Jiayue Yang

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts Viruses are often studied in disease settings, but in the ocean they outnumber cells and shape ecosystems, yet their dynamics remain poorly understood. In this study, high-resolution sampling of blue-...

Bermuda Atlantic Time Series surface waters contain thousands of viral populations with diel rhythms, forming “archetypes” that vary in abundance patterns, predicted hosts, taxonomy, and gene functions @sullivan-lab.bsky.social @joshuasweitz.bsky.social

dx.plos.org/10.1371/jour...

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

Microbial Diversity | Marine Biological Laboratory The goal of the course is to teach professors, postdocs and advanced graduate students how to discover, cultivate, and isolate diverse microorganisms catalyzing a breadth of chemical transformations, ...

Want to ride the front of the wave of all-things-microbiology; field work, cultivation, microscopy, molecular, bioinformatics and AI tools? Me too!
Please join us @mblscience.bsky.social for the 2026 Summer Microbial Diversity Course!
Applications due soon.
www.mbl.edu/education/ad...

The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky

Provirus induction diversifies adaptive variation in Pseudomonas aeruginosa lysogen populations Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that forms chronic infections in people with cystic fibrosis. Often P. aeruginosa strains are lysogens, infected with proviruses, that ...

Happy new year! The second big project of my PhD in Rachel Whitaker's lab is now up! 🎉 We look at how provirus infection affects the evolution of the bacterial chromosome with different types of viral induction – with CRISPRs or antibiotics. Take a peek 🦠 www.biorxiv.org/content/10.6...

Analyses of Genome-Wide Recombination in Sulfolobus islandicus https://www.biorxiv.org/content/10.64898/2025.12.16.694729v1

Environment and physiology shape antiphage system expression Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...

Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.

In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

An archaeal genetic code with all TAG codons as pyrrolysine www.science.org/doi/abs/10.1... #jcampubs

Dynamics of dN/dS within recombining bacterial populations The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often decline...

The first is from former PhD student Zhiru Liu @zzzhiru.bsky.social (now in @bengrbm.bsky.social's group @ MSK) examining the long-term patterns of selective constraint – measured by the classical ratio of nonsynonymous to synonymous mutations (dN/dS) – within recombining populations of bacteria.

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

A new theme issue of #PhilTransB examines the evolutionary history of bacterial immune systems, their modes of action, and the patterns how different bacterial immune systems are distributed across different ecosystems. Read: buff.ly/Z4qdxY1

Our EEB department at the University of Illinois at Urbana-Champaign is hiring an assistant professor in evo-devo. See go.illinois.edu/EEBAsstProf for details. Please share!

Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...

Have you ever wondered what increasing environmental stress will do to microbial communities?

In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...

I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) !
1/n

Special issue in @science.org on #EvolvingImmunity (great illustrations!), with themes addressed by the ERC #IDEM @philinbiomed.bsky.social 10+ years ago: the need to rethink the function of immunity in the context of its physiological roles & co-evo with microbes

www.science.org/toc/science/...

This sounds great! Are the seminars open to the public? Would love to share a link with my lab if so.

I am happy to announce that the Midwest Mathematical Biology Seminar will be returning for the Fall 2025 semester. Our talks will be held on Tuesdays at 11am US/Canada Eastern time (10am Central time).

Please see the link below for more information.

sites.google.com/view/midwest...

Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025

Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...

Critically evaluating the relative importance of phage in shaping microbial community composition The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial com...

Hello new phage phollowers!

I am shamelessly self-promoting mine and Angus Buckling's relatively new review "Critically evaluating the relative importance of phage in shaping microbial community composition"

www.cell.com/trends/micro...

Excited 🥳 to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601