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Beaumelle C, Redman EM, de Rijke J, Wit J, Benabed S, Debias F, Duhayer J, Pardonnet S, Poirel MT, Capron G, Chabot S, Rey B, Yannic G, Gilleard JS, Bourgoin G. Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes. Parasit Vectors 2021; 14:594. [PMID: 34863264 PMCID: PMC8642965 DOI: 10.1186/s13071-021-05087-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Background Gastrointestinal nematodes are ubiquitous for both domestic and wild ungulates and have varying consequences for health and fitness. They exist as complex communities of multiple co-infecting species, and we have a limited understanding of how these communities vary in different hosts, regions and circumstances or of how this affects their impacts. Methods We have undertaken ITS2 rDNA nemabiome metabarcoding with next-generation sequencing on populations of nematode larvae isolated from 149 fecal samples of roe deer of different sex and age classes in the two isolated populations of Chizé and Trois Fontaines in France not co-grazing with any domestic ungulate species. Results We identified 100 amplified sequence variants (ASVs) that were assigned to 14 gastrointestinal nematode taxa overall at either genus (29%) or species (71%) level. These taxa were dominated by parasites classically found in cervids—e.g. Ostertagia leptospicularis, Spiculopteragia spp. Higher parasite species diversity was present in the Trois Fontaines population than in the Chizé population including the presence of species more typically seen in domestic livestock (Haemonchus contortus, Bunostomum sp., Cooperia punctata, Teladorsagia circumcincta). No differences in parasite species diversity or community composition were seen in the samples collected from three zones of differing habitat quality within the Chizé study area. Young roe deer hosted the highest diversity of gastrointestinal nematodes, with more pronounced effects of age apparent in Trois Fontaines. The effect of host age differed between gastrointestinal nematode species, e.g. there was little effect on O. leptospicularis but a large effect on Trichostrongylus spp. No effect of host sex was detected in either site. Conclusions The presence of some livestock parasite species in the Trois Fontaines roe deer population was unexpected given the isolation of this population away from grazing domestic livestock since decades. Overall, our results illustrate the influence of host traits and the local environment on roe deer nemabiome and demonstrate the power of the nemabiome metabarcoding approach to elucidate the composition of gastrointestinal nematode communities in wildlife. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-05087-5.
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Affiliation(s)
- Camille Beaumelle
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France. .,Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France.
| | - Elizabeth M Redman
- Comparative Biology and Experimental Medicine, Host-Parasites Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jill de Rijke
- Comparative Biology and Experimental Medicine, Host-Parasites Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Janneke Wit
- Comparative Biology and Experimental Medicine, Host-Parasites Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Slimania Benabed
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France.,VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, 69280, Marcy l'Etoile, France
| | - François Debias
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France
| | - Jeanne Duhayer
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France
| | - Sylvia Pardonnet
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France
| | - Marie-Thérèse Poirel
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France.,VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, 69280, Marcy l'Etoile, France
| | - Gilles Capron
- Office Français de la Biodiversité, 75008, Paris, France
| | | | - Benjamin Rey
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France
| | - Glenn Yannic
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, 38000, Grenoble, France
| | - John S Gilleard
- Comparative Biology and Experimental Medicine, Host-Parasites Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Gilles Bourgoin
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 69100, Villeurbanne, France.,VetAgro Sup, Campus Vétérinaire de Lyon, Université de Lyon, 69280, Marcy l'Etoile, France
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Duan H, Gao JF, Su X, Fu X, Yue DM, Gao Y, Qiu JH, Wang CR. Genetic variation between and within Triodontophorus brevicauda and Triodontophorus nipponicus revealed by analyses of mtDNA and rDNA gene sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:570-574. [PMID: 27159713 DOI: 10.3109/24701394.2016.1157867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Triodontophorus spp. parasitizes the large intestine of equine, causing strongylid diseases. The present study assessed genetic variation in five gene regions within and between Triodontophorus brevicauda and Triodontophorus nipponicus from Heilongjiang Province and the Inner Mongolia Autonomous region. The five gene markers were three mitochondrial (mt) genes, cytochrome c oxidase subunit I (cox1), NADH dehydrogenase subunit 5 (nad5), cytochrome b (cytb); and two ribosomal RNA genes, the internal transcribed spacer 1 (ITS1) and the internal transcribed spacer 2 (ITS2). Partial (p) sequences of cox1, nad5, cytb and the complete ITS rDNA region were PCR amplified from individual nematodes, and the amplicons were subjected to sequencing in both directions. The size of the three mt genes is identical in both species: 761 bp (p cox1), 505 bp (pnad5) and 562 bp (pcytb); the length of the two ribosomal genes is different: 376 bp and 370 bp (ITS1), and 333 bp and 322 bp (ITS2), respectively. Intraspecific variation between T. brevicauda and T. nipponicus was 0-1.5% and 0-1.1% for pcox1, 0-2.0% and 0-2.0% for pnad5, 0-1.4% and 0-2.2% for pcytb, 0-0.8% and 0-1.1% for ITS1 and 0-0.9% and 0-2.2% for ITS2. Interspecific variation within the nematodes was 13.5-14.3% for pcox1, 15.5-18.7% for pnad5, 16.7-18.6% for pcytb, 11.5-13.1% for ITS1 and 16.0-18.4% for ITS2. Phylogenetic analyses based on the combined mt gene sequences, as well as with the ITS sequences, show each species forming a monophyletic group of individuals. However, samples of different species from the same geographical origin did not always cluster together. These results provide valuable information for further studies of systematics and population genetics of the genus Triodontophorus.
