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Reposted by Morten Kam Dahl Dueholm

The PR2 database @pr2-database.bsky.social · 2d

metaPR2 version 3.0 has just been released.

Here are the major changes:
- Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0).
- 8 new published datasets have been added from the Arctic and from the South West Pacific.

app.metapr2.org

MetaPR2

app.metapr2.org

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Reposted by Morten Kam Dahl Dueholm

Michael Brockhurst @brockhurstlab.bsky.social · 2d

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

www.biorxiv.org

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Reposted by Morten Kam Dahl Dueholm

Vivek Mutalik @vivekmutalik.bsky.social · 3d

#microsky

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

Long-term homeostasis in microbial consortia via auxotrophic cross-feeding - Nature Communications

Synthetic microbial consortia are collections of strains which can segregate metabolic tasks for efficient use in biomaterials, biomanufacturing, and biotherapeutics. Here, the authors present a method to maintain and tune the ratio of two co-cultured bacterial strains via growth medium manipulation.

www.nature.com

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Morten Kam Dahl Dueholm @mkddueholm.bsky.social · 4d

I would blast the ASVs against the 16s rRNA from the genomes and then use the summed relative abundance of either perfect hits or hits with more then 99% identity. You would use the 16S rRNA copy numbers from the genomes to make rough correction. However, it is risky so I would probably not do it.

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Reposted by Morten Kam Dahl Dueholm

Ákos T Kovács @evolvedbiofilm.bsky.social · 10d

Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation

-in Science Advances from Ümit Akbey
with @mkddueholm.bsky.social

www.science.org/doi/10.1126/...

Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation

The structure of FapC reveals how Pseudomonas forms biofilms via a unique β solenoid amyloid fold and dynamic assembly pathway.

www.science.org

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Reposted by Morten Kam Dahl Dueholm

Emmanuele Severi @emmseveri.bsky.social · 12d

www.nature.com/articles/s44...

#microsky #phagesky #synbio

Non-model bacteria as platforms for endogenous gene expression in synthetic biology - Nature Reviews Bioengineering

Microbial synthetic biology might greatly benefit from the application of non-model organisms, which have been evolutionarily optimized for the production of specific proteins and metabolites. This Review discusses the design and application of endogenous production in non-model organisms.

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Marnix Medema @marnixmedema.bsky.social · 13d

Congratulations to #YuzeLi and all co-authors with the publication of rhizoSMASH: a new tool to identify catabolic gene clusters involved in the metabolism of plant root exudates, thus driving rhizosphere colonization. 1/4

rdcu.be/eH8tr

Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH

Nature Communications - Rhizosphere microbiomes are shaped by root exudation of diverse organic compounds. Here, the rhizoSMASH algorithm is introduced, which maps microbial genes involved in their...

rdcu.be

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Reposted by Morten Kam Dahl Dueholm

Nature Microbiology @natmicrobiol.nature.com · 16d

#NewResearch

Structure of a functional archaellum in bacteria of the Chloroflexota phylum

#MicroSky

@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social ‬ @mariejoest.bsky.social @sgribaldo.bsky.social

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

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology

Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Yoann Santin @ysantin.bsky.social · Sep 3

www.nature.com/articles/s42...

On the growth and form of bacterial colonies - Nature Reviews Physics

Most bacteria exist in dense aggregates, yet this lifestyle is relatively poorly understood compared with planktonic cultures. This Review explores biophysical models of aggregate development, and how...

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17d

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Emmanuele Severi @emmseveri.bsky.social · 18d

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

#phagesky #phage

Phages with a broad host range are common across ecosystems - Nature Microbiology

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Nature Microbiology @natmicrobiol.nature.com · 20d

#News&Views

A marine diatom-associated Bradyrhizobium can nodulate a terrestrial legume, expanding understanding of nitrogen-fixing symbioses

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

#microsky

A nitrogen-fixing bacterium forms symbioses on land and at sea - Nature Microbiology

Discovery of a marine diatom-associated Bradyrhizobium that nodulates a terrestrial legume expands our understanding of the environmental and host range of nitrogen-fixing symbioses.

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Emmanuele Severi @emmseveri.bsky.social · Sep 6

www.tandfonline.com/doi/full/10....

