Cool preprint about strain-level metagenome association studies using k-mer containment. Mallawaarachchi et al. from @gerrythill.bsky.social's group. I tried tackling this in our original paper for sylph (sylph-docs.github.io), but this seems to be much more sophisticated. Excited to read!

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5d ago

Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy https://www.biorxiv.org/content/10.64898/2026.08.30.748153v1

The importance of interbacterial relationships in shaping cyanobacterial ecology www.cell.com/trends/micro... #jcampubs 🌊

The importance of interbacterial relationships in shaping cyanobacterial ecology

Cyanobacteria are a globally abundant bacterial phylum that make key contributions to primary production and nutrient cycling in aquatic ecosystems. However, some cyanobacteria also cause substantial ...

cell.com

Designing antimicrobials with programmable mechanism and safety [new] ...conditional diffusion framework controls physicochemical properties & motifs, enabling de novo, analog, and motif-guided design for desired activity and safety.

A genomic catalog of Earth’s bacterial and archaeal symbionts [new] ...is predicted & cataloged by a machine learning tool identifying their symbiotic relationships.

Bacterial genomes are remarkably dynamic, shaped by horizontal transfer of plasmids that follow evolutionary trajectories of their own. This study uses eco-evolutionary perspectives to reveal how #plasmid communities are shaped and contribute to bacterial #evolution. 🧪 #AcademicSky plos.io/4gAJGlB

MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data www.nature.com/articles/s41... #jcampubs

MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data - Nature Microbiology

MetaCAT is a computational framework to assess host–microbiome interaction via a combination of high-accuracy and efficient microbial genome reconstruction and metagenome-wide association studies with...

nature.com

🧬 PanGBank is now available! • 4,600+ prokaryotic #pangenomes, 393,000+ genomes • #PPanGGOLiN graph partitioning, RGPs & Modules • User-friendly web interface, API & CLI 🌐 pangbank.genoscope.cns.fr 🎓 Try it in on #AMR in A. baumannii : shorturl.at/Vw3zc #ABRomics @ifb-elixir-fr.bsky.social

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN https://www.biorxiv.org/content/10.64898/2026.08.05.742796v1

Arnoux, Mainguy, Bazin, Gautreau, Lemane, Vallenet, Calteau: PPanGGOLiN V2: technical enhancement and extended functionalities for prokaryotic pangenome analysis https://arxiv.org/abs/2607.24111 https://arxiv.org/pdf/2607.24111 https://arxiv.org/html/2607.24111

8/ Co-author Jean Mainguy, Laura Bry, Quentin Fernandez De Grado, Yazid Hoblos, @vallenet.bsky.social, Alexandra Calteau @genolabgem.bsky.social

🧬 We're thrilled that PANORAMA has been published! An open-source method to predict & compare biological systems across bacterial pangenomes. Built on PPanGGOLiN, it runs at #pangenome scale in minutes vs. hours for genome-by-genome tools. 📄 doi.org/10.1371/jour... @jpjarnoux.bsky.social

Lossless compression of k-mer matrices enabling random row access https://www.biorxiv.org/content/10.64898/2026.07.03.736306v1

Using protein language models for pangenome construction https://www.biorxiv.org/content/10.64898/2026.06.04.730042v1

A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential www.nature.com/articles/s41...

Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation https://www.biorxiv.org/content/10.64898/2026.07.03.736256v1

7/ From landfills to beaches to insect guts 🐛 the Bioplastomics project explores Brazilian environments to find microbes and enzymes capable of breaking down plastics 🔬♻️ #JOBIM2026 Meet Julia Cantuti-Gendre at poster 47 👋

6/ MetaPanG 🧬 a new tool for strain-level profiling of metagenomic samples, powered by pangenome graphs from PanGBank. Going beyond species ID to reveal which strains — and which genes — are really there 🔬 #pangenomics #JOBIM2026 Meet @tlemane.bsky.social at poster 43 👋

5/ Curious about pangenomes? Check out PangBank, our database built to explore gene content variation across bacterial species and support comparative genomics research 🔬 #pangenomics #JOBIM2026 Meet @j-main-guy.bsky.social at poster 49

Excited to share that our paper on Horizontal Gene Transfer is now out in its final form in @gigascience.bsky.social! 🥳 By analysing 163 high-quality ant genomes, we show that HGT from bacteria is widespread across the ants and likely has adaptive functions! doi.org/10.1093/giga... 🐜📸: Alex Wild

There's also an associated policy briefing, which looks at untangling the international legal frameworks that govern microbial resources. academic.oup.com/sumbio/artic...

Policy Briefing: from access to use—untangling the international legal frameworks that govern microbial resources

Abstract. The wide geographic distribution of microorganisms, combined with their vast taxonomic and functional diversity, make them indispensable reservoi

academic.oup.com

Deep Learning for Protein Complex Prediction and Design [new] ...investigates domain-specific architectures and search algorithms to model hierarchical protein structures, identify interacting homologs, and design protein sequences.

Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach [new] by designing a bio-informed classifier based on L3 rule, using graph prompt learning to reformulate embed pair classification into a graph task.

SCOPE: Siamese Contrastive Operon Pair Embeddings for Functional Sequence Representation and Classification [new] employs PLM embeddings & Siamese MLP for scalable operon pair class. across diverse microbial genomes, aiding annot. & network reconstruction.

Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction [new] Predicts microbiome abundance by aggregating genomic language model embeddings from raw DNA sequences, enabling few-shot learning.

A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...

The Pangenome Is Not a Parts List

The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.

open.substack.com

🧬CroCoDeEL is a new tool for detecting cross-sample contamination in metagenomic data.🐊🦠 The idea behind CroCoDeEL is simple and elegant. Imagine different cocktails poured into a row of glasses...🧵 www.nature.com/articles/s41... #Microbiome #Metagenomics #Contamination

ProtSpace: Protein Universe in Your Browser https://www.biorxiv.org/content/10.64898/2026.05.04.722720v1

Out Now! Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires #MicroSky

Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02318-2Cayman enables computational analysis of carbohydrate-active enzymes (CAZymes) in microbial community data. It revealed novel mucus-foraging gut microorganisms and differences in gut microbial CAZyme repertoires associated with lifestyle and disease.

go.nature.com

Graph Neural Network based Hierarchy-Aware Embeddings of Knowledge Graphs: Applications to Yeast Phenotype Prediction [new] ...leveraging ontology-derived semantic loss to create embeddings that better reflect domain know. and facilitate biological discovery.