Rooftop and surface garden soils in Bangladesh harbor diverse resistome profiles - Environmental Monitoring and Assessment Despite the growing expansion of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles (i.e., resistome) of microbial communities in rooftop and surface garden soi...

Alhamdulillah.
Just published: Our new paper in Environmental Monitoring and Assessment. IF 3.0
A metagenome-based approach to explore environmental AMR. #mtrlabbau #amr #metagenome
link.springer.com/article/10.1...

🔬 Excited to announce the Galaxy #Metagenome Training Course 2026!
💻 Online | 📅 March 5–6, 2025 | ⏰ 10:00–14:00 CET
✨ Covers Galaxy, amplicon & metagenome workflows, assembly, binning, functional annotation & more.
🚀 Beginner-friendly, no participation fee!
🔗 www.denbi.de/training-cou...
#UseGalaxy

This was not done in an afternoon. @ionferrico.bsky.social put in an incredible effort to quality filter, assemble, gene call, dereplicate, bin, MAG and analyse data from over 3 Tb of #metagenome data from 94 samples including time series. Thanks also to @ramalok.bsky.social and all other coauthors

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an as-sembler that operates directly on these sketches. MSR produces...

Another #metagenome assembly algorithm for #PacBio HiFi data - introducing Alice!

I'll be very interested to see how this performs on some of our trickier datasets.

More broadly, I'm happy to see continual development of tools for long-read #metagenomics.

doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

#workflow #genome_assembly #galaxyproject #workflows #metagenome #eosc #fair #open_science (2/2)

Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving...

Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia

#Tuber
#truffles
#Metagenome
#Geotrichum
#Microbiota
#Gleba
#Surfaceoftruffle

pmc.ncbi.nlm.nih.gov/articles/PMC...

Redirecting

New #metagenome assembly comparison of PacBio, ONT, and Illumina in human gut #microbiomes.

- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"

doi.org/10.1016/j.ce...

Can the 'good' bacteria in your mouth act as probiotic cavity fighters? If UC Berkeley's Wenjun Zhang has her way, no one will ever have to brush or floss again.

Can the 'good' #bacteria in your #mouth act as #probiotic cavity fighters? ...

| #oral | #microbes | #microbiome | #teeth | #metagenome | Via @sciencex.bsky.social

Nanopore metagenomics 2026 Learn how to extract DNA from metagenomic samples, prepare libraries, carry out sequencing and analyse data.

Expressions of interest have opened for our #Nanopore #Metagenomics workshop with @nanoporetech.com.

We'll cover experimental methods and sample collection, #DNAextraction, library preparation, and tools for #data analysis and #Metagenome Assembled Genomes.

👉 buff.ly/JfquoNA

#bioinformatics

Shixu He (KU) gave a brilliant talk about the #metagenome of the Greenland population, revealing unique microbial signatures. Seems like ice-cream can improve your health!?

Nanopore metagenomics 2026 In this in-person workshop, learn how to extract DNA from metagenomic samples, prepare libraries, carry out nanopore sequencing and analyse data.

📣 New dates announced for our #Nanopore #Metagenomics workshop in 2026 covering:

🧪 Experimental methods & sample collection
🧬 #DNAextraction & library prep
📊 Data analysis & visualisation
💻 Tools for #Metagenome Assembled #Genomes

Register your interest 👇
buff.ly/RDdTq11

@nanoporetech.com

OUTPOST: A comprehensive analysis software for whole‐metagenome shotgun sequencing incorporating group stratification The whole metagenOme shotgun seqUencing sTream Pipeline that is cOmprehensive and uSeful for mulTi groups experiments (OUTPOST) is a comprehensive analysis software for whole-metagenome shotgun seque....

OUTPOST: A comprehensive analysis software for whole‐metagenome shotgun sequencing incorporating group stratification #iMetaOmics
onlinelibrary.wiley.com/doi/10.1002/...
#metagenome #microbiome #Bioinformatics

Comparative multiomics analyses reveal the breed effect on the colonic host–microbe interactions in pig The colon contents of the Jiaxing Black (JXB) and the Duroc × Landrace × Yorkshire (DLY) pigs were collected for transcriptomic and metagenomic analyses. By using Weighted Gene Co-expression Network ...

Comparative #multiomics analyses reveal the breed effect on the colonic host–microbe interactions in pig #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#transcriptomics #microbiome #Bioinformatics #metagenome

Characterisation of the thermophilic P450 CYP116B305 identified using metagenomics-derived sequence data from an Australian hot spring - Applied Microbiology and Biotechnology Abstract Cytochrome P450 enzymes (P450s) have gained significant attention due to their remarkable ability to oxidise unactivated C-H bonds with high regio- and stereoselectivity. Their industrial uti...

New paper investigating a new #biocatalyst from a #metagenome
Characterisation of the #thermophilic #P450 CYP116B305 identified using metagenomics-derived sequence data from an Australian hot spring. Appl Microbiol Biotechnol 109, 133 (2025). doi.org/10.1007/s002...

A multi‐centered prospective birth cohort study in Western China The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a regi...

