The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Metabarcoding and Metagenomics, Journal Year: 2024, Volume and Issue: 8

Published: Dec. 30, 2024

Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data metadata makes results difficult to reproduce synthesise. A working group scientists have collaborated produce set minimum reporting guidelines the constituent steps workflows, physical layout laboratories through archiving. We emphasise how suite should adhere findable, accessible, interoperable reproducible (FAIR) standards, thereby providing context evaluating understanding study results. An overview considerations each workflow step is presented then summarised in checklist that can accompany published or report. Ensuring workflows are transparent documented critical research allow more efficient uptake into management decision-making.

Language: Английский

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mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 11, 2024

Abstract We developed a python package called mbctools , designed to offer cross-platform tool for processing amplicon data from various organisms in the context of metabarcoding studies. It can handle most common tasks pipelines such as paired-end merging, primer trimming, quality filtering, sequence denoising, zero-radius operational taxonomic unit (ZOTU) and has capability process multiple genetic markers simultaneously. is menu-driven program that eliminates need expertise command-line skills ensures documentation each analysis reproducibility purposes. The software, run console, offers an interactive experience, guided by keyboard inputs, assisting users along way through hiding complexity command lines letting them concentrate on selecting parameters apply step process. In our workflow, VSEARCH utilized fastq files derived amplicon-based Next-Generation Sequencing data. This software versatile open-source sequences, offering advantages high speed, efficient memory usage, ability large datasets. provides functions dereplication, clustering, chimera detection, assignment. thus very retrieving overall diversity sample. To adapt projects metabarcoding, we facilitate reprocessing datasets with possibility adjust parameters. also be launched headless mode, making it suited integration into running High-Performance Computing environments. available at https://github.com/GuilhemSempere/mbctools https://pypi.org/project/mbctools/ .

Language: Английский

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Inventorizing marine biodiversity using eDNA data from Indonesian coral reefs: comparative high throughput analysis using different bioinformatic pipelines

Marine Biodiversity, Journal Year: 2024, Volume and Issue: 54(3)

Published: April 5, 2024

Language: Английский

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Optimization of environmental DNA-based methods: A case study for detecting brook trout (Salvelinus fontinalis).

Authorea (Authorea), Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR ddPCR) passive sequencing approaches metabarcoding). However, the lack optimized standardized methods reduces sensitivity this approach precludes reliable comparison findings across studies, respectively. DNA extraction a prime target optimization efforts because method highly variable studies despite being most influential factor in detection efficiency entire post-collection workflow. Sequence analysis arguably least step workflow, with new bioinformatics pipelines frequently emerging literature implemented innumerable unique combinations parameter values. current study aimed to support standardization by assessing two commercial kits manufactured Qiagen Macherey-Nagel on cost, time, performance specifications comparing success brook trout metabarcoding three pipelines, qPCR, ddPCR. Our protocols were effective detecting all 20 samples analyzed. Brook was detected ddPCR nine (90%) extracts but only seven (70%) extracts. In comparison, equal (100%). performed equally well no significant differences read numbers associated species. Under our experimental conditions, kit selected as preferred due its overall good considerably lower cost slightly longer time.

Language: Английский

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Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems

Research in Microbiology, Journal Year: 2024, Volume and Issue: 175(7), P. 104217 - 104217

Published: June 9, 2024

Language: Английский

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