Ann Gregory, PhD
@gregoryannc.bsky.social
Asst. Prof. at the Uni of Calgary in the Dept. of Biological Sciences | Viromics & One Health | www.integrativeviromicslab.com
Reposted by Ann Gregory, PhD
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
November 20, 2025 at 9:24 PM
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.
Reposted by Ann Gregory, PhD
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
November 5, 2025 at 2:39 AM
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
Reposted by Ann Gregory, PhD
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...
@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
September 27, 2025 at 6:10 PM
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...
@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...
Reposted by Ann Gregory, PhD
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
September 17, 2025 at 1:39 AM
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.
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.
September 17, 2025 at 1:13 AM
🚨 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.
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.
Reposted by Ann Gregory, PhD
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...
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 ...
www.cell.com
September 9, 2025 at 5:05 PM
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...
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...
Reposted by 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!
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!
July 13, 2025 at 7:49 AM
📢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!
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!
Reposted by Ann Gregory, PhD
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...
#ScienceMatters
www.nature.com/articles/s41...
Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis - Nature Medicine
A novel personalized phage therapy strategy that selects phages for a predicted evolutionary trade-off may represent a viable alternative approach for the treatment of antimicrobial-resistant bacteria...
www.nature.com
April 30, 2025 at 1:57 PM
Reposted by Ann Gregory, PhD
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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
March 31, 2025 at 5:07 AM
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
🌐https://bfvd.foldseek.com
💾https://bfvd.steineggerlab.workers.dev/
1/3
Last day back at home in the USA #internationalwomensday #tucson #arizona #womensrightsarehumanrights #notmypresident
March 8, 2025 at 5:43 PM
Last day back at home in the USA #internationalwomensday #tucson #arizona #womensrightsarehumanrights #notmypresident
Reposted by Ann Gregory, PhD
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...
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...
www.nature.com
March 5, 2025 at 11:00 PM
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...
www.nature.com/articles/s41...
Reposted by Ann Gregory, PhD
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:
#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.
www.nature.com
February 18, 2025 at 11:02 AM
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:
#metagenomics #microbiome #microbiomesky
So what is MEDI? A combination of two things:
Reposted by Ann Gregory, PhD
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)
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)
December 2, 2024 at 2:44 PM
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)
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)
Reposted by Ann Gregory, PhD
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" 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.
www.nature.com
February 4, 2025 at 8:52 PM
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" now out in Nature Microbiology.
We wanted a way to measure bacteria and phage in metagenomes 1/
www.nature.com/articles/s41...
Reposted by Ann Gregory, PhD
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
January 28, 2025 at 3:03 PM
Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
Reposted by Ann Gregory, PhD
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...
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...
www.cell.com
January 22, 2025 at 5:12 PM
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...
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...
Reposted by Ann Gregory, PhD
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
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
January 22, 2025 at 6:11 AM
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
@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social
Reposted by Ann Gregory, PhD
RNA control of reverse transcription in a diversity-generating retroelement
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 8, 2025 at 6:36 PM
RNA control of reverse transcription in a diversity-generating retroelement
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ann Gregory, PhD
January 3, 2025 at 10:38 AM
Reposted by Ann Gregory, PhD
Reposted by Ann Gregory, PhD
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...
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.
www.nature.com
January 2, 2025 at 5:38 PM
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...
by Justin Sonnenburg, Matt Olm, Sean Spencer & co
#microsky
www.nature.com/articles/s41...
Reposted by Ann Gregory, PhD
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...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
December 23, 2024 at 4:39 PM
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...
📄 www.biorxiv.org/content/10.1...
💾 github.com/steineggerla...
Reposted by Ann Gregory, PhD
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…👇🏼
December 20, 2024 at 4:51 PM
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…👇🏼
Reposted by Ann Gregory, PhD
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...
www.biorxiv.org
December 18, 2024 at 8:08 PM
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...
Reposted by Ann Gregory, PhD
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...
www.science.org
December 12, 2024 at 7:22 PM
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/...