Faecal egg counts and nemabiome metabarcoding highlight the genomic complexity of equine cyathostomin communities and provide insight into their dynamics in a Scottish native pony herd

Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing

“…This estimate matched observations made in Kentucky horses using the nemabiome metabarcoding approach ( Poissant et al, 2021 ). In contrast, independent reports using the nemabiome metabarcoding approach found C. goldi as a minor species, either absent ( Sargison et al, 2022 ) or with relative abundance of 0.2% ( Malsa et al, 2022 ), 1.88% and 0.03% in Canadian horse populations ( Poissant et al, 2021 ). We suppose that the low fecundity of most Cylicostephanus species including C. goldi ( Kuzmina et al, 2012 ) can explain why the species that actually dominated in the horse strongylid community are underestimated in nemabiome metabarcoding studies when DNA is extracted from pools of eggs or larvae.…”

“…In addition to this higher resolutive power, the protein-coding nature of the COI barcode can be leveraged to denoise sequencing data ( Ramirez-Gonzalez et al, 2013 ). To date, metabarcoding experiments on strongylid species of equids have exclusively focused on the ITS-2 rDNA gene region, including community description in wild and domesticated equine populations ( Poissant et al, 2021 ; Sargison et al, 2022 ), the study of bioactive forage effect on cyathostomin species ( Malsa et al, 2022 ), the evaluation of drug efficacy in cyathostomin population ( Nielsen et al, 2022 ) or investigation of parasitic nematode community in plain zebras ( Tombak et al, 2021 ). This may owe to the existence of universal primers and the amplicon length that is a good fit for short-read sequencing platforms.…”

Species interactions, stability, and resilience of the gut microbiota - Helminth assemblage in horses

“…The initial resident nemabiome community identified by the internal transcribed spacer-2 (ITS-2) rDNA metabarcoding encompassed 14 co-infecting Cyathostominae species and three genera, represented by 239 abundant ASVs ( Table S3 ; Figure S2 ). Similar to recently published equine nemabiome studies, 59 , 60 , 61 , 62 , 63 the Cyathostominae community included Coronocyclus coronatus, Coronocyclus labiatus, Coronocyclus labratus, Cyathostomum catinatum, Cyathostomum pateratum, Cylicocyclus ashworthi, Cylicocyclus insigne, Cylicocyclus leptostomum, Cylicocyclus nassatus, Cylicostephanus calicatus, Cylicostephanus goldi, Cylicostephanus longibursatus, and Cylicostephanus minutus ( Figure 2 B) . The prevalence was high, with a core of eight species found in more than 17 of 19 high shedders, namely C. nassatus, C. minutus, C. longibursatus, C. catinatum, C. pateratum, C. coronatus, C. goldi , C. ashworthi .…”

Evaluation of genome skimming to detect and characterise human and livestock helminths

“…This is likely attributable to the stringent matching parameters applied, that required the vast majority of the sequencing read to match the ITS2 reference sequence and discounted the greater proportion of legitimate but partial sequencing read matches. The direct sequencing of ITS2 PCR products, such as the nemabiome sequencing toolkit developed for selected livestock parasites (Avramenko et al, 2015;Redman et al, 2019;Sargison et al, 2022) has proven highly sensitive to detecting and discriminating species within mixed helminth populations; however, to date, no comparable assays for diagnosis of human parasites are available. All three approaches relied on the availability of a reference sequence from a known helminth species for comparative analyses; therefore, genome skimming approaches are intrinsically limited by the availability of high-quality reference genomes.…”