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Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis

Baltrusis, Paulius and Halvarsson, Peter and Höglund, Johan (2022). Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis. Parasites and Vectors. 15 , 290
[Research article]

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Abstract

Background: Next-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.Methods: In 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.Results: For 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.Conclusions: The 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.

Authors/Creators:Baltrusis, Paulius and Halvarsson, Peter and Höglund, Johan
Title:Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis
Series Name/Journal:Parasites and Vectors
Year of publishing :2022
Volume:15
Article number:290
Number of Pages:12
Publisher:BMC
ISSN:1756-3305
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 403 Veterinary Science > Pathobiology
Keywords:Nemabiome, PacBio, Ivermectin, Albendazole, Monepantel, Anthelmintic resistance, Bioinformatic pipeline, NGS
URN:NBN:urn:nbn:se:slu:epsilon-p-118750
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-118750
Additional ID:
Type of IDID
DOI10.1186/s13071-022-05399-0
Web of Science (WoS)000839652200001
ID Code:28811
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Department of Biomedical Science and Veterinary Public Health
Deposited By: SLUpub Connector
Deposited On:09 Sep 2022 08:30
Metadata Last Modified:09 Sep 2022 08:31

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