-borne pathogens. BMC Genomics 17:481. https://doi.org/10.1186/s12864-016-2744-9
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495. https://doi.org/10.1093/nar/gkt1178
Lu BL, Wu HY (2003) Classification and Identification of Important Medical Insects of China. Henan Science and technology publishing House, pp. 661–665 (in Chinese).
Luo LM, Sun JM, Yan JB, Wang CW, Zhang ZT, Zhao L, Han HJ, Tong ZD, Liu MM, Wu YY, Wen HL, Zhang R, Xue ZF, Sun XF, Li KF, Ma DQ, Liu JW, Huang YT, Ye L, Li WQ, Jiang JM, Yu XJ (2016) Detection of a novel Ehrlichia species in Haemaphysalis longicornis tick from China. Vector-Borne Zoonotic Dis 16:363–367. https://doi.org/10.1089/vbz.2015.1898
McMullan LK, Folk SM, Kelly AJ, MacNeil A, Goldsmith CS, Metcalfe MG, Batten BC, Albariño CG, Zaki SR, Rollin PE, Nicholson WL, Nichol ST (2012) A new phlebovirus associated with severe febrile illness in Missouri. New Engl J Med 367(9):834–841. https://doi.org/10.1056/NEJMoa1203378
Narasimhan S, Fikrig E (2015) Tick microbiome: the force within. Trends Parasitol 31:315–23. https://doi.org/10.1016/j.pt.2015.03.010
Narasimhan S, Rajeevan N, Liu L, Zhao YO, Heisig J, Pan J, Eppler-Epstein R, Deponte K, Fish D, Fikrig E (2014) Gut microbiota of the tick vector Ixodes scapularis modulate colonization of the Lyme disease spirochete. Cell Host Microbe 15:58–71. https://doi.org/10.1016/j.chom.2013.12.001
Obregón D, Bard E, Abrial D, Estrada-Peña A, Cabezas-Cruz A (2019) Sex-specific linkages between taxonomic and functional profiles of tick gut microbiomes. Front Cell Infect Microbiol 9:298. https://doi.org/10.3389/fcimb.2019.00298
Pimentel V, Afonso R, Nunes M, Vieira ML, Bravo-Barriga D, Frontera E, Martinez M, Pereira A, Maia C, Paiva-Cardoso MDN, Freitas FB, Abecasis AB, Parreira R (2019) Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences. Ticks Tick Borne Dis 10(4):942–948. https://doi.org/10.1016/j.ttbdis.2019.05.001
Salvetti E, Campanaro S, Campedelli I, Fracchetti F, Gobbi A, Tornielli GB, Torriani S, Felis GE (2016) Whole-metagenome-sequencing-based community profiles of Vitisvinifera L cv Corvina berries withered in two post-harvest conditions. Front Microbiol 7:937. https://doi.org/10.3389/fmicb.2016.00937
Smith TA, Driscoll T, Gillespie JJ, Raghavan R (2015) A Coxiella-like endosymbiont is a potential vitamin source for the Lone Star tick. Genome Biol Evol 7:831–838. https://doi.org/10.1093/gbe/evv016
Stark K, Niedrig M, Biederbick W, Merkert H, Hacker J (2009) Climate changes and emerging diseases. What new infectious diseases and health problem can be expected? Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 52:699–714. https://doi.org/10.1007/s00103-009-0874-9
Sun J, Liu Q, Lu L, Ding G, Guo J, Fu G, Zhang J, Meng F, Wu H, Song X, Ren D, Li D, Guo Y, Wang J, Li G, Liu J, Lin H (2008) Coinfection with four genera of bacteria (Borrelia, Bartonella, Anaplasma, and Ehrlichia) in Haemaphysalis longicornis and Ixodes sinensis ticks from China. Vector Borne Zoonotic Dis 8:791–795
Swei A, Kwan JY (2017) Tick microbiome and pathogen acquisition altered by host blood meal. ISME J 11:813–816. https://doi.org/10.1038/ismej.2016.152
Takahashi T, Maeda K, Suzuki T, Ishido A, Shigeoka T, Tominaga T, Kamei T, Honda M, Ninomiya D, Sakai T, Senba T, Kaneyuki S, Sakaguchi S, Satoh A, Hosokawa T, Kawabe Y, Kurihara S, Izumikawa K, Kohno S, Azuma T, Suemori K, Yasukawa M, Mizutani T, Omatsu T, Katayama Y, Miyahara M, Ijuin M, Doi K, Okuda M, Umeki K, Saito T, Fukushima K, Nakajima K, Yoshikawa T, Tani H, Fukushi S, Fukuma A, Ogata M, Shimojima M, Nakajima N, Nagata N, Katano H, Fukumoto H, Sato Y, Hasegawa H, Yamagishi T, Oishi K, Kurane I, Morikawa S, Saijo M (2014) The first identification and retrospective study of severe fever with thrombocytopenia syndrome in Japan. J Infect Dis 209(6):816-827. https://doi.org/https://doi.org/10.1093/infdis/jit603
