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🆕 New to metagenomics? Check our beginner-friendly training material and learn to run typical metagenomic analyses—right in your browser, no complex installs needed! 🚀
Step by step, you’ll use SimpleVM for preconfigured workflows on de.NBI cloud resources. Perfect for students & life scientists with little or no bioinformatics experience.
🔗 Course material: https://denbi-nfdi-simplevm-metagenomics-workshop.readthedocs.io/en/latest/
#Metagenomics #Bioinformatics #Training

🎉 Huge shout out to everyone who instructed and participated in yesterday's online Meta-*omics #Nextflow Pipeline Community Exhibition Day!

🧑‍🏫 Over 9 hours, we had 15 different pipelines demo'd by their lead developers, and giving an international cohort of participants hands-on experience on running diverse pipelines spanning #metataxonomics, #metagenomics, #metatranscriptomics, and #metaproteomics, as well as a crash-course on the different ways to configure Nextflow pipelines.

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Meta-*omics Nextflow pipeline community exhibition day

Organised by James Fellows Yates

Supported by NFDI4Microbiota, Nextflow Ambassador program, and deNBI

Recovering DNA from ancient plants is tough, but this new method makes it work! A new extraction workflow improves recovery of fragmented endogenous plant aDNA while preserving library complexity and read yield.
https://www.nature.com/articles/s41598-025-21743-7

#MetagenomicsMonday #SPAAM #aDNA #metagenomics #archaeobotany #ancientplants #DNA

Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.3.0

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Ancient microbe DNA as a record of climate change 🦠🧬: mountain lake sedaDNA from the past 430 years reveals major microbial shifts since 1960, following climate shifts.
https://doi.org/10.1007/s00248-025-02612-2
#MetagenomicsMonday #SPAAM #aDNA #climate #change #metagenomics #sediment #sedaDNA #mountain #lake

Pipeline release! nf-core/proteinfamilies v2.1.0 - Iron Goat!
Generation and updating of protein families
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.1.0

#metagenomics #proteinfamilies #proteomics #nfcore #openscience #nextflow #bioinformatics

We are hiring! If you're interested in exploring the #biogeography of #prokaryotes using #genomics and #metagenomics, are interested in biology and geographic information systems, and are passionate about #OpenScience, this is for you! We have just opened a PhD and a PostDoc position in my lab at Aalborg University!

PhD: https://www.vacancies.aau.dk/phd-positions/show-vacancy/vacancyId/879120

Postdoc: https://www.vacancies.aau.dk/scientific-positions/show-vacancy/vacancyId/879146

Feel free to reach out with questions or apply directly in the links

What can ancient chewing gum reveal about life in the Neolithic Alps? 🌲🧬 This study of birch bark tar uncovers traces of human, microbial, plant & animal DNA, revealing who chewed it and why. #MetagenomicsMonday #SPAAM #aDNA #neolithic #metagenomics
https://doi.org/10.1098/rspb.2025.0092

Pipeline release! nf-core/taxprofiler v1.2.5 - v1.2.5 - Bouncy Basenji Patch!
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.5

#classification #illumina #longreads #metagenomics #microbiome #nanopore #pathogen #profiling #shotgun #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/createtaxdb v2.0.0 - v2.0.0 - Charming Chaac - [2025-11-14]!

Parallelised and automated construction of metagenomic classifier databases of different tools

Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/2.0.0

#database #databasebuilder #metagenomicprofiling #metagenomics #profiling #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

This new study takes a closer look at eukaryotic reference genomes. 🧬 By mapping microbial-like regions across thousands of plant & animal assemblies, it helps make ancient eDNA analyses more accurate. #MetagenomicsMonday #SPAAM #aDNA #metagenomics #eDNA
https://doi.org/10.1093/gigascience/giaf108

Happy to share our new paper by Clarisse Lemonnier et al.:
Comparison of #Metabarcoding and #Shotgun Sequencing Confirms the Relevance of Chloroplastic rRNA Genes to Assess Community Structure of #Lake #Phytoplankton
https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.70077
#metagenomics
in Mol Ecol Res

Schematic resuming the different analyses done in this study, using 23S as an example. (A) Metabarcoding steps with DNA amplification, MiSeq sequencing, DADA2 pipeline and taxonomic assignment using assign. taxonomy() command and Phytool reference databases. (B) The metagenomic steps to recover taxonomic composition of phytoplankton with DNA fragmentation, NovaSeq sequencing, SortMeRNA to recover rRNA reads and taxonomic assignment with blast of the extracted rRNA reads against Phytool. (C) A fine comparison of the ASV sequence and abundance using mapping of the shotgun reads. A sequence with a colour means that it was assigned taxonomically.

Comparison of the relative abundances obtained for the main phytoplankton phyla based on metabarcoding and shotgun sequencing. As the relative abundances obtained in shotgun did not differ depending on the barcode, here, values of the 23S were taken as a reference for shotgun values. R-squared and the equation of the linear model are indicated for each group and each barcode.

