Luke Hillary

Any UK plan for partial Horizon association ‘a profound error’ - Research Professional News Academic leaders warn against UK abandoning participation in collaborative part of EU R&I programme

UKRI's chief executive said recently that the UK "may wish to explore" paring back its association to the EU's research programme, to make it partial.

That would be a "profound strategic error", critics now warn.

By @clanicholson.bsky.social

www.researchprofessionalnews.com/rr-news-euro...

Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.

Our paper "Ecosystem health shapes viral ecology in peatland soils" is out in Nature Microbiology!

We show that peatland health strongly structures viral communities, shaping virus–host networks, and carbon and nutrient cycling. Please share.

www.nature.com/articles/s41...

#phagesky #Microsky

Data Discovery Tool Helps Identify Microbial Roles within Metagenomes | Joint Genome Institute Protein annotations provide insights into environmental tendencies

The Metagenome Stability Diagram uses gene markers across ecosystems to understand how environmental conditions constrain metabolic activity in microbiomes. 🖥️🧬🦠

https://jgi.doe.gov/user-science/science-stories/data-discovery-tool-helps-identify-microbial-roles-within-metagenomes

Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.

Soil viruses are important regulators of ecosystem function, but what are their roles in environments that face long-term degradation and restoration? In our paper published today in Nature Micro, we asked how soil viruses influence peatland recovery, and vice versa. www.nature.com/articles/s41...

Huge thanks to co-authors Trina Knotts, Sean Adams, Mohammed Ali, @mattolm.bsky.social, and to my PI, Joanne Emerson, who handled all of the wet-lab sample processing.
🧵 5/5

Viromes and metagenomes captured partially overlapping but differently biased components of the total gut viral community. This has significant implications for inter-study comparisons.

🧵 4/5

DNase treating your viromes? Unlike soil viromes, this looks like it might not have as big an effect in stool (at least in our study).

🧵 3/5

Firing up the MDA kit? We got STRONG compositional distortions and reduced richness. Whilst this effect is generally known, MDA continues to be used. Filtering out ssDNA viruses partially compensated for this, but at a cost in downstream data analyses.

🧵 2/5

📢 New preprint is out on bioRxiv 📢:

How much does virome prep influence our view of the human gut virome?

Short answer: a lot.

Long answer:
doi.org/10.1101/2025...

Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.

🧵 1/5

Huge thanks to co-authors Trina Knotts, Sean Adams, Mohammed Ali, @mattolm.bsky.social, and to my PI, Joanne Emerson, who handled all of the wet-lab sample processing.

🧵 5/5

Viromes and metagenomes capture partially overlapping but differently biased components of the total gut viral community. This has significant implications for inter-study comparisons.

🧵 4/5

DNase treating your viromes? Unlike soil viromes, this looks like it might not have as big an effect in stool (at least in our study).

🧵 3/5

Firing up the MDA kit? Get STRONG compositional distortions and reduced richness. Whilst this effect is generally known, MDA continues to be used. Filtering out ssDNA viruses can compensate, but it’ll cost you in downstream data analyses.

🧵 2/5

An upland landscape in Scotland with trees and open areas.

PhD opportunity with me at University of Edinburgh linked with Forest Research, funded by E5 DTP.

On the microbial mechanisms of soil carbon cycling in tree-planted upland soils. Apply before 14th Dec. Please share with your network.

Pic: one of our Scottish sites.

e5-dtp.ed.ac.uk/project?item...

We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...

Black box of phage–bacterium interactions: exploring alternative phage infection strategies | Open Biology The canonical lytic–lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and ...

No problem. A temperate phage can switch between being lysogenic or lytic, so can be either. A virulent phage can only be in a lytic lifecycle. There are also a bunch of alternatives doi.org/10.1098/rsob...

Same. It’s not helped when lots of biotech companies, including Illumina, misuse the term.

Also, as always, 16S rRNA gene amplicon sequencing != metagenomics

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...

Love this new paper from @gtrubl.bsky.social and @alexjprobst.bsky.social on the importance of accurate use of terminology in microbial ecology. I’ve seen a lot of use of lysogenic instead of temperate recently so it’s nice to see that distinction being made. doi.org/10.1111/1462...

🎉Woot woot 🎉Finished a 2 week writing challenge with sending a manuscript off to co-authors/ submitting data to NCBI. Onto the next one 😁

Learn more about EcoFABs in this episode of our #GenomeInsider podcast ⬇️ 🖥️🧬

Fitting that Google has DNA in today’s doodle,the same day Marie Skłodowska-Curie postdoc fellowship proposals are due in 😁🧬

ISVC2026 International Soil Virus Conference 2026! We are excited to announce and provide RSVP details for the next International Soil Virus Conference that will be held in Saint-Loup Lamaire, France on Jun…

📢 We are thrilled to announce the International Soil Virus Conference 2026 in conjunction with the Saint Loup Research Institute.
🗓️ June 16 – 18, 2026
📍 Château de Saint Loup sur Thouet, France
👇 RSVP by October 31st, 2025
#virus #phage #ISVC2026

Assistant Professor Plant-Microbe Interactions We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!

jobs.colostate.edu/postings/165...

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

#Perspective

A discussion on virus-encoded auxiliary metabolic genes and a framework for the biological interpretation of these genes.

#MicroSky 🦠

www.nature.com/articles/s41...

Awesome looking review on RNA phage discovery 😁

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

Efficient detection and typing of phage-plasmids Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...

🚨 New preprint! 🧬

𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.

We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use

📖 www.biorxiv.org/content/10.1...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

It’s life @jgi.doe.gov 🖖 but not as we know it. This symposium looks fascinating! (couldn’t resist making the Trek reference)