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Affiliation(s)
- Hong Duan
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Jun-Feng Gao
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Xin Su
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Xue Fu
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Dong-Mei Yue
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Yuan Gao
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Jian-Hua Qiu
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
| | - Chun-Ren Wang
- a College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing , Heilongjiang Province , PR China
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Xu WW, Qiu JH, Liu GH, Zhang Y, Liu ZX, Duan H, Yue DM, Chang QC, Wang CR, Zhao XC. The complete mitochondrial genome of Strongylus equinus (Chromadorea: Strongylidae): Comparison with other closely related species and phylogenetic analyses. Exp Parasitol 2015; 159:94-9. [PMID: 26366671 DOI: 10.1016/j.exppara.2015.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 07/14/2015] [Accepted: 08/16/2015] [Indexed: 11/25/2022]
Abstract
The roundworms of genus Strongylus are the common parasitic nematodes in the large intestine of equine, causing significant economic losses to the livestock industries. In spite of its importance, the genetic data and epidemiology of this parasite are not entirely understood. In the present study, the complete S. equinus mitochondrial (mt) genome was determined. The length of S. equinus mt genome DNA sequence is 14,545 bp, containing 36 genes, of which 12 code for protein, 22 for transfer RNA, and two for ribosomal RNA, but lacks atp8 gene. All 36 genes are encoded in the same direction which is consistent with all other Chromadorea nematode mtDNAs published to date. Phylogenetic analysis based on concatenated amino acid sequence data of all 12 protein-coding genes showed that there were two large branches in the Strongyloidea nematodes, and S. equinus is genetically closer to S. vulgaris than to Cylicocyclus insignis in Strongylidae. This new mt genome provides a source of genetic markers for the molecular phylogeny and population genetics of equine strongyles.
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Affiliation(s)
- Wen-Wen Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Jian-Hua Qiu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Yan Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Ze-Xuan Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Hong Duan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Dong-Mei Yue
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China.
| | - Xing-Cun Zhao
- Animal and Plant Department, Quanzhou Entry-Exit Inspection and Quarantine Bureau, Quanzhou, Fujian Province, 362000, PR China.
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Wang CR, Lou Y, Zhang Y, Wang WT, Zheng X, Xu WW, Zhang Y, Tian SQ, Na L, Chang QC. Genetic variability among Syphacia obvelata isolates from laboratory mice in four different geographical locations of China revealed by sequence analyses of five mitochondrial genes. ACTA ACUST UNITED AC 2014; 26:213-6. [PMID: 24708136 DOI: 10.3109/19401736.2014.905861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Syphacia obvelata is a rodent nematode with high prevalence in laboratory mice. In the present study, we examined the genetic variability of S. obvelata from naturally infected laboratory mice in four different provinces, China. Five mitochondrial (mt) DNA regions, namely cytochrome c oxidase subunit 1 (pcox1), cytochrome b (pcytb), large subunit ribosomal RNA (prrnL) and NADH dehydrogenase subunits 1 and 5 (pnad1 and pnad5), were amplified separately from individual nematodes by PCR, and then sequenced directly. The size of the sequences of pcox1, pcytb, prrnL, pnad1 and pnad5 was 628 bp, 555 bp, 548 bp, 548 bp and 561 bp, respectively. While the intra-specific sequence variations within S. obvelata were 0-1.0% for pcox1, 0-1.6% for pcytb, 0-2.8% for prrnL, 0-2.0% for pnad1 and 0-1.8% for pnad5, the inter-specific sequence differences among members of the Oxyuridae were significantly higher, being 14.0-17.5% for pcox1, 27.5-32.9% for pcytb, 35.8-37.2% for prrnL, 22.2-26.8% for pnad1 and 22.3-25.2% for pnad5, respectively. Phylogenetic analyses based on combined sequences of four mt protein-coding genes, using Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) methods, indicated that all of the S. obvelata samples grouped together with high statistical support, but samples from the same geographical origin did not always cluster together. These findings demonstrated the existence of low-level intra-specific variation in five mtDNA sequences among S. obvelata isolates from laboratory mice, but no obvious geographical distinction among S. obvelata isolates from laboratory mice in different geographic regions in China. These results provide basic information for further studies of systematics and population genetics of S. obvelata.
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Affiliation(s)
- Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University , Daqing, Heilongjiang Province , P.R. China
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Chang QC, Gao JF, Sheng ZH, Lou Y, Zheng X, Wang CR. Sequence variability in three mitochondrial genes among four roundworm species from wild animals in China. ACTA ACUST UNITED AC 2013; 26:75-8. [DOI: 10.3109/19401736.2013.823171] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Qiao-Cheng Chang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Xinfeng Road, Daqing, Heilongjiang Province, P. R. China and
| | - Jun-Feng Gao
- Department of Parasitology, Heilongjiang Institute of Veterinary Science, Qiqihar, P. R. China
| | - Zhong-Hua Sheng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Xinfeng Road, Daqing, Heilongjiang Province, P. R. China and
| | - Yan Lou
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Xinfeng Road, Daqing, Heilongjiang Province, P. R. China and
| | - Xu Zheng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Xinfeng Road, Daqing, Heilongjiang Province, P. R. China and
| | - Chun-Ren Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Xinfeng Road, Daqing, Heilongjiang Province, P. R. China and
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