Co-inertia analysis describing the co-structure between phytoplankton communities characterised by metabarcoding and shotgun approaches, for each marker gene (16S and 23S). The dot in the graph corresponds to metabarcoding samples and the end of the arrows to shotgun-mapping samples.

Pipeline release! nf-core/mag v5.2.0 - mag 5.2.0 - Puce Pangolin!
Assembly and binning of metagenomes
Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.2.0

#annotation #assembly #binning #longreadsequencing #metagenomes #metagenomics #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics

Metalog: curated and harmonised contextual data for global metagenomics samples

#metagenomics #microbiome

https://doi.org/10.1093/nar/gkaf1118

In this new paper, researchers extended the sedaDNA analysis beyond cave sediments: bone-adhered deposits preserved human, microbial, plant & animal sequences. #MetagenomicsMonday #SPAAM #aDNA #sedaDNA #metagenomics #cave #sediment
https://doi.org/10.1093/molbev/msaf202

Did you miss the ISBA11? Or maybe you want to refresh your memories from the symposium? 🧬 SPAAM members gathered for a debriefing session to share our impressions and feedback on the ISBA conference program. Check it out!
https://www.spaam-community.org/blog/2025/10/23/isba11-debrief/
#SPAAM #ancientDNA #ISBA11 #aDNA #sedaDNA #metagenomics

A new study explores the secrets hidden in concretions coating ancient teeth. 🦷 The researchers found microbial & protein traces, but human DNA remains elusive… #MetagenomicsMonday #SPAAM #aDNA #proteomics #metagenomics
https://doi.org/10.1016/j.isci.2025.113182

🚨 New release of AncientMetagenomeDir! (v25.09.0, Site of Palmyra)
https://github.com/SPAAM-community/AncientMetagenomeDir/releases/tag/v25.09.0
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below:

📈 Release v25.09.0:
📚 211 (+5) publications
🧬 1705 (+33) ancient host-associated metagenome samples
🦠 810 (+40) ancient microbial genomes
🌅 803 (+90) ancient environmental samples

#AncientDNA #palaeogenomics #aDNA #metagenomics(🧵 1/2)

Join us on December 10th for an online ‘Meta-*omics #Nextflow #pipeline community exhibition day’, for an intro and hands-on tutorial of #metagenomics #metataxonomics #metaproteomics #metatranscriptomics pipelines directly from the developers!

Since the first advert: we also have an additional pipeline that will be exhibited (metagenomics-toolkit)

We are almost oversubscribed, so register ASAP, deadline to register is Oct 24th: https://tally.so/r/31qJyQ

Poster advertising an event

Meta-*omics
Nextflow Pipeline
Community Exhibition Day
Do you work with . Want to find out how to
metagenomics, metaxaxonomics, make your analysis more
metaproteomics, metatranscriptomics efficient, scalable, and
datasets? reproducible?
Meet developers for an introduction and practical hands-on demonstration of their meta-*omics Nextflow pipelines!
When is it happening?
December 10th 2025. Times pending
Where is happening?
Online! Platform pending

What do you need?
- Ability to navigate the UNIX command line Online
- Be already familiar with basic theory/concepts pjatform pending of the analysis of your meta-*omics data
- A computer, and an internet connection

Interested? Register your interest and choose your pipeline(s)
https://tally.so/r/31gJyQ

Supported by NFDI4MIcrobiota and NextflowAmbassadors

Poster advertising event

Featured pipelines

nf-core/createtaxdb (nf-co.re/createtaxdb)
nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input FASTA reference genome set in a highly automated and parallelised manner.

Biobakery-nextflow (github.com/BonhamLab/biobakery-nextflow)
Shotgun metagenomics community profiling (taxonomic and functional) of Illumina short read data using the Biobakery suite of tools and databases.

epi2me-labs/wf-metagenomics (github.com/epi2me-labs/wf-metagenomics)
Taxonomic classification of Nanopore sequenced metagenomic sequencing data and identification of antimicrobial resistance (AMR) or virulence genes. It includes an optional step to remove host sequences. It can also be run through the EPI2ME Desktop Application.

nf-core/taxprofiler (nf-co.re/taxprofiler)
nf-core/taxprofiler is a pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It performs in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, with standardised output profiles.

(and more! Please contact James Fellows Yates for the rest of the list - hitting Alt text limits now)

🦠 Are tiny gut protists rewriting what we know about “good” and “bad” microbes?

🔗 Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.006

📚 CSBJ: https://www.csbj.org/

#Microbiome #GutHealth #Metagenomics #Protists #Blastocystis #Giardia #NGS #Microbiota #MicrobialEcology #NGS #ComputationalBiology #MolecularBiology

#metagenomics

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