Deep untargeted wastewater metagenomic sequencing from sewersheds across the United States Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this cap...

Happy to report that we submitted a new manuscript this week.

The manuscript is abour our work untargeting wastewater sequencing as a technique for monitoring viral pathogens from wastewater. @lennijusten.bsky.social
1/
medrxiv.org/cgi/content/...

A phage protein screen identifies triggers of the bacterial innate immune system Nature Microbiology, Published online: 16 January 2026; doi:10.1038/s41564-025-02239-6A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

Out Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection Auxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...

Major contribution of particle‐associated microbes to deep‐sea organic carbon degradation The biological carbon pump mediates the export of particulate organic carbon from the euphotic zone to the deep ocean, where it provides the base of the food web. Although deep-sea microbial metaboli...

Very happy that our paper was published in Limnology & Oceanography #ASLO_LO
Huge shoutout to my co-authors🫰
& big thanks to reviewers and editors!
May the year keep up this energy 🙌
@microbialoceanv.bsky.social @aslo.org @davehambright.bsky.social
aslopubs.onlinelibrary.wiley.com/doi/10.1002/...

Ecological ubiquity and phylogeny drive nestedness in phages–bacteria networks and shape the bacterial defensome Author summary Viruses that infect bacteria, known as phages, are part of microbial communities and influence the abundance, diversity, and traits of their hosts. In an agriculture-related context, th...

#microsky #phagesky #phage
At last! Great to see this one out: journals.plos.org/plospathogen...

Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social

Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.

I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome:
doi.org/10.1093/isme...

Phage defence-system abundances vary across environments and increase with viral density | Philosophical Transactions of the Royal Society B: Biological Sciences The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain ...

Phage defence-system abundances vary across environments and increase with viral density

Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social

royalsocietypublishing.org/doi/10.1098/...

very nice, it's a natural spike-in! I wonder what are the GDPR implications, though, of sharing human reads.

I guess participants now will be asked to consent to their genomic data being shared.

Happy to team up with @microbe-enjoyer.bsky.social to highlight fantastic work by @gibbological.bsky.social, Alex Carr, and colleagues using community scale metabolic models to predict risk for C. difficile colonization!

See the initial study here: www.cell.com/cell-systems...

Protein Structure Informed Bacteriophage Genome Annotation with Phold Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

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

Electron micrograph of two phage infecting a host cell side-by-side, with hearts between them

Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊

𝗕𝗿𝗶𝗻𝗴𝗶𝗻𝗴 𝗣𝗵𝗮𝗴𝗲 𝗟𝘆𝘁𝗶𝗰 𝗖𝘆𝗰𝗹𝗲 𝘁𝗼 𝗟𝗶𝗳𝗲 🦠🧬

Dive into the lytic cycle! A bacteriophage injects DNA, hijacks the host, and rapidly replicates until the bacterium lyses, releasing a new swarm of virulent phages!

#blender #3D #cgi #science #research #biology #phage #lyticcycle #bacteria #scicomm #sciart

Viromics approaches for the study of viral diversity and ecology in microbiomes Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

Excited to try this one!

How little we’ve seen: A visual coverage estimate of the deep seafloor In decades of deep-sea exploration, humans have observed only 0.001% of the deep seafloor, leaving 66% of planet Earth unseen.

"How Little We've Seen"

Imagine measuring an area the size of Houston, then making generalizations about the entire globe.

From analysis of Bell et al., that's just what we're doing with the deep seafloor.

www.science.org/doi/full/10....

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.

Please see the official job ad here, and spread the word:

jobs.awi.de/Vacancies/20...

Simons Graduate Fellowships in Ecology and Evolution The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

Simons Graduate Fellowships in Ecology and Evolution www.simonsfoundation.org/grant/simons...
Application Deadline July 31, 2025

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Tapping the treasure trove of atypical phages With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncover…

#phagesky

Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF

Tapping the treasure trove of atypical phages

www.sciencedirect.com/science/arti...

Time to catch up on the past week’s news about science and medicine in the US. Whew. 1/10

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!

(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)

ecoevorxiv.org/repository/v...

CoverM: Read alignment statistics for metagenomics AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r

CoverM is published!

CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

GitHub - shandley/awesome-virome: A listing of software, tools and databases useful for virome analysis A listing of software, tools and databases useful for virome analysis - shandley/awesome-virome

Check out this list of awesome #virome tools and be sure to add yours!

github.com/shandley/awe...

#phagesky #microsky

MIUViG Update Survey Since the development of the Minimum Information about an Uncultured Viral Genome (MIUViG) standard (Roux et al. 2019), there has been an explosion in the number of genomic data generated on unculture...

We're looking for suggestions on how to update and adapt the Minimum Information about an Uncultured Viral Genome (MIUVIG) reporting standard. What works? What needs updating? Check out the survey forms.gle/DPHvMFe8Gsdj... 🧵

Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇

www.nature.com/articles/s43...

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

Venn diagram illustrating microbial diversity of bacteria and archaea captured by isolates, metagenome-assembled genomes (MAGs) from NCBI and IMG, and metagenomes from IMG. A large portion of microbial diversity, labeled as 'Microbial Dark Matter,' represents species not captured by isolates or MAGs. Image modified from https://www.science.org/doi/10.1126/sciadv.adq2166

Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes

...BUT: they still don't capture a lot of the 🦠 species that are out there

New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...

Phage-induced disturbance of a marine sponge microbiome - PubMed Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic …

Phage-induced disturbance of a marine sponge microbiome.

DOI: 10.1186/s40793-024-00637-7

https://pubmed.ncbi.nlm.nih.gov/39593141/

If you had a really nice looking alignment of about thirty 100kb virus genomes and you wanted to find recombination breakpoints, what software/methods would you use?

All suggestions, snark, links to papers etc. welcome. Trying to navigate a new field...

Please repost!

🧪