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#Metabarcoding

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Public
Frédéric Rimet

Une offre de post-doc de 1 an renouvelable 1 an :
> Finaliser le développement d’une méthode d’identification moléculaire du phytoplancton utilisant le séquençage ADN haut-débit #metabarcoding

> CDD post-doc de 1 an, reconductible 1 an : démarrage à partir de mai 2025, Lieu : UMR Carrtel, Thonon fr-carrtel.lyon-grenoble.hub.i

> Projet pluriannuel #OFB et le projet européen #eDNAquaPlan

> candidature : frederic.rimet@inrae.fr

> plus de détails : filesender.renater.fr/?s=downl

fr-carrtel.lyon-grenoble.hub.inrae.frAccueilAccueil
Public
Lukas VFN 🇪🇺

Researchers partner with #IndigenousKnowledge holders to protect threatened great desert skink Tjakuṟa phys.org/news/2025-01-partner-

#Metabarcoding clarifies the diet of the elusive and vulnerable Australian #tjakura (Great Desert #Skink, Liopholis kintorei) frontiersin.org/journals/ecolo

"Tjakuṟa is a large #lizard that lives in multi-tunneled communal burrows in #Australia... scientists rely on #Aṉangu Traditional Knowledge to locate Tjakuṟa burrows, estimate burrow occupancy, identify predator tracks"

photo of a lizard next to a burrow in dry red soil
Public
Teresita Porter 🙋🏻‍♀️

A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria

link.springer.com/article/10.1

SpringerLinkA new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria - International MicrobiologyMetabarcoding is a powerful tool to characterize biodiversity in biological samples. The interpretation of taxonomic profiles from metabarcoding data has been hindered by their compositional nature. Several strategies have been proposed to transform compositional data into quantitative data, but they have intrinsic limitations. Here, I propose a workflow based on bacterial and fungal cellular internal standards (spike-ins) for absolute quantification of the microbiota in soil samples. These standards were added to the samples before DNA extraction in amounts estimated after qPCRs, to target around 1–2% coverage in the sequencing run. In bacteria, proportions of spike-in reads in the sequencing run were very similar (< 2-fold change) to those predicted by the qPCR assessment, and for fungi they differed up to 40-fold. The low variation among replicates highlights the reproducibility of the method. Estimates based on multiple bacterial spike-ins were highly correlated (r = 0.99). Procrustes analysis evidenced significant biological effects on the community composition when normalizing compositional data. A protocol based on qPCR estimation of input amounts of cellular spikes is proposed as a cheap and reliable strategy for quantitative metabarcoding of biological samples.
#quantitative#metabarcoding#bacteria
Public
Teresita Porter 🙋🏻‍♀️

What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying *Fagus sylvatica* Bark as Case Study

mdpi.com/2309-608X/10/10/708

MDPIWhat Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case StudyNanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE’s species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve.
#nanopore#metabarcoding#fungi
Public
Lukas VFN 🇪🇺

Saving the #bats: Researchers find #bacteria and #fungi on #bat wings that could help fight deadly white-nose syndrome phys.org/news/2024-10-bacteria

DNA #metabarcoding analyses reveal fine-scale #microbiome structures on Western Canadian bat wings journals.asm.org/doi/10.1128/s

"Healthy wings are critical for the survival and reproduction of bats and the wing microbiome is believed to play a major role in their susceptibility to #WhiteNoseSyndrome"

person holding a bat with an outstretched wing
Public
AquaEcOmics

Register for the upcoming AquaEcOmics Symposium and come listen to great keynote speakers who will discuss the use of environmental omics for microbial network analyses, assessing functional diversity and evolutionary diversification and gaining insights into spatial and temporal community dynamics. aquaecomics.symposium.inrae.fr #aquaecomics2025 #eDNA #omics #metagenomics #metabarcoding #dPCR #marine #freshwater #ecology #biomonitoring

Public
Lukas VFN 🇪🇺

New study reveals the crucial role of #jellyfish in Greenlandic waters rcinet.ca/eye-on-the-arctic/20

A belly full of jelly? DNA #metabarcoding shows evidence for gelatinous #zooplankton predation by several #fish species in #Greenland waters royalsocietypublishing.org/doi

"Scientists have commonly regarded jellyfish as a secondary food source for predatory fish, due to their low energy density and nutritional value. But... fish consume jellyfish much more frequently than previously thought."

underwater photo of a jellyfish
Public
nf-core

🦠 Interested in #nextflow & anything 'meta-' ?(#metagenomics, #metabarcoding, #metatranscriptomics, #metaproteomics, #microbes #MicrobialEcology & more!)

📆 Join us next Tuesday 13:00 CEST (3rd September) for an nf-core #bytesize for the #metaomics #nfcore special interest group! (Also on YouTube after!)

🤝 We will introduce how we want the community to work together with #users and #bioinformatics developers to make the best pipelines for anything 'meta-'

ℹ️ Zoom: nf-co.re/events/2024/bytesize_

nf-co.reBytesize: Special Interest Group meta-omicsDaniel Lundin (Linnaeus University / Stockholm University), James Fellows Yates (HKI Jena / MPI-EVA Leipzig) and Carson J. Miller (University of Washington)
Public
Frédéric Rimet

AquaEcOmics - Registrations for the 2025 AquaEcOmics Symposium are now open! Register now to learn and discuss about recent advancements and challenges of omic tools and how they can be used to address pertinent scientific and management questions in aquatic ecosystems.
aquaecomics.symposium.inrae.fr
#aquaecomics2025 #eDNA #omics #metagenomics #metabarcoding #dPCR #marine #freshwater #ecology #biomonitoring #metabolomics

aquaecomics.symposium.inrae.frAquaEcOmicsHome Page
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