Open Access
Issue
Parasite
Volume 31, 2024
Article Number 28
Number of page(s) 11
DOI https://doi.org/10.1051/parasite/2024028
Published online 30 May 2024
  1. Achatz TJ, Martens JR, Kostadinova A, Pulis EE, Orlofske SA, Bell J, Fecchio A, Oyarzún-Ruiz P, Syrota YY, Tkach VV. 2022. Molecular phylogeny of Diplostomum, Tylodelphys, Austrodiplostomum and Paralaria (Digenea: Diplostomidae) necessitates systematic changes and reveals a history of evolutionary host switching events. International Journal for Parasitology, 52(1), 47–63. [Google Scholar]
  2. Allsopp BA, Baylis HA, Allsopp MT, Cavalier-Smith T, Bishop RP, Carrington DM, Sohanpal B, Spooner P. 1993. Discrimination between six species of Theileria using oligonucleotide probes which detect small subunit ribosomal RNA sequences. Parasitology, 107(Pt 2), 157–165. [Google Scholar]
  3. An R, Liu Y, Pan C, Da Z, Zhang P, Qiao N, Zhao F, Ba S. 2023. Water quality determines protist taxonomic and functional group composition in a high-altitude wetland of international importance. Science of the Total Environment, 880, 163308. [Google Scholar]
  4. Bass D, Stentiford GD, Littlewood DTJ, Hartikainen H. 2015. Diverse applications of environmental DNA methods in parasitology. Trends in Parasitology, 31(10), 499–513. [Google Scholar]
  5. Briscoe AG, Nichols S, Hartikainen H, Knipe H, Foster R, Green AJ, Okamura B, Bass D. 2021. High-throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds. Molecular Ecology Resources, 22(4), 1303–1318. [Google Scholar]
  6. Bu XL, Zhao WS, Li WX, Zou H, Wu SG, Li M, Wang GT. 2023. Mitochondrial metabolism of the facultative parasite Chilodonella uncinata (Alveolata, Ciliophora). Parasites & Vectors, 16(1), 92. [Google Scholar]
  7. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583. [Google Scholar]
  8. Cannon MV, Bogale H, Rutt L, Humphrys M, Korpe P, Duggal P, Ravel J, Serre D. 2018. A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples. Microbiome, 6(1), 195. [Google Scholar]
  9. Çapar S. 2012. Morphology and morphometry of Bresslauides pratensis n. sp., a new soil ciliate (Ciliophora, Colpodea) from Turkey. European Journal of Protistology, 48(3), 252–260. [Google Scholar]
  10. Carvalho EL, Santana RLS, Pinheiro R, Giese EG. 2019. Eucoleus contortus (Nematoda: Capillariidae), a parasite of Cairina moschata domestica (Anseriformes: Anatidae) on Marajó Island, Pará State, in Brazilian Amazon. Revista Brasileira de Parasitologia Veterinaria, 28(4), 692–699. [Google Scholar]
  11. Chai JY, Jung BK. 2020. Foodborne intestinal flukes: A brief review of epidemiology and geographical distribution. Acta Tropica, 201, 105210. [Google Scholar]
  12. Chapman HD, Rathinam T. 2022. Focused review: The role of drug combinations for the control of coccidiosis in commercially reared chickens. International Journal for Parasitology – Drugs and Drug Resistance, 18, 32–42. [Google Scholar]
  13. Chaúque BJM, Dos Santos DL, Anvari D, Rott MB. 2022. Prevalence of free-living amoebae in swimming pools and recreational waters, a systematic review and meta-analysis. Parasitology Research, 121(11), 3033–3050. [Google Scholar]
  14. Chen JJ, Pu Z, Huang ZH, Yu FQ, Zhang JJ, Xu DH, Xu JQ, Shang P, Parhati D, Li YJ, Tshering J, Guo YM. 2023. Global distribution and number of overwintering black-necked crane (Grus nigricollis). Biodiversity Science, 31(6), 97–106. [Google Scholar]
  15. Childs-Sanford S, Lejeune M, Abdu A, Buckles E, Renshaw R, Ford D, Bunting E. 2019. Oral capillariosis due to Eucoleus dispar in migrating Sharp-shinned Hawks (Accipiter striatus) in New York, USA, 2016–18. Journal of Wildlife Diseases, 55(4), 928–934. [Google Scholar]
