In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...
📄 doi.org/10.1093/nsr/...
February 22, 2025 at 5:47 AM
In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...
📄 doi.org/10.1093/nsr/...
OUT NOW: Metagenomic immunoglobulin sequencing (MIg-seq) reveals IgA coating of microbial strains in the healthy human gut
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology
Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.
www.nature.com
January 2, 2025 at 5:38 PM
OUT NOW: Metagenomic immunoglobulin sequencing (MIg-seq) reveals IgA coating of microbial strains in the healthy human gut
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...
Let the games begin.
First World Cup wastewater metagenomic plate will be done tomorrow.
43 samples (23 from WC host cities).
First World Cup wastewater metagenomic plate will be done tomorrow.
43 samples (23 from WC host cities).
June 13, 2026 at 9:09 PM
Let the games begin.
First World Cup wastewater metagenomic plate will be done tomorrow.
43 samples (23 from WC host cities).
First World Cup wastewater metagenomic plate will be done tomorrow.
43 samples (23 from WC host cities).
It is 2025, and @elsevierconnect.bsky.social is still happily publishing AI-generated crap and asking money for this.
Come on, Elsevier, where is your commitment to publishing quality articles and book chapters?
pubpeer.com/publications...
Come on, Elsevier, where is your commitment to publishing quality articles and book chapters?
pubpeer.com/publications...
April 28, 2025 at 11:28 PM
It is 2025, and @elsevierconnect.bsky.social is still happily publishing AI-generated crap and asking money for this.
Come on, Elsevier, where is your commitment to publishing quality articles and book chapters?
pubpeer.com/publications...
Come on, Elsevier, where is your commitment to publishing quality articles and book chapters?
pubpeer.com/publications...
Excited to release METAGENE-1, a 7B parameter metagenomic foundation model, built to aid in pathogen detection & pandemic monitoring. Pretrained on 1.5 trillion base pairs of DNA/RNA sequenced from wastewater.
A collab w/ USC, PrimeIntellect, & the Nucleic Acid Observatory.
metagene.ai
A collab w/ USC, PrimeIntellect, & the Nucleic Acid Observatory.
metagene.ai
Metagenomic Foundation Model
Metagenomic Foundation Model for Pandemic Monitoring
metagene.ai
January 7, 2025 at 8:58 PM
Excited to release METAGENE-1, a 7B parameter metagenomic foundation model, built to aid in pathogen detection & pandemic monitoring. Pretrained on 1.5 trillion base pairs of DNA/RNA sequenced from wastewater.
A collab w/ USC, PrimeIntellect, & the Nucleic Acid Observatory.
metagene.ai
A collab w/ USC, PrimeIntellect, & the Nucleic Acid Observatory.
metagene.ai
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 13, 2025 at 8:53 PM
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
science.org
November 14, 2025 at 2:25 PM
1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs
Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery - Nature Communications
Benchmarking metagenomic binning tools with simulated and real datasets reveals factors affecting genome recovery and provides practical guidelines for improving metagenome assembled genome reconstruc...
www.nature.com
April 14, 2026 at 11:23 PM
Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs
Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes - Nature Communications
Metagenomic binning is the process of grouping metagenomic sequences by their organism of origin. Here the authors benchmark 13 metagenomic binning tools using seven data-binning combinations on five ...
www.nature.com
March 31, 2025 at 1:30 PM
Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Good job. You didn't use "dysbiosis" or "metagenomic space" even once. Totally =normal= conversation.
May 14, 2026 at 7:52 PM
Good job. You didn't use "dysbiosis" or "metagenomic space" even once. Totally =normal= conversation.
Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social
UKHSA launches new metagenomic surveillance for health security
The UK launches mSCAPE, a world-first metagenomics initiative by UKHSA to enhance health security through rapid pathogen detection and surveillance.
www.gov.uk
January 30, 2025 at 4:54 PM
Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper www.nature.com/articles/s41... #jcampubs
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology
Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.
www.nature.com
July 16, 2025 at 5:21 PM
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper www.nature.com/articles/s41... #jcampubs
If you use Kraken for profiling microbial / environmental / ancient metagenomic data, please check this preprint where I benchmark filtering strategies of Kraken outputs on simulated microbial and environmental metagenomic samples, and provide recommendations for optimal filtering thresholds
April 10, 2025 at 6:57 AM
If you use Kraken for profiling microbial / environmental / ancient metagenomic data, please check this preprint where I benchmark filtering strategies of Kraken outputs on simulated microbial and environmental metagenomic samples, and provide recommendations for optimal filtering thresholds
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
www.nature.com
September 16, 2025 at 1:25 PM
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
Every week I get a metagenomic readout of the most elevated viruses from wastewater collected the week before (44 sites).
COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.
COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.
September 21, 2026 at 7:44 PM
Every week I get a metagenomic readout of the most elevated viruses from wastewater collected the week before (44 sites).
COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.
COVID was on the list today for the first time since last winter, along with D68 and a bunch of rhinoviruses.
We passed 3,000 metagenomic samples this week.
I need a few hundred more hard drives.
I need a few hundred more hard drives.
July 16, 2026 at 2:32 AM
We passed 3,000 metagenomic samples this week.
I need a few hundred more hard drives.
I need a few hundred more hard drives.
Interested in bioinformatics method development for proteins, structures or metagenomic analysis? Please check out my lab’s starter pack!
🔗 go.bsky.app/VJhXcSs
🔗 go.bsky.app/VJhXcSs
November 28, 2024 at 12:36 PM
Interested in bioinformatics method development for proteins, structures or metagenomic analysis? Please check out my lab’s starter pack!
🔗 go.bsky.app/VJhXcSs
🔗 go.bsky.app/VJhXcSs
I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:
anvio.org/tutorials/co...
anvio.org/tutorials/co...
Competitive metagenomic read recruitment explained
A tutorial on the nuts and bolts of competitive read recruitment
anvio.org
October 25, 2025 at 10:50 AM
I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:
anvio.org/tutorials/co...
anvio.org/tutorials/co...
A really cool study just published used metagenomic sequencing to uncover viral causes of unexplained fevers in Uganda. Of 230 patients who had tested negative for common infections, 19% had viral pathogens—ranging from respiratory and GI viruses to deadly viruses.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing - Nature Communications
Acute febrile illness is common in sub-Saharan Africa and causative agents are often unknown. Here, the authors perform metagenomic sequencing on samples from patients with acute febrile illness in Ug...
www.nature.com
March 27, 2025 at 9:35 PM
A really cool study just published used metagenomic sequencing to uncover viral causes of unexplained fevers in Uganda. Of 230 patients who had tested negative for common infections, 19% had viral pathogens—ranging from respiratory and GI viruses to deadly viruses.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇
Evolution of gut microbiota across honeybee species revealed by comparative metagenomics
Nature Communications - Here, the authors perform metagenomic analysis of honeybee gut microbes, uncovering many previously unidentified species and host specific differences in composition and...
rdcu.be
October 14, 2025 at 7:04 PM
Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇
Happy to report that we submitted a new manuscript this week.
The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...
The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...
Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States
Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this cap...
medrxiv.org
March 7, 2026 at 10:23 PM
Happy to report that we submitted a new manuscript this week.
The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...
The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...
Nature research paper: A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion
https://go.nature.com/4jODjvX
https://go.nature.com/4jODjvX
A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion - Nature
A metalloenzyme capable of oxidatively cleaving cellulose, found in a microbial community specialized in lignocellulose degradation, could enable sustainable biofuel production.
go.nature.com
February 12, 2025 at 9:10 PM
Nature research paper: A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion
https://go.nature.com/4jODjvX
https://go.nature.com/4jODjvX
A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion www.nature.com/articles/s41... #jcampubs
A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion - Nature
A metalloenzyme capable of oxidatively cleaving cellulose, found in a microbial community specialized in lignocellulose degradation, could enable sustainable biofuel production.
www.nature.com
February 13, 2025 at 2:31 PM
A metagenomic ‘dark matter’ enzyme catalyses oxidative cellulose conversion www.nature.com/articles/s41... #jcampubs
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies www.biorxiv.org/content/10.6... #jcampubs
July 27, 2026 at 2:57 PM
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies www.biorxiv.org/content/10.6... #jcampubs