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Reposted

Rob Finn @robdfinn.bsky.social · Jul 22

Now we have what I call the big three biomes represented in @mgnifydb.bsky.social, soil, marine and human. We are constantly looking for MAGs to add to our catalogues. Talk to @tgurbich.bsky.social if you have data you want to contribute.

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 21

@johannavw.bsky.social will also speak in the MICROBIOME session, presenting gemsparcl, an ultra-fast, MAG-aware tool for clustering millions of bacterial genomes in rapid time.
📍 MICROBIOME session
Weds evening | Room 01B

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 21

@tgurbich.bsky.social will present MGnify Genomes — our biome-specific genome catalogues built with @nextflow.io, featuring rich annotations & several sequence search tools.
📍 MICROBIOME session
Weds evening | Room 01B

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 21

@mberacochea.bsky.social will talk about @mgnifydb.bsky.social's infrastructure evolution - working towards service sustainability while balancing scale, data provenance, and operational constraints.
📍ELIXIR/NIH-ODSS session
Weds afternoon | Room 12

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 21

MGnify are at ISMB/ECCB 2025 this week!
Catch our talks on Wednesday to learn about our latest services and tools. 👇 #ISMB2025 #ISMBECCB2025

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Reposted

Tatiana Gurbich @tgurbich.bsky.social · Jul 17

With the addition of the soil genome catalogue, MGnify now hosts over half a million genomes - exciting milestone for the resource.

mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 17

The genome catalogue for the soil microbiome is now live on MGnify! Built from MAGs & isolate genomes across 21 studies (including the recently published SMAG and Microflora Danica catalogues), it features 19,472 species.

MGnify - EBI

www.ebi.ac.uk

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 17

A big thank you to the open data community who made this possible. Explore the catalogue here: www.ebi.ac.uk/metagenomics...

MGnify - EBI

www.ebi.ac.uk

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 17

The genome catalogue for the soil microbiome is now live on MGnify! Built from MAGs & isolate genomes across 21 studies (including the recently published SMAG and Microflora Danica catalogues), it features 19,472 species.

MGnify - EBI

www.ebi.ac.uk

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

Mettannotator academic.oup.com/bioinformati... provides a rich set of annotations for prokaryotic genomes, within a comprehensive NextFlow pipeline leveraging tools, databases and customised scripts to tap into gene functions for novel species.

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

AbstractSummary. In recent years, there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. T

academic.oup.com

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

Microbes can be difficult to culture in the laboratory. To tackle this we assemble their genomes directly from metagenomic data. These are called MAGs: metagenome-assembled genomes. Explore the novelty of uncultivated microbes in our biome-specific genome catalogues. www.ebi.ac.uk/metagenomics...

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

Functions are derived from proteins and the MGnify protein database now contains almost 2.5 billion protein sequences from microbiome data! www.ebi.ac.uk/metagenomics...

phmmer search | EBI metagenomics

Search our non-redundant protein database using HMMER

www.ebi.ac.uk

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

The MGnify analysis pipelines help researchers explore these microbial communities and understand what’s present and what they do in a diverse range of environments.

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

The microbiome is the community of microbes - bacteria, archaea, viruses & micro-eukaryotes - that live in almost all environments. So how do we untangle the complex puzzle in each environment?

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

It’s #WorldMicrobiomeDay! This year’s theme is Microbiome 101: What You Need to Know — here we present MGnify’s guide to microbiome data! 🔬

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Reposted

Europe PMC @europepmc.org · Jan 30

4/ We link publications with data from established repositories, including:
🔎Protein structures @pdbeurope.bsky.social
🌍Metagenomic data @Mgnifydb.bsky.social
🔎Protein families & functional sites @interprodb.bsky.social
🧪Bioactive molecules & drug discovery @chembl.bsky.social
And more!!

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Reposted

Martín @mberacochea.bsky.social · Jan 21

I've recently joined the Nextflow Ambassador program, we are using Nextflow in our team at @mgnifydb.bsky.social extensively. I'm excited to help grow the community around Nextflow. Being originally from 🇺🇾 (but now living in 🇬🇧), I want to help grow the LATAM Nextflow community.

Nextflow @nextflow.io · Jan 21

🎉 We are excited to kick off the 2025 Nextflow Ambassador Program with a vibrant, diverse new cohort from 35+ countries! 🌍

Read the blog post: seqera.io/blog/welcome...

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jan 7

At ELIXIR Europe's 2024 BioHackathon, we co-led work to improve how the metagenomics community can use RO-Crates to collectively describe and analyse more datasets, more efficiently. Our preprint envisions this as a federated microbiome analysis service: osf.io/preprints/bi...

OSF

osf.io

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mgnifydb.bsky.social @mgnifydb.bsky.social · Dec 2

Presenting at the "Metagenomics in spaceflight" workshop at NASA, Lorna- @microbiodata.bsky.social presented the vast microbiome resources available at @ebi.embl.org and MGnify to assist discussions to develop a roadmap for integration of metagenomic sequencing into planetary protection.

Metagenomics in spaceflight NASA workshop

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mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

MGnify Proteins – our vast database of protein sequences derived from metagenomic sequencing – is now accessible via the web () and via @googlecloud BigQuery Public Datasets.
For the full news, see

ebi.ac.uk/metagenomics/p… ebi.ac.uk/about/news/upd…

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mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

MGnify Genomes’ #marine catalogue has been updated to v2, with 33x the number of genomes compared to v1. It covers nearly 9x more species, and brings new annotations from our updated pipeline. This work is part of @BlueRemediomics and @EU_AtlantECO.

ebi-metagenomics.github.io/blog/2024/08/0…

mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

Food production systems play a vital role in the food we consume. @FindingPhenoEU uses statistical methods to assess how host-microbiome interactions for a variety of crops and animals can be leveraged for healthy and sustainable food production. 🐔🐷🐟🌽🍅🐝#WorldMicrobiomeDay

mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

We're celebrating @UNBiodiversity's #BiodiversityDay with a milestone for our #PartOfThePlan: MGnify has now analysed over 5000 studies of publicly available data, characterising microbial biodiversity in a wide range of environments around the Earth and beyond.

mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

Our annual #metagenomics #bioinformatics at MGnify course, running virtually in September, covers the lifecycle of metagenomics projects from experimental design through quality control & annotation to MAG generation & more. Apply by 9 June:

ebi.ac.uk/training/event…

mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

There is still time to register for the COS-EMBL workshop on Plant Macro and Microbiomes - exploring plant biotic interactions. Registration has been extended until 12th April.

embl.org/events/cos-emb…

mgnifydb.bsky.social @mgnifydb.bsky.social · Nov 25

Presenting MGnify Genomes' new catalogue comprising 112,951 genomes (2,847 species level clusters) derived from public mouse gut datasets with contributions from
@SilasKieser, @StrowigLab, @PedicordLab, generated as part of our work with @MRCMouseNetwork.

ebi-metagenomics.github.io/blog/2024/03/0…