  16. da Silva Costa F, Júnio Pedroso Dias R, Fonseca Rossi M. 2021. Macroevolutionary analyses of ciliates associated with hosts support high diversification rates. International Journal for Parasitology, 51(11), 967–976. [Google Scholar]
  17. Díaz-Rodríguez J, Donaire-Barroso D, Jowers MJ. 2018. First report of Euryhelmis parasites (Trematoda, Heterophyidae) in Africa: conservation implications for endemic amphibians, Parasitology Research, 117(8), 2569–2576. [Google Scholar]
  18. Dixon P. 2003. VEGAN, a package of R functions for community ecology. Journal of Vegetation Science, 14(6), 927–930. [Google Scholar]
  19. Dong HY, Lu GY, Zhong XY, Yang XJ. 2016. Winter diet and food selection of the Black-necked Crane Grus nigricollis in Dashanbao, Yunnan, China. PeerJ, 4, e1968. [Google Scholar]
  20. Feyer S, Bartenschlager F, Bertram CA, Ziegler U, Fast C, Klopfleisch R, Müller K. 2021. Clinical, pathological and virological aspects of fatal West Nile virus infections in ten free-ranging goshawks (Accipiter gentilis) in Germany. Transboundary and Emerging Diseases, 68(2), 907–919. [Google Scholar]
  21. Gogarten JF, Calvignac-Spencer S, Nunn CL, Ulrich M, Saiepour N, Nielsen HV, Deschner T, Fichtel C, Kappeler PM, Knauf S, Müller-Klein N, Ostner J, Robbins MM, Sangmaneedet S, Schülke O, Surbeck M, Wittig RM, Sliwa A, Strube C, Leendertz FH, Roos C, Noll A. 2020. Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny. Molecular Ecology Resources, 20(1), 204–215. [Google Scholar]
  22. Grabensteiner E, Hess M. 2006. PCR for the identification and differentiation of Histomonas meleagridis, Tetratrichomonas gallinarum and Blastocystis spp. Veterinary Parasitology, 142(3–4), 223–230. [Google Scholar]
  23. Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, Del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WH, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(Database issue), D597–D604. [Google Scholar]
  24. Harder CB, Rønn R, Brejnrod A, Bass D, Al-Soud WA, Ekelund F. 2016. Local diversity of heathland Cercozoa explored by in-depth sequencing. ISME Journal, 10(10), 2488–2497. [Google Scholar]
  25. Hawxhurst CJ, Micciulla JL, Bridges CM, Shor M, Gage DJ, Shor LM. 2023. Soil protists can actively redistribute beneficial bacteria along Medicago truncatula roots. Applied Environmental Microbiology, 89(3), e0181922. [Google Scholar]
  26. Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. 2019. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing. Scientific Reports, 9(1), 12783. [Google Scholar]
  27. Honma H, Suyama Y, Watanabe Y, Matsumoto F, Nakai Y. 2011. Accurate analysis of prevalence of coccidiosis in individually identified wild cranes in inhabiting and migrating populations in Japan. Environmental Microbiology, 13(11), 2876–2887. [Google Scholar]
  28. Honma H, Yokoyama T, Inoue M, Uebayashi A, Matsumoto F, Watanabe Y, Nakai Y. 2007. Genetical identification of coccidia in red-crowned crane, Grus japonensis. Parasitology Research, 100(3), 637–640. [Google Scholar]
  29. Hu X, Xu Y, Liu G, Hu D, Wang Y, Zhang W, Zheng Y. 2020. The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon. Applied Microbiology Biotechnology, 104(21), 9239–9250. [Google Scholar]
  30. Huang YX, Wang S, Gao YQ, Chen JH, Wang XL, Li RJ. 2021. Comparison of mitochondrial genome and development of specific PCR primers for identifying two scuticociliates, Pseudocohnilembus persalinus and Uronema marinum. Parasites & Vectors, 14(1), 318. [Google Scholar]
  31. Imanian B, Donaghy J, Jackson T, Gummalla S, Ganesan B, Baker RC, Henderson M, Butler EK, Hong Y, Ring B, Thorp C, Khaksar R, Samadpour M, Lawless KA, MacLaren-Lee I, Carleton HA, Tian R, Zhang W, Wan J. 2022. The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems. NPJ Science of Food, 6(1), 35. [Google Scholar]
