Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Zahedi, Alireza; Liu, Dandan; Yang, Rongchang; Austen, Jill M.; Potter, Abbey; Ryan, Una

doi:10.1007/s00436-022-07764-5

Cited by 5 publications

(3 citation statements)

References 44 publications

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“…The scope of molecular scatology has been significantly broadened by the recent advancements in high-throughput next-generation sequencing (NGS) approaches (e.g. Bohmann et al, 2014;Dunisławska et al, 2017;Kartzinel et al, 2015;Khan & Tyagi, 2021;Liu et al, 2021;Scasta et al, 2019;Zahedi et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…The scope of molecular scatology has been significantly broadened by the recent advancements in high‐throughput next‐generation sequencing (NGS) approaches (e.g. Bohmann et al., 2014 ; Dunisławska et al., 2017 ; Kartzinel et al., 2015 ; Khan & Tyagi, 2021 ; Liu et al., 2021 ; Scasta et al., 2019 ; Zahedi et al., 2022 ). One such application of NGS that has gained notable attention recently is the assessment of an animal species' (defined as target species henceforth) fine‐scale dietary spectrum (e.g.…”

Section: Introductionmentioning

confidence: 99%

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An experimental design for obtaining DNA of a target species and its diet from a single non‐invasive genetic protocol

Paul,

Shahar,

Seifan

et al. 2023

Ecology and Evolution

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Next‐generation sequencing technology has enabled accurate insights into the diet of wildlife species. The protocols for faecal sample collection and DNA extraction for diet analysis have differed from those focusing on target species, even in most studies combining questions on both aspects. We designed an experiment to evaluate two protocols using 11 parameters and select a single one that will generate both target species (Asiatic wild ass, Equus hemionus, in Israel) and diet DNA, as an effective strategy to minimise time, effort, and cost without hampering efficiency. In Protocol A, we swabbed the outer surface of faecal boluses and extracted DNA using a Stool Kit, while for Protocol B, we homogenised faecal matter from inside the bolus followed by extraction using a Powersoil Kit. Protocol A performed significantly better for four parameters, which included, for the target species, microsatellite amplification success and the quantity of the GAPDH gene; and for its diet, the number of exact sequence variants (ESVs) obtained at genus level and plant genus richness. However, there was no significant difference in the amplification success of sex‐linked and plant markers, total reads at genus level, number of genera obtained and plant genus composition. Although we chose Protocol A, both protocols yielded results for the target species and its diet, demonstrating that one single protocol can be used for both purposes, although a pilot study is recommended to optimise the protocol for specific systems. This strategy may also be useful for studies combining target species and their gut microbiome and parasitic load.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An experimental design for obtaining DNA of a target species and its diet from a single non‐invasive genetic protocol

Paul,

Shahar,

Seifan

et al. 2023

Ecology and Evolution

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“…Commonly applied to bacteria in intestinal systems and eukaryotes in terrestrial and aquatic systems, it is surprising how rarely amplicon sequencing is used for intestinal parasites. Amplicon sequencing identified Eimeria species in chickens [ 4 , 5 ] and in other livestock and wildlife [ 6 ], but fewer studies have simultaneously estimated parasite abundance from the same data (but see [ 7 – 9 ] for other parasites). While a main focus of bacterial microbiome studies has been on intestinal “ecosystems” within human and animal hosts, sequencing of symbiotic eukaryotes from intestinal contents or faecal samples is less frequently used for detection of (e.g.…”

Section: Introductionmentioning

confidence: 99%

Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria)

2023

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Background Quantifying infection intensity is a common goal in parasitological studies. We have previously shown that the amount of parasite DNA in faecal samples can be a biologically meaningful measure of infection intensity, even if it does not agree well with complementary counts of transmission stages (oocysts in the case of Coccidia). Parasite DNA can be quantified at relatively high throughput using quantitative polymerase chain reaction (qPCR), but amplification needs a high specificity and does not simultaneously distinguish between parasite species. Counting of amplified sequence variants (ASVs) from high-throughput marker gene sequencing using a relatively universal primer pair has the potential to distinguish between closely related co-infecting taxa and to uncover the community diversity, thus being both more specific and more open-ended. Methods We here compare qPCR to the sequencing-based amplification using standard PCR and a microfluidics-based PCR to quantify the unicellular parasite Eimeria in experimentally infected mice. We use multiple amplicons to differentially quantify Eimeria spp. in a natural house mouse population. Results We show that sequencing-based quantification has high accuracy. Using a combination of phylogenetic analysis and the co-occurrence network, we distinguish three Eimeria species in naturally infected mice based on multiple marker regions and genes. We investigate geographical and host-related effects on Eimeria spp. community composition and find, as expected, prevalence to be largely explained by sampling locality (farm). Controlling for this effect, the novel approach allowed us to find body condition of mice to be negatively associated with Eimeria spp. abundance. Conclusions We conclude that amplicon sequencing provides the underused potential for species distinction and simultaneous quantification of parasites in faecal material. The method allowed us to detect a negative effect of Eimeria infection on the body condition of mice in the natural environment. Graphical Abstract

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Conservation of parasites: A primer

Lymbery

Smit

2023

International Journal for Parasitology: Parasites and Wildlife

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Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Cited by 5 publications

References 44 publications

An experimental design for obtaining DNA of a target species and its diet from a single non‐invasive genetic protocol

An experimental design for obtaining DNA of a target species and its diet from a single non‐invasive genetic protocol

Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria)

Conservation of parasites: A primer

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