Excited to share my lab's new #MGen review! Evolving Strategies for Virus Discovery explores how virus identification is moving beyond sequence similarity toward AI- and protein structure-based approaches to uncover hidden viral diversity. doi.org/10.1099/mgen...

Evolving strategies for virus discovery

Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack ...

doi.org

The Integrative Viromics Lab at the University of Calgary is recruiting MSc and PhD students to study viruses in lakes, glaciers, permafrost, and other changing environments. Strong computational skills are preferred. Send a CV and cover letter to ann.gregory[at]ucalgary.ca

Love seeing some @natureportfolio.nature.com journals allow author names in non-Roman characters. Such a simple change, but huge for representation and proper attribution!

Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.

Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises

Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

pubs.acs.org

Breaking news: Democratic socialist Zohran Mamdani is elected as the next mayor of New York City, defeating former New York governor Andrew Cuomo and becoming the first Muslim and first of Indian descent to hold the office. https://wapo.st/47rlrDf

Microbes without borders: uniting societies for climate action @femsjournals.bsky.social Microbiol Ecol by @jaytlennon.bsky.social et al @leonorabit.bsky.social @vscooper.micropopbio.org @gilbertjacka.bsky.social academic.oup.com/femsec/artic...

Microbes without borders: uniting societies for climate action

The climate crisis is one of the most urgent and complex challenges of our time. Although often overlooked in models and policy, microorganisms play a crit

academic.oup.com

Why are some species widespread while others are found only in small, isolated areas? A study in Nature Communications shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, poor dispersers, and have evolved relatively recently. #evosky 🧪

Evolutionary age correlates with range size across plants and animals - Nature Communications

Why are some species widespread while others are found only in small, isolated areas? This study shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, poor dispersers, and have evolved relatively recently.

go.nature.com

🚨 We’re hiring! 🚨 The Integrative Viromics Lab @UCalgary 🇨🇦 is looking for a Lab Technician! 🔬 Phage isolation & culture 🧫 Anaerobic chamber work 📦 Lab management & student mentoring Apply now & help us explore the virosphere! You must have work authorization to work in Canada already.

Thrilled to share our two latest papers with the @tcostalab.bsky.social lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species. @imperialcollegeldn.bsky.social www.cell.com/cell/fulltex...

Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization

Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...

cell.com

📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!

#phage #phagesky

KaminskiMed@kaminskimed.bsky.social · last yr.

A phage therapy using naturally occurring bacteryophages that not only kill but also selects for less resistant bacteria, shows promise in Cystic Fibrosis patients infected with drug resistant Pseudomonas. Kudos Dr. Chen, Stanley, Turner and Koff!!! #ScienceMatters www.nature.com/articles/s41...

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3

Last day back at home in the USA #internationalwomensday #tucson #arizona #womensrightsarehumanrights #notmypresident

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social. www.nature.com/articles/s41...

Genome duplication in a long-term multicellularity evolution experiment - Nature

In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

nature.com

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:

Metagenomic estimation of dietary intake from human stool - Nature Metabolism

Diener et al. present a method that allows the estimation of dietary intake from human stool by detecting food-derived DNA in faecal metagenomes.

nature.com

Delighted to share this paper out via Virus Evolution: academic.oup.com/ve/advance-a... in which we develop and assess a quantitative method to infer phage and bacterial mutations driving changes in infection phenotypes arising in coevolutionary dynamics. a 🧵 about people (and some science)

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...

Longitudinal phage–bacteria dynamics in the early life gut microbiome - Nature Microbiology

Reanalysis of 12,262 longitudinal infant gut microbiome samples using the Marker-MAGu pipeline revealed phage–bacteria dynamics over the first year of life.

nature.com

Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors

Diverse and novel phages were recovered from anaerobic fatty acid–fed reactors. Phages linked to hosts in all three functional groups primarily consisted of generalists and temperate species, especia...

enviromicro-journals.onlinelibrary.wiley.com

Today we report a new compendium of human gut microbiomes with >168,000 samples By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria Now out in Cell: www.cell.com/cell/fulltex...

Integration of 168,000 samples reveals global patterns of the human gut microbiome

The Human Microbiome Compendium is a unified database of publicly available human gut microbiome 16S samples, built with the integrated data from hundreds of independent projects. The compendium is us...

cell.com

Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX... @benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social

RNA control of reverse transcription in a diversity-generating retroelement www.nature.com/articles/s41...

And I finally got round to updating the GitHub links... github.com/RyanCook94/i...

GitHub - RyanCook94/inphared: Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.

Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines. - RyanCook94/inphared

github.com

Andrew Millard@milja001.bsky.social · 2y ago

New year ... new lot of genomes. With @ryancook94.bsky.social updated what we can find in Genbank millardlab.org/phage-genome-j… With entire set annotated with PHROGs millardlab-inphared.s3.climb.ac.uk/GenomesDB_Jan2…

Blood DNA virome associates with autoimmune diseases and COVID-19 www.nature.com/articles/s41...

Blood DNA virome associates with autoimmune diseases and COVID-19 - Nature Genetics

Analysis of the blood DNA virome in patients with COVID-19 and autoimmune disease associates endogenous HHV-6 (eHHV-6) and high anellovirus load with increased disease risk, most notably for systemic ...

nature.com

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...

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.

nature.com

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...

Delighted that @tarnopol.bsky.social’s paper (dissertation ch.) is online @currentbiology.bsky.social! “Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.” Phage toxin genes became a feature of insect immune systems millions of years ago…👇🏼

I’m so excited to share that some of my grad work in the @aaronwhiteley lab is now available on bioRxiv! We used an AlphaFold-multimer screen to uncover how a bacterial NLR-related proteins senses multiple phage-encoded proteins to confer phage protection. Link: www.biorxiv.org/content/10.1...

A bacterial NLR-related protein recognizes multiple unrelated phage triggers to sense infection

Immune systems must rapidly sense viral infections to initiate antiviral signaling and protect the host. Bacteria encode >100 distinct viral (phage) defense systems and each has evolved to sense cruci...

biorxiv.org

Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...

Diverse phage communities are maintained stably on a clonal bacterial host

Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

science.org

It’s hard to believe the Integrative Viromics Lab is close to wrapping up its first year! This December has been full of celebrations—three birthdays, a festive winter holiday party, and so many milestones to reflect on and be proud of. Here’s to an even more exciting 2025! 🎉✨

EvoMIL uses protein language models & deep learning to predict virus-host associations with improved accuracy & highlights critical viral proteins. #VirusHostInteractions #DeepLearning #Bioinformatics 📄 doi.org/10.1371/jour... EVBC👤: @davidlrobertson.bsky.social

Prediction of virus-host associations using protein language models and multiple instance learning

Author summary Being able to predict which viruses can infect which host species, and identifying the specific proteins that are involved in these interactions, are fundamental tasks in virology. Trad...

doi.org