ArticleParasites & vectors2022
Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis.
Article in Parasites & vectors, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 11 citations in OpenAlex.
- QIIME2 pipeline for ITS2-based nemabiome sequencing in veterinary species and the importance of analysis parameters.Parasites & vectors · 2025Article
- Old world camels in Germany: parasitic nematode communities characterized by nemabiome analysis showed reduced anthelmintic efficacy according to the fecal egg count reduction test.Parasites & vectors · 2025Article
- A Pilot Study for the Characterization ofMicroorganisms · 2024Article
- A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.Molecular ecology resources · 2024Review
- Wireless sensor network-based health monitoring and smart home assistance for the older adults in sports and wellness towns.Frontiers in public health · 2024Article
- Parasitic strongyle nemabiome communities in wild ruminants in Sweden.Parasites & vectors · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundNext-generation sequencing (NGS) has provided an alternative strategy to study the composition of nematode communities with increased resolution and sensitivity. However, the handling and processing of gigabytes worth of amplicon sequence data produced by an NGS platform is still a major hurdle, limiting the use and adoption of faster and more convenient analysis software.
methodsIn total 32 paired, fecal samples from Swedish sheep flocks were cultured and the larvae subsequently harvested subjected to internal transcribed spacer 2 (ITS2) amplicon sequencing using the PacBio platform. Samples were analyzed with three different bioinformatic pipelines, i.e. the DADA2, Mothur and SCATA pipelines, to determine species composition and richness.
resultsFor the the major species tested in this study (Haemonchus contortus, Teladorsagia circumcinta and Trichostrongylus colubriformis) neither relative abundances nor species diversity differed significantly between the three pipelines, effectively showing that all three analysis pipelines, although different in their approaches, yield nearly identical outcomes. In addition, the samples analyzed here had especially high frequencies of H. contortus (90-95% across the three pipelines) both before and after sample treatment, followed by T. circumcinta (3.5-4%). This shows that H. contortus is the parasite of primary importance in contemporary Swedish sheep farms struggling with anthelmintic resistance. Finally, although on average a significant reduction in egg counts was achieved post-treatment, no significant shifts in major species relative frequencies occurred, indicating highly rigid community structures at sheep farms where anthelmintic resistance has been reported.
conclusionsThe findings presented here further contribute to the development and application of NGS technology to study nemabiome compositions in sheep, in addition to expanding our understanding about the most recent changes in parasite species abundances from Swedish sheep farms struggling with anthelmintic resistance.
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