Ann Gregory, PhD

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...

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.

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 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

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...

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.

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 🧪

🚨 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.

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 ...

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...

📢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

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

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...

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...

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.

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:

Predicted infections with phage/host mutation models

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)

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.

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...

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...

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

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...

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...

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...

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 ...

Blood DNA virome associates with autoimmune diseases and COVID-19

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.

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...

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…👇🏼

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...

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...

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...

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/...

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! 🎉✨

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...

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

A tuneable minimal cell membrane reveals that two lipid species suffice for life Nature Communications - All cells are encapsulated by a membrane of complex lipidic composition, and understanding the roles of different lipids in membrane function is experimentally challenging...

All cells are encapsulated by a membrane of complex lipidic composition, right?

Not anymore! @JamesSaenz.bsky.social et al. show that a ‘minimal’ bacterial cell only needs 2 lipid species

#microNatComms #Microbiology #CellBiology #lipids

Read the paper:
www.nature.com/artic...

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️

So how can we ever achieve #gender #equality?

We discuss various strategies in this #Cell Commentary

#WomeninSTEM

www.cell.com/cell/fulltex...
🧵 1/

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web.
🌐 bfvd.foldseek.com
💾 bfvd.steineggerlab.workers.dev
📄 academic.oup.com/nar/advance-...