Simultaneous analysis of the intestinal parasites and diet through eDNA metabarcoding

Abstract

Agricultural expansion and intensification are having a huge impact on plant and arthropod diversity and abundance, affecting food availability for farmland birds. Difficult food access, in turn, can lead to immunosuppression and a higher incidence of parasites. In the studies designed to examine changes in the diet of birds and their parasites, metabarcoding is proving particularly useful. This technique requires mini‐barcodes capable of amplifying the DNA of target organisms from fecal environmental DNA. To help to understand the impact of agricultural expansion on biodiversity, this study sought to design and identify mini‐barcodes that might simultaneously assess diet and intestinal parasites from the feces of farmland birds. The capacity to identify diet and parasites of 2 existing and 3 newly developed mini‐barcodes was tested “in silico” in relation to the behavior of a reference eukaryotic barcode. Among the newly designed mini‐barcodes, MiniB18S_81 showed the higher taxonomic coverage of eukaryotic taxa and a greater amplification and identification capacity for diet and parasite taxa. Moreover, when it was tested on fecal samples from 5 different steppe bird species, MiniB18S_81 showed high taxonomic resolution of the most relevant diet and parasite phyla, Arthropoda, Nematoda, Platyhelminthes, and Apicomplexa at the order level. Thus, the mini‐barcode developed emerges as an excellent tool to simultaneously provide detailed information regarding the diet and parasites of birds, essential for conservation and management.

Dietary niche overlap and resource partitioning among six steppe passerines of Central Spain using DNA metabarcoding

“…The eukaryotic mini‐barcode miniB18S_81 designed by Cabodevilla et al . (2022) was used to amplify prey DNA, targeting the 18S rRNA gene. This marker was initially selected because steppe birds can feed on a wide range of invertebrates (insects, spiders and snails), but also on plants, so we were interested in amplifying both the invertebrate and the plant components of the diet.…”

“…A second PCR was performed to index each amplified product and attach Illumina adaptors (Illumina, San Diego, CA, USA). Amplification was carried out according to Cabodevilla et al (2022). The resulting fragments were checked in a Bioanalyzer before pooling in equimolar amounts.…”

Foster innovation and facilitate publications for zoology

“…The degree of sexual size dimorphism decreased with a decrease in latitude (Krasnov et al 2022). Cabodevilla et al (2022) design a eukaryotic mini-barcode (MiniB18S_81), which provides high taxonomic resolution of the most relevant diet and parasite phyla, Arthropoda, Nematoda, Platyhelminthes, and Apicomplexa, at the order level. This is an excellent tool to simultaneously provide detailed information regarding the diet and parasites of birds, essential for conservation and management.…”

“…Overall, this issue will help researchers to investigate parasitology through new methods, such as eDNA metabarcoding (Cabodevilla et al. 2022). The importance of this topic is likely to continue in light of increasing concern over the effects of parasitic diseases in recent years.…”

An Overview of Microbial Source Tracking Using Host-Specific Genetic Markers to Identify Origins of Fecal Contamination in Different Water Environments

“…It became a functional measure in environmental DNA (eDNA) studies since fecal matter is considered one of the predominant origins of eDNA [18]. In this regard, MST defines host-specific signatures of fecal eDNA (anthropo-zoogenic origins and sources), which are essential for the assessment of the environmental impacts of microbial pollution and the health risks of enteric pathogens [19][20][21][22].…”