Reposted by Phil Hugenholtz
A feature in Nature outlines the advances that suggest usable quantum computers could be here in a decade. ⚛️ 🧪
Quantum computers will finally be useful: what’s behind the revolution
A string of surprising advances suggests usable quantum computers could be here in a decade.
go.nature.com
February 6, 2026 at 2:09 PM
A feature in Nature outlines the advances that suggest usable quantum computers could be here in a decade. ⚛️ 🧪
Reposted by Phil Hugenholtz
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
www.nature.com
February 6, 2026 at 3:15 PM
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Phil Hugenholtz
Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...
February 2, 2026 at 8:55 AM
Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...
Reposted by Phil Hugenholtz
A surface-exposed cardiolipin synthase provides an unexpected paradigm for maintaining the Gram-negative outer membrane www.pnas.org/doi/abs/10.1... #jcampubs
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
January 26, 2026 at 4:34 PM
A surface-exposed cardiolipin synthase provides an unexpected paradigm for maintaining the Gram-negative outer membrane www.pnas.org/doi/abs/10.1... #jcampubs
Reposted by Phil Hugenholtz
Out Now! Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation #MicroSky
Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation
Nature Microbiology, Published online: 26 January 2026; doi:10.1038/s41564-025-02241-yLarge-scale computational and in vitro analyses identify commensal type III secretion systems and substrates in the human gut microbiome that can interact with human proteins to modulate immune pathways.
go.nature.com
January 26, 2026 at 6:28 PM
Out Now! Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation #MicroSky
Reposted by Phil Hugenholtz
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
January 26, 2026 at 7:00 PM
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
Reposted by Phil Hugenholtz
An eye-popping discovery: early vertebrates had four eyes rather than two www.nature.com/articles/d41...
An eye-popping discovery: early vertebrates had four eyes rather than two
Eyes on a face’s front or side enable a brain to perceive images. Fossil evidence suggests that two light-sensitive organs on top of ancient vertebrate heads generated images, too.
www.nature.com
January 26, 2026 at 4:50 AM
An eye-popping discovery: early vertebrates had four eyes rather than two www.nature.com/articles/d41...
Reposted by Phil Hugenholtz
Description of Spongorhabdus gen. nov., a novel genus within the Endozoicomonadaceae family, and its type species Spongorhabdus nitratireducens sp. nov., isolated from marine sponges www.microbiologyresearch.org/content/jour... #jcampubs
January 21, 2026 at 7:02 PM
Description of Spongorhabdus gen. nov., a novel genus within the Endozoicomonadaceae family, and its type species Spongorhabdus nitratireducens sp. nov., isolated from marine sponges www.microbiologyresearch.org/content/jour... #jcampubs
Reposted by Phil Hugenholtz
The ISME Early Career Scientist Committee is glad to begin the year by spotlighting @aroneys.bsky.social, a Postdoctoral Researcher at QUT, and his paper, “Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.”
doi.org/10.1038/s415...
(1/2)
doi.org/10.1038/s415...
(1/2)
January 20, 2026 at 4:49 PM
The ISME Early Career Scientist Committee is glad to begin the year by spotlighting @aroneys.bsky.social, a Postdoctoral Researcher at QUT, and his paper, “Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.”
doi.org/10.1038/s415...
(1/2)
doi.org/10.1038/s415...
(1/2)
Reposted by Phil Hugenholtz
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
github.com
January 20, 2026 at 1:37 AM
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
Reposted by Phil Hugenholtz
A molecular inventory of the faecal microbiomes of 23 marsupial species
#microbiology #microbiome #marsupials #MicroSky
@microbiologysociety.org
doi.org/10.1099/mgen...
#microbiology #microbiome #marsupials #MicroSky
@microbiologysociety.org
doi.org/10.1099/mgen...
January 18, 2026 at 7:06 PM
A molecular inventory of the faecal microbiomes of 23 marsupial species
#microbiology #microbiome #marsupials #MicroSky
@microbiologysociety.org
doi.org/10.1099/mgen...
#microbiology #microbiome #marsupials #MicroSky
@microbiologysociety.org
doi.org/10.1099/mgen...
This is such a shock. Such a smart and generous guy gone too soon.
