Ann Gregory, PhD

📢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-...

Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵

Weekly to biweekly

Spatially restricted immune and microbiota-driven adaptation of the gut - Nature Intestinal regionalization is characterized by robust and resilient structural cell states and the intestine can adapt to environmental stress in a spatially controlled manner through crosstalk betwee...

1/ Keen to share the story of my postdoc research out in @natureportfolio.bsky.social! We built a massive resource characterizing the spatial landscape of the gut—and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇
www.nature.com/articles/s41...

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae A study of how the complex interaction between capsules and mobile genetic elements shapes gene flow in populations of Klebsiella pneumoniae reveals that capsule inactivation by phage pressure facilit...

This morning #Klebsiella2024 @olayarendueles.bsky.social is presenting work on the interactions between capsule, fitness and Horizontal Gene Transfer in Klebsiella pneumoniae. Great story, some of it published journals.plos.org/plosbiology/...

📢 REMINDER: The CSV Early Career Researcher Virtual Seminar Series on Friday, Nov 22 @ 10:30 AM PST / 1:30 PM EST! 📢

Featuring talks from Bryce Warner and Mariya Goncheva.

A Zoom link has been sent to CSV members! Don't miss out and come support your fellow Canadian virologists!

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination - Nature Communications Microbial communities are predominantly composed of species and intraspecies units, but the mechanisms behind the formation and persistence of these units are unclear. Here, the authors provide experi...

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination www.nature.com/articles/s41... #jcampubs