A multi‐centered prospective #birth #cohort study in Western China onlinelibrary.wiley.com/doi/10.1002/... #MultiOmics #genome #metabolome #metagenome #scRNA

We got great results on the bioanalyzer today from the genomic and metagenomic museum samples! 🧬

Thanks to @madeleinebergstrom.bsky.social! Now we're looking forward to send these off for sequencing; they're part of a small pilot project.
#microbiome #metagenome #hologenome

High-quality metagenome assembly from nanopore reads with nanoMDBG Third-generation long-read sequencing technologies, have been shown to significantly enhance the quality of metagenome assemblies. The results obtained using the highly accurate reads generated by…

📄 A new preprint from scientists at the Earlham Institute, @pasteur.fr, @ukceh.bsky.social, and @quadraminstitute.bsky.social presents nanoMDBG - an evolution of their earlier metaMDBG #metagenome assembler - now designed to support @nanoporetech.com #sequencing data.

buff.ly/MrTyegs

Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of Mesomycoplasma hyopneumoniae strains causing pig lung lesions In this study, we utilized 744 metagenomic sequencing data from lower respiratory tract microbial samples of 675 well-phenotyped pigs across five cohorts. From these, we constructed a microbial gene ...

Comprehensive #lung microbial gene and #genome catalogs assist the mechanism survey of #Mesomycoplasma hyopneumoniae strains causing #pig lung lesions onlinelibrary.wiley.com/doi/10.1002/...
#microbiome #metagenome #adhesion

Honoring Earth Day, Every Day 🌍

PacBio is committed to contributing to a better future for our planet and global health. Watch how researchers are uncovering thousands of microbial genomes in complex soil #microbiome communities using HiFi #longread #metagenome assembly.

Watch: bit.ly/3Gxlxhm

Transforming metagenome assembly from long reads with metaMDBG Researchers at The Earlham Institute and Institut Pasteur in France have developed a new tool to uncover microbial diversity. MetaMDBG allows for more efficient assembly of highly accurate long reads…

💬 "de Bruijn graphs are a computationally efficient way to represent overlaps and relationships between reads.” @gaetanbenoit.bsky.social

Researchers at the Earlham Institute and Institut Pasteur have developed metaMDBG to enhance #metagenome assembly from @pacbio.bsky.social #HiFi sequencing. 🖥️🧬

Group Leader Dr Chris Quince, one of the developers of metaMDBG

💬 "The efficiency of the assembler allows us to work with bigger data sets and to start thinking about co-assembling data sets and retrieving strain-level genomes."

Transforming #metagenome assembly from #longreads with metaMDBG 🖥️ 🧬
➡️ buff.ly/iYiWTEf

Transforming metagenome assembly from long reads with metaMDBG Researchers at The Earlham Institute and Institut Pasteur in France have developed a new tool to uncover microbial diversity. MetaMDBG allows for more efficient assembly of highly accurate long reads…

In a new article, scientists at the Earlham Institute and @pasteur.fr discuss the computational tools they're developing to enable highly-accurate #metagenome assembly from #longread PacBio and ONT #sequencing.
buff.ly/RPKbZtz

🧪 🖥️ 🧬

Interesting pre-print looking at shallow shotgun #metagenomics with short reads for #metagenome profiling, assembly, and function. Pretty clear limitations, but assembly was particularly bad.

Long reads have advantages in all three areas; similar benchmarking approaches would prove useful here.

Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena Abstract. Tillage erosion poses threats to crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosyste

MicGeo NEWS.
Our second study on
biogeography of microbiome functions on field scale is out!

@zalf.bsky.social

#cereal #microbiome #Ncyle #nitrifiers #denitrifiers #diazotrophs #fertlization #remotesensing #metagenome

academic.oup.com/ismecommun/a...

Transforming metagenome assembly from long reads with metaMDBG Researchers at The Earlham Institute and Institut Pasteur in France have developed a new tool to uncover microbial diversity.

💬 "de Bruijn graphs are a computationally efficient way to represent overlaps and relationships between reads.” @gaetanbenoit.bsky.social

Researchers at the Earlham Institute and Institut Pasteur have developed metaMDBG to enhance #metagenome assembly from @pacbio.bsky.social #HiFi sequencing. 🖥️🧬

Transforming metagenome assembly from long reads with metaMDBG Researchers at The Earlham Institute and Institut Pasteur in France have developed a new tool to uncover microbial diversity.

🆕 In a new article, scientists at the Earlham Institute and @pasteur.fr discuss the computational tools they're developing to enable highly-accurate #metagenome assembly from #longread #sequencing.
buff.ly/RrRTfW8

@gaetanbenoit.bsky.social

🧪 🖥️ 🧬

Extremely happy to be part of this amazing study!

#Cancertherapy #Microbiome #Metagenome

bsky.app/profile/medc...

Glad we can share some project results in #Zenodo and make research and scientific knowledge available for everyone! 👉https://zenodo.org/records/14864574

#bioremediation #soilhealth #metagenome #microbiome #data #bacteria
@cnrs.fr @rtds-group.bsky.social