Tenquisf JD, Charleston WAG (2001) A revision of the annotated checklist of ectoparasites of terrestrial mammals in New Zealand. J R Soc N Z 31:481–542
Vayssier-Taussat M, Cosson JF, Degeilh B, Eloit M, Fontanet A, Moutailler S, Raoult D, Sellal E, Ungeheuer MN, Zylbermann P (2015) How a multidisciplinary‘One Health’ approach can combat the tick-borne pathogen threat in Europe. Future Microbiol 10:809–818. https://doi.org/10.2217/fmb.15.15
Wang YH, Mao LH, Peng Y, Sun YW, Wang ZJ, Zhang JY, Zhang JB, Tian J (2016) Francisella tularensis was detected in Haemaphysalis longicornis from Liaoning province. Chin J Vector Biol Control 27:529–532 ((in Chinese))
Wei F, Song M, Liu H, Wang B, Wang S, Wang Z, Ma H, Li Z, Zeng Z, Qian J, Liu Q (2016) Molecular detection and characterization of zoonotic and veterinary pathogens in ticks from Northeastern China. Front Microbiol 7:1913. https://doi.org/10.3389/fmicb.2016.01913
Weiss B, Aksoy S (2011) Microbiome influences on insect host vector competence. Trends Parasitol 27:514–522. https://doi.org/10.1016/j.pt.2011.05.001
Weiss BL, Maltz MA, Vigneron A, Wu Y, Walter KS, O’Neill MB, Wang J, Aksoy S (2019) Colonization of the tsetse fly midgut with commensal Kosakonia cowanii Zambiae inhibits trypanosome infection establishment. PLoS Pathog 15:e1007470. https://doi.org/10.1371/journal.ppat.1007470
Yu XJ, Liang MF, Zhang SY, Liu Y, Li JD, Sun YL, Zhang L, Zhang QF, Popov VL, Li C, Qu J, Li Q, Zhang YP, Hai R, Wu W, Wang Q, Zhan FX, Wang XJ, Kan B, Wang SW, Wan KL, Jing HQ, Lu JX, Yin WW, Zhou H, Guan XH, Liu JF, Bi ZQ, Liu GH, Ren J, Wang H, Zhao Z, Song JD, He JR, Wan T, Zhang JS, Fu XP, Sun LN, Dong XP, Feng ZJ, Yang WZ, Hong T, Zhang Y, Walker DH, Wang Y, Li DX (2011) Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med 364:1523–1532. https://doi.org/10.1056/NEJMoa1010095
Zhang XC, Yang ZN, Lu B, Ma XF (2014) The composition and transmission of microbiome in hard tick, Ixodes persulcatus, during blood meal. Ticks Tick Borne Dis 5:864–870. https://doi.org/10.1016/j.ttbdis.2014.07.009
Zhang RL, Huang ZD, Yu GF, Zhang Z (2019) Characterization of the bacterial community in Haemaphysalis longicornis (Acari: Ixodidae) throughout developmental stages. Exp Appl Acarol 77(2):173–186. https://doi.org/10.1007/s10493-019-00339-7
Zhong J, Jasinskas A, Barbour AG (2007) Antibiotic treatment of the tick vector Amblyomma americanum reduced reproductive fitness. PLoS One 2:e405. https://doi.org/10.1371/journal.pone.0000405
Zolnik CP, Prill RJ, Falco RC, Daniels TJ (2016) Microbiome changes through ontogeny of a tick pathogen vector. Mol Ecol 25:4963–4977. https://doi.org/10.1111/mec.13832
Zou Y, Jin H, Wang Q, Fu Z, Gao H, Liu P, Liu Q, Chen L (2011) Molecular detection of Anaplasma phagocytophilum in Ixodid ticks in Hebei Province, China. Vector Borne Zoonotic Dis 11:1323–1327
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This research was supported by Development Plan Project of Shandong Province Science and Technology (No. 2017GSF221017).
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ZRL and ZZ conceived and designed the experiment. ZQ and YGF performed laboratory work, interpreted results, and compiled tables and figures. ZRL and ZQ wrote the first draft of the manuscript, and YGF and ZZ contributed to finalizing the paper. All authors contributed critically to the drafts and gave final approval for publication.
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Zhang, R., Zhang, Q., Yu, G. et al. Metagenomic deep sequencing obtains taxonomic and functional profiles of Haemaphysalis longicornis that vary in response to different developmental stages and sexes. Exp Appl Acarol 83, 285–300 (2021). https://doi.org/10.1007/s10493-020-00582-3
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DOI: https://doi.org/10.1007/s10493-020-00582-3