A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

A Hakimzadeh, A Abdala Asbun… - Molecular Ecology …, 2024 - Wiley Online Library
Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for
monitoring biodiversity in ecology. However, taxa identifications produced through …

Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring

M Couton, L Lévêque, C Daguin-Thiébaut, T Comtet… - Biofouling, 2022 - Taylor & Francis
Marinas are high-priority targets for marine non-indigenous species (NIS), where they
compose a large portion of the biofouling communities. The practicality of water samples …

Opportunities and inherent limits of using environmental DNA for population genetics

M Couton, F Viard, F Altermatt - Environmental DNA, 2023 - Wiley Online Library
Molecular techniques using DNA retrieved from community or environmental samples, in
particular environmental DNA (eDNA), are becoming increasingly popular for detecting …

Comparative analysis of the bacterial diversity of Chinese fermented sausages using high-throughput sequencing

QQ Zhang, D Li, W Zhang, M Jiang, XH Chen… - Lwt, 2021 - Elsevier
Chinese dry fermented sausage is a spontaneously fermented food with complex microbial
diversity. In this study, the bacterial diversity of long-and round-type Chinese dry fermented …

Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies

A Bonin, A Guerrieri, GF Ficetola - Molecular Ecology …, 2023 - Wiley Online Library
Clustering approaches are pivotal to handle the many sequence variants obtained in DNA
metabarcoding data sets, and therefore they have become a key step of metabarcoding …

[PDF][PDF] Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps

L Sire, PS Yáñez, A Bézier, B Courtial, S Mbedi… - PeerJ, 2023 - peerj.com
Background. Broad-scale monitoring of arthropods is often carried out with passive traps
(eg, Malaise traps) that can collect thousands of specimens per sample. The identification of …

Environmental gradients and optimal fixation time revealed with DNA metabarcoding of benthic sample fixative

O Vargovčík, Z Čiamporová-Zaťovičová, P Beracko… - Scientific Reports, 2024 - nature.com
Assessments of biodiversity and ecosystem status can benefit from DNA metabarcoding as a
means to streamline sample processing and specimen identification. Moreover, processing …

Testing the applicability of environmental DNA metabarcoding to landscape genetics

S Nakajima, K Tsuri - Molecular Ecology Resources, 2024 - Wiley Online Library
Landscape genetics is a field dealing with local genetic differences and contributes to
strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has …

Diet Diversity of the Fluviatile Masu Salmon, Oncorhynchus masou (Brevoort 1856) Revealed via Gastrointestinal Environmental DNA Metabarcoding and …

L Li, X Yin, Q Wan, D Rusitanmu, J Han - Biology, 2024 - mdpi.com
Simple Summary Masu salmon (Oncorhynchus masou), a commercially important fish
endemic to the North Pacific Ocean, received national second-level protected animal status …

Non-destructive DNA metabarcoding of arthropods using collection medium from passive traps

L Sire, P Schmidt Yáñez, A Bézier, B Courtial, S Mbedi… - bioRxiv, 2023 - biorxiv.org
Background Broad-scale monitoring of arthropods is often carried out with passive traps (eg.
Malaise traps) that can collect thousands of specimens per sample. The identification of …