Ilnam Kang

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions.

We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

This was a fantastic collaboration between MIT and @tattabio.bsky.social . Read the preprint here: www.biorxiv.org/content/10.6... and checkout the github repo: github.com/TattaBio/Fla.... A huge thanks to the team: @microyunha.bsky.social , Matt Tranzillo, Nicolo Zulaybar, and Imane Bouzit.

This scalability unlocks extensive cross-proteome discovery. By querying viral proteomes against host genomes, FlashPPI identifies host-virus interactions involving previously uncharacterized proteins. 6/

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.

We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

New preprint! We propose "anergiobiosis" to describe microbial life at thermodynamic limits as a way of separating the physiological state from questions about aeonophilic extremophile specialization. ecoevorxiv.org/repository/v...
#Microbiology #Extremophiles #SubsurfaceMicrobiology #MicroSky

Phage–host interactions are a key driver of microbial ecology, but observing them in nature is hard!
With metaHi-C, we detect freshwater phage–host pairs and link their infection dynamics to evolution.

Together with @nadal-molero.bsky.social & Ana Martin-Cuadrado

www.biorxiv.org/content/10.6...

We're Looking to Sponsor Postdoc Fellows in AI-Driven Microbial Cultivation NSF Postdoctoral Research Fellowships in Biology

We're looking to sponsor applications to the new NSF PRFB who are interested in using AI to tackle microbiology's "Great Plate Count Anomaly"

Details below. Please share.

#microsky #postdoc #AI #microbiology

open.substack.com/pub/carinila...

Submit to our session "The art and science of microbial persuasion" focusing on microbial cultivation!

New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...

Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning | Nature Biotechnology https://www.nature.com/articles/s41587-026-03005-7

Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation | Nature Communications https://www.nature.com/articles/s41467-026-68859-6

Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae Insertion sequence (IS) elements are transposable regions of DNA present in a majority of bacterial genomes. It is hypothesized that differences in distributions of IS elements across bacterial strain...

Hey y’all,

New paper out from the lab in Microbial Genomics, starting down the rabbit hole of IS elements in Paeudomonas syringae

www.microbiologyresearch.org/content/jour...

Iranians are experiencing a collective trauma. Thousands have been killed/injured in recent events, the economy is crippled & the threat of a wider conflict is real. This is especially difficult for those living in Iran, as many have lost (or fear losing) loved ones. www.nature.com/articles/d41...

Reposting w/alt text.

Iranians are experiencing collective trauma. Thousands have been killed/injured, the economy is crippled & the threat of a wider conflict is real. It’s especially difficult for those living in Iran, as many have lost (or fear losing) loved ones. www.nature.com/articles/d41...

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...

This paper originated from a simple idea: Since we want to study SAR11 growth physiology, let’s look at how one SAR11 bacterium becomes two SAR11 bacteria, inspired by the quote from François Jacob, “The dream of a bacterium: to produce two bacteria”.

We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...

GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

Announcing a new tool for "denoising" long-read amplicon sequences: savont.

Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.

1/4

github.com/bluenote-157...

Application of Nanopore sequencing to intact caspid-packaged DNA reveals that bacterial DNA encapsulation is widespread in the human gut #microbiome

www.nature.com/articles/s41...

#microbiome friends, is there a database of cultured microbes that is readily searchable? Or a simple way to limit NCBI searches to cultured microbes?

Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments?

My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.

Please share around for visibility.

Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n
📃 doi.org/10.64898/2026.01.26.701724

Luo Lab - Microbial Ecology - join Lab members will have access to state-of-the art wet lab, and computing, and sequencing resources, including in-house sequencing for both short and long reads (Illumina NextSeq and Nanopore GridION). ...

Our lab has an opening for a fully funded postdoc position! Start date is flexible; ideally summer 2026. Apply by Feb 20th for full consideration. For more about the lab and how to apply:

sites.google.com/uncc.edu/mic...

Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth’s history | PNAS The transition from anaerobic to aerobic life was a pivotal adaptation in Earth’s history, yet the timing and genomic drivers remain poorly resolve...

Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth’s history | PNAS https://www.pnas.org/doi/10.1073/pnas.2515709123?utm_source=twitter&utm_medium=social&utm_term=pnasnews&utm_content=ed5e288c-e569-461d-9a1d-160b0d6facad&utm_campaign=hootsuite

Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan - Nature Microbiology Limiting phosphate concentrations could be a strategy to protect and sequester carbon dioxide as fucoidan, a polysaccharide produced by marine algae.

Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan | Nature Microbiology https://www.nature.com/articles/s41564-025-02240-z

Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions - Nature Microbiology Mathematical representations of overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification recapitulate dynamics in co-cultures of Prochlorococcus and eight heterotrophic b...

Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions www.nature.com/articles/s41...

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊

Cross-cohort analysis reveals conserved gut virome signatures and phage-encoded auxiliary functions in ulcerative colitis https://www.biorxiv.org/content/10.64898/2026.01.21.700755v1

This paper may be relevant, though it is largely about metagenome assembly.
doi.org/10.1038/s415...
anvio.org/m/anvi-scrip...

A nirK–cbb3 genomic region links SAR11 to nitrogen loss in the northern Benguela Upwelling System www.microbiologyresearch.org/content/jour... #jcampubs 🌊