Anders Ogechi Hostrup Daugberg

City, Biofilm of Humans (Part I) by Roberto — The title of today's post is a twist on the opinion article Paula Watnick and I wrote at the turn of the century: Biofilm, City of Microbes. As I contemplate population dynamics, from bac...

schaechter.asmblog.org/schaechter/2...
#MicroSky

Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity - Nature Microbiology Deep, long-read metagenome sequencing of 154 soil and sediment samples from diverse habitats in Denmark enabled recovery of 4,894 high-quality and highly contiguous microbial genomes. The vast untappe...

#ResearchBriefing

Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity

#MicroSky

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

Break the selective silence on the genocide in Gaza Substantial and well-documented evidence indicates a catastrophic public health emergency in Gaza (appendix pp 1–5), marked by severe food insecurity and alarming levels of malnutrition-related deaths...

Gaza has recorded the most health-care worker deaths (over 1400 deaths), UN deaths (295) & journalist deaths (212) than in any recent conflict zone.

Life expectancy at birth dropped 35 yrs in 2024. From Oct '23-May '25, there were 720 attacks on healthcare targets www.thelancet.com/journals/lan...

Graphical illustration of how EPS is enzymatically degraded in multiple steps into smaller fragments, fueling the growth of non-degrading species: EPS degraders break down EPS into larger oligomers for oligomer consumers; further degradation into monomers and small oligomers supports non-degrading consumers.

What is the role of extracellular polymeric substances (EPS) in carbon exchange among microbial species? @sammy-pontrelli.bsky.social &co show that #EPS, formed via #chitin degradation, drives #MicrobialDiversity by acting as a sequentially degraded #CarbonSource @plosbiology.org 🧪 plos.io/3J9kbuu

Someone on here compared AI produced material as "digital asbestos " which in a few decades' time we will have to work out how to eradicate from the fabric of research.

Was talking to a student who wasn't sure about why one would get a PhD. So I wrote up a list of reasons!
www.eugenevinitsky.com/posts/reason...

Why scientists need to be better at data visualization The scientific literature is riddled with bad charts and graphs, leading to misunderstanding and worse. Avoiding design missteps can improve understanding of research.

knowablemagazine.org/content/arti... My favorite advice piece.

I compile this and other useful advice articles on my lab website: lowepowerlab.ucdavis.edu/resources

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

A periodic table of bacteria?: Mapping bacterial diversity in trait space Bacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental prefe...

New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...

well this is kinda cool 🦠✨

Awesome story, biofilms are so fascinating! 🦠🧬🧫

Logo for the Sandpiper website

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE www.biorxiv.org/content/10.1... #jcampubs

Python Rgonomics | Emily Riederer Switching languages is about switching mindsets - not just syntax. New developments in python data science toolings, like polars and seaborn’s object interface, can capture the ‘feel’ that converts from R/tidyverse love while opening the door to truly pythonic workflows

If you are an R user and want to use python This blog is for you www.emilyriederer.com/post/py-rgo/

De Novo Glycan Annotation of Mass Spectrometry Data Carbohydrates are fundamental molecules of life that are involved in virtually all biological processes. The chemical diversity of glycans─carbohydrate chains─enables diverse functions but also challe...

Congrats to @margotbligh.bsky.social 🎉 terrific work on a complex problem in mass spectrometry - See her new GlycoAnnotateR tool for De Novo #Glycan Annotation of Mass Spectrometry Data // it works for all, #LCMS #MSI pubs.acs.org/doi/10.1021/...
@mpimarinemicrobio.bsky.social

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity Abstract. Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and med

GATOR-GC is out at @narjournal.bsky.social!! Check out our new targeted genome mining tool featuring a novel similarity metric to efficiently compare and deduplicate gene clusters.

We uncover biosynthetic diversity missed by other genome mining tools

academic.oup.com/nar/article/...

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio

Very excited to share the first paper out of my Postdoc @CMR:

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social

doi.org/10.1093/isme...

🧵1/7

gutSMASH might be a good addition to the list, depending on what you want to do. It identifies primary metabolic gene clusters in gut bacteria 😊🦠

The 3-decade-old competition that enabled the emergence and evaluate of AlphaFold has run out of NIH funding.

The program will be terminated in weeks.

This is terminating success.

www.science.org/content/arti...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

Overview of paper revealing role of arginine in regulating K. pneumoniae mucoidy.

Our paper reporting a highly conserved mechanism by which arginine positively regulates hypervirulent K. pneumoniae mucoid phenotype is now fully online.
rdcu.be/euiWG

Summary picture is below, but details in the 🧵

Scihub stopped uploading new articles. SciDB is a continuing effort which has the entire scihub collection AND new papers.

annas-archive.org/scidb

I'd like to be added 😊

#GeneSky #MicroSky #MicrobiomeSky

🧬FapC amyloid protein structure unveiled🦠

I am proud to have performed the bioinfo part of this very impressive paper which not only shows the structure of an important functional amyloid protein, but also investigates its fibrillation mechanics and catalytic activity! 🖥
doi.org/10.1002/adma...

InterPro just got one of its biggest updates ever.

Now with 1.8 billion AI-driven protein annotations, AlphaFold-based TED domains, and viral proteins from the Big Fantastic Virus Database (BFVD).

See it all at www.ebi.ac.uk/interpro

🖥️🧬

@interprodb.bsky.social

I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

Christ