Julia M. Brown
@viraljules.bsky.social
(mostly) marine microbial and viral ecology via all the 'omics Mainer from away check out my lab webpage at juliambrown.github.io
Check out the conversation I had with Kate Dickerson of the Maine Discovery Museum. A fun conversation about viruses, career, research "cruises", foundational research and more.
Julia Brown | Maine Science Podcast
A conversation with Julia Brown, Senior Research Scientist at Bigelow Laboratory of Ocean Sciences
maine-science-podcast.simplecast.com
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/...
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...
medrxiv.org
Out Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky
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.
go.nature.com
Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...
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...
cell.com
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/...
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...
aslopubs.onlinelibrary.wiley.com
#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
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...
journals.plos.org
Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.
Beate Kraft @beatekraft.bsky.social · 10mo ago📣Postdoc opportunity @nordcee.bsky.social , University of Southern Denmark! 📣 Join us and work with Bo Thamdrup and me on microbial dark oxygen production in marine oxygen minimum zones! Please share widely! Deadline: 17 November More information can be found here: tinyurl.com/2vuur3wh
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 Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social royalsocietypublishing.org/doi/10.1098/...
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 ...
royalsocietypublishing.org
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.
Sean Gibbons 🦠💩@gibbological.bsky.social · last yr.You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements. Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal. journals.asm.org/doi/10.1128/... 🧵
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...
Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut
Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...
cell.com
Connor Tiffany@microbe-enjoyer.bsky.social · 12mo agoHappy to see the preview @joeyzacks.bsky.social and I wrote on the excellent paper recently published by the Gibbons Lab @gibbological.bsky.social is in press! I'd encourage folks interested in bacterial pathogenesis or microbial ecology to check out the preview and the research article!
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...
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...
biorxiv.org
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 🦠🌊
New online! Viromics approaches for the study of viral diversity and ecology in microbiomes
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.
nature.com
"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....
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.
science.org
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...
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
jobs.awi.de
Simons Graduate Fellowships in Ecology and Evolution www.simonsfoundation.org/grant/simons... Application Deadline July 31, 2025
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...
simonsfoundation.org
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.
#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...
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…
sciencedirect.com
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...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
ecoevorxiv.org
CoverM is published! CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs
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
academic.oup.com
Check out this list of awesome #virome tools and be sure to add yours! github.com/shandley/awe... #phagesky #microsky
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
github.com
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... 🧵
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...
forms.gle
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 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
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. DOI: 10.1186/s40793-024-00637-7 https://pubmed.ncbi.nlm.nih.gov/39593141/
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 …
pubmed.ncbi.nlm.nih.gov
