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Reposted by Julia M. Brown

Ramunas Stepanauskas @rstepanauskas.bsky.social · Sep 7

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...

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Reposted by Julia M. Brown

Ákos T Kovács @evolvedbiofilm.bsky.social · Sep 5

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

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Reposted by Julia M. Brown

Leo Martins (he/him) @leomrtns.bsky.social · Aug 22

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 · Jul 31

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/...
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Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems

In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

journals.asm.org

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Reposted by Julia M. Brown

Joe Zackular @joeyzacks.bsky.social · Aug 20

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...

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Reposted by Julia M. Brown

George Bouras @gbouras13.bsky.social · Aug 8

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...

www.biorxiv.org

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Reposted by Julia M. Brown

Mya Breitbart @viromegirl.bsky.social · Aug 1

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 🦠🌊

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

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Reposted by Julia M. Brown

Queralt Tolosa, PhD @queralttolosa.bsky.social · Jul 30

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

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Reposted by Julia M. Brown

Nature Reviews Genetics @natrevgenet.nature.com · Jul 21

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.

www.nature.com

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Julia M. Brown @viraljules.bsky.social · Jul 17

Excited to try this one!

Nature Biotechnology @natbiotech.nature.com · Jul 16

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - @benjwoodcroft.bsky.social go.nature.com/3IwOxHh

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology

Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

go.nature.com

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Reposted by Julia M. Brown

Nick Record @seascapescience.bsky.social · Jun 11

"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.

www.science.org

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Reposted by Julia M. Brown

A. Murat Eren (Meren) @merenbey.bsky.social · Jun 5

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

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Reposted by Julia M. Brown

Emil Ruff @emilruff.bsky.social · Jun 2

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...

www.simonsfoundation.org

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Reposted by Julia M. Brown

Sean Eddy @cryptogenomicon.bsky.social · May 22

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.

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Vivek Mutalik @vivekmutalik.bsky.social · Nov 21

#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…

www.sciencedirect.com

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Reposted by Julia M. Brown

Carl Zimmer @carlzimmer.com · May 1

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

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Matthew Hahn @3rdreviewer.bsky.social · Apr 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

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Reposted by Julia M. Brown

Cameron Thrash @jcamthrash.bsky.social · Apr 9

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

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Reposted by Julia M. Brown

Rob Edwards @linsalrob.bsky.social · Mar 12

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

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Reposted by Julia M. Brown

Luke Hillary @lukehillary.bsky.social · Feb 11

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

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Reposted by Julia M. Brown

Ran Blekhman @blekhman.bsky.social · Jan 27

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...

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Reposted by Julia M. Brown

Cameron Thrash @jcamthrash.bsky.social · Jan 28

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

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Reposted by Julia M. Brown

Axel Visel @axelvisel.bsky.social · Jan 17

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/...

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

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Reposted by Julia M. Brown

Phage papers @phagepapers.bsky.social · Dec 1

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

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Reposted by Julia M. Brown

Rob Lanfear @roblanfear.bsky.social · Nov 26

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!

🧪

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Reposted by Julia M. Brown

Samuel Aroney @aroneys.bsky.social · Nov 26

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla.
doi.org/10.1101/2024...
@wwood @rhysnewell @CMR_QUT
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