Electronic Resource
Amplicon sequencing allows differential quantification of closely related parasite species
| العنوان: | Amplicon sequencing allows differential quantification of closely related parasite species |
|---|---|
| Additional Titles: | an example from rodent Coccidia (Eimeria) |
| المؤلفون: | Ferreira, Susana C. M., Jarquín-Díaz, Víctor Hugo, Heitlinger, Emanuel |
| بيانات النشر: | Humboldt-Universität zu Berlin 2023-06-17 |
| نوع الوثيقة: | Electronic Resource |
| مستخلص: | The article processing charge was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 491192747 and the Open Access Publication Fund of Humboldt-Universität zu Berlin. 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 Peer Reviewed |
| مصطلحات الفهرس: | Eimeria, Parasite infection, Microbiome, Parasite quantification, Amplicon sequencing, qPCR, Body condition, 570 Biologie, ddc:570, article, doc-type:article, publishedVersion |
| URL: | |
| الاتاحة: | Open access content. Open access content (CC BY 4.0) Attribution 4.0 International https://creativecommons.org/licenses/by/4.0 |
| ملاحظة: | application/pdf English |
| Other Numbers: | FBU oai:edoc.hu-berlin.de:18452/28194 urn:nbn:de:kobv:11-110-18452/28194-8 1756-3305 10.1186/s13071-023-05800-6 1417744971 |
| المصدر المساهم: | BIBLIOTHEK DER HUMBOLDT-UNIVERSITAT BER From OAIster®, provided by the OCLC Cooperative. |
| رقم الانضمام: | edsoai.on1417744971 |
| قاعدة البيانات: | OAIster |
| الوصف غير متاح. |