  32. Kang HS, Itoh N, Limpanont Y, Lee HM, Whang I, Choi KS. 2019. A novel paramyxean parasite, Marteilia tapetis sp. nov. (Cercozoa) infecting the digestive gland of Manila clam Ruditapes philippinarum from the southeast coast of Korea. Journal of Invertebrate Pathology, 163, 86–93. [Google Scholar]
  33. Kechin A, Boyarskikh U, Kel A, Filipenko M. 2017. cutPrimers: A new tool for accurate cutting of primers from reads of targeted next generation sequencing. Journal of Computational Biology, 24(11), 1138–1143. [Google Scholar]
  34. Kim SL, Choi JH, Yi MH, Lee S, Kim M, Oh S, Lee IY, Jeon BY, Yong TS, Kim JY. 2022. Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius. Parasites & Vectors, 15(1), 486. [Google Scholar]
  35. Kolde R. 2019. pheatmap: pretty heatmaps. R package version 1.0.12. [Google Scholar]
  36. Kong D, Luo W, Liu Q, Li Z, Huan G, Zhang J, Yang X. 2018. Habitat use, preference, and utilization distribution of two crane species (Genus: Grus) in Huize National Nature Reserve, Yunnan-Guizhou Plateau, China. PeerJ, 6, e5105. [Google Scholar]
  37. Kounosu A, Murase K, Yoshida A, Maruyama H, Kikuchi T. 2019. Improved 18S and 28S rDNA primer sets for NGS-based parasite detection. Scientific Reports, 9(1), 15789. [Google Scholar]
  38. Landman WJ, Molenaar RJ, Cian A, van der Heijden HM, Viscogliosi E. 2016. Granuloma disease in flocks of productive layers caused by Tetratrichomonas gallinarum. Avian Pathology, 45(4), 465–477. [Google Scholar]
  39. Landman WJM, Gantois N, van Eck JHH, van der Heijden H, Viscogliosi E. 2019. Tetratrichomonas gallinarum granuloma disease in a flock of free range layers. Veterinary Quarterly, 39(1), 153–160. [Google Scholar]
  40. Li W, Zhao J, Tian H, Shen Y, Wang Y, Shao M, Xiong T, Yao Y, Zhang L, Chen X, Xiao H, Xiong Y, Yang S, Tan C, Xu H. 2023. Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration. Applied Microbiology Biotechnology, 107(14), 4635–4646. [Google Scholar]
  41. Liang Y, Zhao Z, Hu J, Esch GW, Peng M, Liu Q, Chen J. 2018. Prevalence and genetic characterization of eimeriid coccidia from feces of black-necked cranes, Grus nigricollis. Parasitology Research, 117(3), 869–874. [Google Scholar]
  42. Liu W, Jin Y, Wu Y, Zhao C, He X, Wang B, Ran J. 2020. Home range and habitat use of breeding Black-Necked Cranes. Animals, 10(11). [Google Scholar]
  43. Martinez A. 2020. pairwiseAdonis: pairwise multilevel comparison using adonis. R package version 0:4. [Google Scholar]
  44. Matsubayashi M, Takami K, Abe N, Kimata I, Tani H, Sasai K, Baba E. 2005. Molecular characterization of crane Coccidia, Eimeria gruis and E. reichenowi, found in feces of migratory cranes. Parasitology Research, 97(1), 80–83. [Google Scholar]
  45. Mima D, Ci Z, Qiong R. 2012. Investigation of parasitic infections in black-necked cranes in Tibet. Work & Study Abroad, 06, 214. [Google Scholar]
  46. Minardi D, Ryder D, Del Campo J, Garcia Fonseca V, Kerr R, Mortensen S, Pallavicini A, Bass D. 2022. Improved high throughput protocol for targeting eukaryotic symbionts in metazoan and eDNA samples. Molecular Ecology Resources, 22(2), 664–678. [Google Scholar]
  47. Morgan JA, Blair D. 1995. Nuclear rDNA ITS sequence variation in the trematode genus Echinostoma: an aid to establishing relationships within the 37-collar-spine group. Parasitology, 111(Pt 5), 609–615. [Google Scholar]
  48. Morgan JA, Blair D. 1998. Relative merits of nuclear ribosomal internal transcribed spacers and mitochondrial CO1 and ND1 genes for distinguishing among Echinostoma species (Trematoda). Parasitology, 116(Pt 3), 289–297. [Google Scholar]