#microsky #microbiome #glycotime

Cell surface polysaccharides in the gut microbiota: occurrence, structure and role

The gastrointestinal (GI) tract is colonized by trillions of microorganisms living in a symbiotic relationship with the host. Commensal bacteria in the gut engage in cross-talks with epithelial and...

www.tandfonline.com

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Reposted by Morten Kam Dahl Dueholm

Ákos T Kovács @evolvedbiofilm.bsky.social · Sep 2

Behind the Paper by Michaela M Salcher
Why cultivation still matters in microbiology
communities.springernature.com/posts/why-cu...

Why cultivation still matters in microbiology

The majority of aquatic microbes are still uncultivated. Here, we cultivated 627 strains of abundant freshwater bacteria from 14 lakes, thus generating a collection that includes many previously uncul...

communities.springernature.com

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Reposted by Morten Kam Dahl Dueholm

Emmanuele Severi @emmseveri.bsky.social · Aug 22

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

#microsky

Discovery of a widespread chemical signalling pathway in the Bacteroidota - Nature

The N-acyl-cyclolysine system regulates the expression of co-localized operons encoding diverse secreted molecules in Bacteroidota.

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Niranjan Nagarajan @niranjantw.bsky.social · Aug 22

Our work on direct @nanoporetech.com sequencing of non-canonical bases in now out in @natcomms.nature.com!

Read all about it here: nature.com/articles/s41...

Great collab with Chew and Hirao lab

x.com/NiranjanTW/s...

Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning - Nature Communications

Perez, Kimoto, Rajakumar and colleagues present a fast and accurate DNA sequencing method that reads canonical and non-canonical bases using AI and nanopore technology. The approach enables an expande...

nature.com

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Reposted by Morten Kam Dahl Dueholm

Nature Microbiology @natmicrobiol.nature.com · Aug 21

#News&Views

Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.

#MicroSky

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

Amyloids in bacterial antiphage defence - Nature Microbiology

Bacterial prions form amyloids in response to phage infection and induce cell death to prevent viral replication, similar to the processes in fungi and across the tree of life.

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Cameron Thrash @jcamthrash.bsky.social · Aug 13

High-Density Microdroplet Cultivation Reveals the Essential Role of Microbial Interactions in the Growth of Environmental Microbes www.biorxiv.org/content/10.1... #jcampubs

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Morten Kam Dahl Dueholm @mkddueholm.bsky.social · Aug 11

MitSorter: a standalone tool for accurate discrimination of mtDNA and NuMT ONT reads based on differential methylation
academic.oup.com/bioinformati...

MitSorter: a standalone tool for accurate discrimination of mtDNA and NuMT ONT reads based on differential methylation

AbstractMotivation. The accurate differentiation between mitochondrial DNA (mtDNA) and nuclear mitochondrial DNA segments (NuMTs) is a critical challenge i

academic.oup.com

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Morten Kam Dahl Dueholm @mkddueholm.bsky.social · Aug 4

In connection with obtaining a Nagoya approval for sequencing metagenomes on Indian wastewater treatment plant samples. I need to print and sign the agreement on Indian Rs. 20/- Non Judicial Stamp Paper. Can anyone direct me to where I can obtain such stamp paper?😅

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Reposted by Morten Kam Dahl Dueholm

Ákos T Kovács @evolvedbiofilm.bsky.social · Jul 23

Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes

-in #FEMS Microbiology Rev from Nico Boon

academic.oup.com/femsre/advan...

Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes

Abstract. Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities—shedding light on cell-to-cell va

academic.oup.com

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Reposted by Morten Kam Dahl Dueholm

Kassiani Panagiotou @kassipan.bsky.social · Jul 20

Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.

The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky

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Reposted by Morten Kam Dahl Dueholm

Noah Fierer @noahfierer.bsky.social · Jul 18

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...

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...

www.biorxiv.org

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Reposted by Morten Kam Dahl Dueholm

Tom Booth @boothicus.bsky.social · Jul 9

🏺

Previously a preprint now a paper led by the Copenhagen group- ancient DA extracted from 1313 ancient humans shows the dynamics of different infectious diseases across Eurasia over the last 37,000 years.

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

The spatiotemporal distribution of human pathogens in ancient Eurasia - Nature

Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens coi...

www.nature.com

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Reposted by Morten Kam Dahl Dueholm

Rob Waterhouse @rmwaterhouse.bsky.social · Jul 11

BUSCO v6.0.0 has been released. busco.ezlab.org

BUSCO - from QC to gene prediction and phylogenomics

from QC to gene prediction and phylogenomics

busco.ezlab.org

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