Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes

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...

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Autores principales:	Camille Beaumelle, Elizabeth M. Redman, Jill de Rijke, Janneke Wit, Slimania Benabed, François Debias, Jeanne Duhayer, Sylvia Pardonnet, Marie-Thérèse Poirel, Gilles Capron, Stéphane Chabot, Benjamin Rey, Glenn Yannic, John S. Gilleard, Gilles Bourgoin
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Strongyle Ungulate Parasitism Amplicon sequence variants Haemonchus contortus Wildlife Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/5fd2601b9f6d4b6cad132b9128578f14
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spelling	oai:doaj.org-article:5fd2601b9f6d4b6cad132b9128578f142021-12-05T12:17:03ZMetabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes10.1186/s13071-021-05087-51756-3305https://doaj.org/article/5fd2601b9f6d4b6cad132b9128578f142021-12-01T00:00:00Zhttps://doi.org/10.1186/s13071-021-05087-5https://doaj.org/toc/1756-3305Abstract 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 AbstractCamille BeaumelleElizabeth M. RedmanJill de RijkeJanneke WitSlimania BenabedFrançois DebiasJeanne DuhayerSylvia PardonnetMarie-Thérèse PoirelGilles CapronStéphane ChabotBenjamin ReyGlenn YannicJohn S. GilleardGilles BourgoinBMCarticleStrongyleUngulateParasitismAmplicon sequence variantsHaemonchus contortusWildlifeInfectious and parasitic diseasesRC109-216ENParasites & Vectors, Vol 14, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Strongyle Ungulate Parasitism Amplicon sequence variants Haemonchus contortus Wildlife Infectious and parasitic diseases RC109-216
spellingShingle	Strongyle Ungulate Parasitism Amplicon sequence variants Haemonchus contortus Wildlife Infectious and parasitic diseases RC109-216 Camille Beaumelle Elizabeth M. Redman Jill de Rijke Janneke Wit Slimania Benabed François Debias Jeanne Duhayer Sylvia Pardonnet Marie-Thérèse Poirel Gilles Capron Stéphane Chabot Benjamin Rey Glenn Yannic John S. Gilleard Gilles Bourgoin Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
description	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
format	article
author	Camille Beaumelle Elizabeth M. Redman Jill de Rijke Janneke Wit Slimania Benabed François Debias Jeanne Duhayer Sylvia Pardonnet Marie-Thérèse Poirel Gilles Capron Stéphane Chabot Benjamin Rey Glenn Yannic John S. Gilleard Gilles Bourgoin
author_facet	Camille Beaumelle Elizabeth M. Redman Jill de Rijke Janneke Wit Slimania Benabed François Debias Jeanne Duhayer Sylvia Pardonnet Marie-Thérèse Poirel Gilles Capron Stéphane Chabot Benjamin Rey Glenn Yannic John S. Gilleard Gilles Bourgoin
author_sort	Camille Beaumelle
title	Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
title_short	Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
title_full	Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
title_fullStr	Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
title_full_unstemmed	Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
title_sort	metabarcoding in two isolated populations of wild roe deer (capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes
publisher	BMC
publishDate	2021
url	https://doaj.org/article/5fd2601b9f6d4b6cad132b9128578f14
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Metabarcoding in two isolated populations of wild roe deer (Capreolus capreolus) reveals variation in gastrointestinal nematode community composition between regions and among age classes

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