  49. O’Brien MF, Brown MJ, Stidworthy MF, Peirce MA, Marshall RN, Honma H, Nakai Y. 2011. Disseminated visceral coccidiosis in Eurasian cranes (Grus grus) in the UK. Veterinary Record, 168(8), 216. [Google Scholar]
  50. Otero-Ruiz A, Gonzalez-Zuñiga LD, Rodriguez-Anaya LZ, Lares-Jiménez LF, Gonzalez-Galaviz JR, Lares-Villa F. 2022. Distribution and current state of molecular genetic characterization in pathogenic free-living amoebae. Pathogens, 11(10). [Google Scholar]
  51. Paknejad N, Hajialilo E, Saraei M, Javadi A. 2020. Isolation and identification of Acanthamoeba genotypes and Naegleria spp. from the water samples of public swimming pools in Qazvin, Iran. Journal of Water Health, 18(2), 244–251. [Google Scholar]
  52. Poinar G, Duarte D, Santos MJ. 2010. Halomonhystera parasitica n. sp. (Nematoda: Monhysteridae), a parasite of Talorchestia brito (Crustacea: Talitridae) in Portugal. Systematic Parasitology, 75(1), 53–58. [Google Scholar]
  53. Qian FW, Wu HQ, Gao LB, Zhang HG, Li FS. 2010. Migration routes and stopover sites of Black-necked Cranes determined by satellite tracking. Journal of Field Ornithology, 80(1), 19–26. [Google Scholar]
  54. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(Database issue), D590–D596. [Google Scholar]
  55. R Core Team. 2023. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org. [Google Scholar]
  56. Randag AC, van Rooij J, van Goor AT, Verkerk S, Wisse RPL, Saelens IEY, Stoutenbeek R, van Dooren BTH, Cheng YYY, Eggink CA. 2019. The rising incidence of Acanthamoeba keratitis: A 7-year nationwide survey and clinical assessment of risk factors and functional outcomes. PLoS One, 14(9), e0222092. [Google Scholar]
  57. Ruan Y, Li Y, Xia Y, Yu T, Dai C. 2022. Students’ knowledge of and conservation attitude toward the black-necked crane (Grus nigricollis) in Guizhou, China: Insights for conservation. Journal of Ethnobiology and Ethnomedicine, 18(1), 37. [Google Scholar]
  58. Sah R, Khadka S, Hamal R, Poudyal S. 2018. Human echinostomiasis: a case report BMC Research Notes, 11(1), 17. [Google Scholar]
  59. Sakaguchi S, Yunus M, Sugi S, Sato H. 2020. Integrated taxonomic approaches to seven species of capillariid nematodes (Nematoda: Trichocephalida: Trichinelloidea) in poultry from Japan and Indonesia, with special reference to their 18S rDNA phylogenetic relationships. Parasitology Research, 119(3), 957–972. [Google Scholar]
  60. Samba-Louaka A, Delafont V, Rodier MH, Cateau E, Héchard Y. 2019. Free-living amoebae and squatters in the wild: ecological and molecular features. FEMS microbiology reviews, 43(4), 415–434. [Google Scholar]
  61. Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB. 2020. Perspectives from ten years of protist studies by high-throughput metabarcoding. Journal of Eukaryotic Microbiology, 67(5), 612–622. [CrossRef] [PubMed] [Google Scholar]
  62. Sato H, Ihara S, Inaba O, Une Y. 2010. Identification of Euryhelmis costaricensis metacercariae in the skin of Tohoku hynobiid salamanders (Hynobius lichenatus), northeastern Honshu, Japan. Journal of Wildlife Diseases, 46(3), 832–842. [Google Scholar]
  63. Schroeder JM, Booton GC, Hay J, Niszl IA, Seal DV, Markus MB, Fuerst PA, Byers TJ. 2001. Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge. Journal of Clinical Microbiology, 39(5), 1903–1911. [Google Scholar]
  64. Schuster FL, Visvesvara GS. 2004. Free-living amoebae as opportunistic and non-opportunistic pathogens of humans and animals. International Journal for Parasitology, 34(9), 1001–1027. [Google Scholar]
  65. Sente C, Erume J, Naigaga I, Mulindwa J, Ochwo S, Magambo PK, Namara BG, Kato CD, Sebyatika G, Muwonge K, Ocaido M. 2016. Prevalence of pathogenic free-living amoeba and other protozoa in natural and communal piped tap water from Queen Elizabeth protected area, Uganda. Infectious Diseases of Poverty, 5(1), 68. [Google Scholar]
  66. Tantrawatpan C, Saijuntha W. 2020. Multiplex PCR development for the differential detection of four medically important echinostomes (Trematoda: Echinostomatidae) in Thailand. Acta Tropica, 204, 105304. [Google Scholar]
  67. Tchoumbou MA, Mayi MPA, Malange ENF, Foncha FD, Kowo C, Fru-Cho J, Tchuinkam T, Awah-Ndukum J, Dorazio R, Nota Anong D, Cornel AJ, Sehgal RNM. 2020. Effect of deforestation on prevalence of avian haemosporidian parasites and mosquito abundance in a tropical rainforest of Cameroon. International Journal for Parasitology, 50(1), 63–73. [Google Scholar]
  68. Tedersoo L, Albertsen M, Anslan S, Callahan B. 2021. Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Applied Environmental Microbiology, 87(17), e0062621. [Google Scholar]
  69. Toledo R, Esteban JG. 2016. An update on human echinostomiasis. Transactions of the Royal Society of Tropical Medicine and Hygiene, 110(1), 37–45. [Google Scholar]
  70. Tyml T, Dyková I. 2018. Sappinia sp. (Amoebozoa: Thecamoebida) and Rosculus sp. (SAR: Cercozoa) isolated from King Penguin guano collected in the Subantarctic (South Georgia, Salisbury Plain) and their coexistence in culture. Journal of Eukaryotic Microbiology, 65(4), 544–555. [Google Scholar]
  71. Wang Y, Jiang L, Zhao Y, Ju X, Wang L, Jin L, Fine RD, Li M. 2023. Biological characteristics and pathogenicity of Acanthamoeba. Frontiers in Microbiology, 14, 1147077. [Google Scholar]
  72. Wang Y, Mi C, Guo Y. 2020. Satellite tracking reveals a new migration route of black-necked cranes (Grus nigricollis) in Qinghai-Tibet Plateau. PeerJ, 8, e9715. [Google Scholar]
  73. Watson SE, Hailer F, Lecomte N, Kafle P, Sharma R, Jenkins EJ, Awan M, L’Hérault V, Perkins SE. 2020. Parasites of an Arctic scavenger; the wolverine (Gulo gulo). International Journal for Parasitology-Parasites and Wildlife, 13, 178–185. [Google Scholar]
  74. Wickham H. 2016. ggplot2: Elegant graphics for data analysis. R package version 3.4.2. [Google Scholar]
  75. Wong SS, Fung KS, Chau S, Poon RW, Wong SC, Yuen KY. 2014. Molecular diagnosis in clinical parasitology: When and why?. Experimental Biology and Medicine, 239(11), 1443–1460. [Google Scholar]
  76. Yang Y, Xie C, Shen C, Tian B, Wang S, Bian X, Guo Y, Zhu Y, Fang H. 2023. Changes in the landscape patterns of Black-necked Crane habitat and its correlation with their individual population numbers during the past 40 years in China. Ecology and Evolution, 13(6), e10125. [Google Scholar]
  77. Gao Y, Zhang G, Jiang S, Liu YX. 2024. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. iMeta, (3), e175. [Google Scholar]
  78. Zahedi A, Greay TL, Paparini A, Linge KL, Joll CA, Ryan UM. 2019. Identification of eukaryotic microorganisms with 18S rRNA next-generation sequencing in wastewater treatment plants, with a more targeted NGS approach required for Cryptosporidium detection. Water Research, 158, 301–312. [Google Scholar]
  79. Zhao J, Wang Y, Zhang M, Yao Y, Tian H, Sang Z, Wang L, Xu H. 2021. Structural changes in the gut microbiota community of the black-necked crane (Grus nigricollis) in the wintering period. Archives of Microbiology, 203(10), 6203–6214. [Google Scholar]
  80. Zhou X, Wang L, Wang Z, Zhu P, Chen Y, Yu C, Chen S, Xie Y. 2023. Impacts of Eimeria coinfection on growth performance, intestinal health and immune responses of broiler chickens. Veterinary Parasitology, 322, 110019. [Google Scholar]

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