We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 17, 2026 at 3:17 AM
This is such a shock. Such a smart and generous guy gone too soon.
Reposted by Phil Hugenholtz
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
Reposted by Phil Hugenholtz
Why does life explore so few of the forms it could possibly take? Using fractal descriptors, this #scienceadvances paper shows that Earth’s biosphere clusters around simple shapes, reflecting deep evolutionary constraints. @artemyte.bsky.social @manlius.bsky.social www.science.org/doi/pdf/10.1...
January 11, 2026 at 1:23 PM
Why does life explore so few of the forms it could possibly take? Using fractal descriptors, this #scienceadvances paper shows that Earth’s biosphere clusters around simple shapes, reflecting deep evolutionary constraints. @artemyte.bsky.social @manlius.bsky.social www.science.org/doi/pdf/10.1...
Reposted by Phil Hugenholtz
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
The scientific lead will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪
The scientific lead will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪
January 9, 2026 at 6:06 AM
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
The scientific lead will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪
The scientific lead will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪
Reposted by Phil Hugenholtz
While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting
Reconciliation algorithms infer the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizont...
www.biorxiv.org
January 7, 2026 at 11:22 AM
While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
Reposted by Phil Hugenholtz
It's finally out today in Nature Medicine - a huge shout out to Jess Bryant and the entire Seres team, past and present, on this post hoc analysis of microbiome omics data across all three clinical trials of VOWST (aka SER-109).
Read it here:
www.nature.com/articles/s41...
Read it here:
www.nature.com/articles/s41...
The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome - Nature Medicine
An exploratory analysis of the phase 3 ECOSPOR III trial shows that a higher dosage of the oral microbiome therapeutic VOWST led to enhanced pharmacokinetics, increased species engraftment and altered...
www.nature.com
January 6, 2026 at 2:53 AM
It's finally out today in Nature Medicine - a huge shout out to Jess Bryant and the entire Seres team, past and present, on this post hoc analysis of microbiome omics data across all three clinical trials of VOWST (aka SER-109).
Read it here:
www.nature.com/articles/s41...
Read it here:
www.nature.com/articles/s41...
Reposted by Phil Hugenholtz
Ever wondered if your favorite bacteria 🧫🦠 produce exopolysaccharides? You can now easily check that with epsSMASH, our new bioinformatic tool built on the antiSMASH framework. It detects both known and novel exoPS BGCs. Check out and share the preprint! www.biorxiv.org/content/10.6...
epsSMASH uncovers exopolysaccharide biosynthetic gene clusters in environmental and human microbiomes
Biofilms represent the default mode of bacterial life in natural and built environments, with extracellular polysaccharides (exoPS) serving as essential structural and functional components of the bio...
www.biorxiv.org
January 5, 2026 at 10:26 AM
Ever wondered if your favorite bacteria 🧫🦠 produce exopolysaccharides? You can now easily check that with epsSMASH, our new bioinformatic tool built on the antiSMASH framework. It detects both known and novel exoPS BGCs. Check out and share the preprint! www.biorxiv.org/content/10.6...
Reposted by Phil Hugenholtz
Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...
github.com
June 1, 2025 at 7:28 PM
Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...
Reposted by Phil Hugenholtz
Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!
[1/3] Is your favorite bacterial isolate hiding a surprise lytic virus with a VERY different lifestyle? Finally I can proudly say that our paper on persistent phages is out in Nature Microbiology. rdcu.be/eWJEp. Well done @peterdoug.bsky.social
Persistent virulent phages exist across bacterial isolates
Nature Microbiology - The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical...
rdcu.be
December 29, 2025 at 3:18 PM
Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!
Reposted by Phil Hugenholtz
Authors published a paper in Biorxiv, they used GTDB-Tk in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
www.biorxiv.org
December 25, 2025 at 5:37 PM
Authors published a paper in Biorxiv, they used GTDB-Tk in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #reproducibility #RRID
Reposted by Phil Hugenholtz
If you want an example of gold standard genomics across every aspect of a paper, read this. It levelled me up.
Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too.
www.nature.com/articles/s41...
Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too.
www.nature.com/articles/s41...
December 21, 2025 at 10:09 PM
If you want an example of gold standard genomics across every aspect of a paper, read this. It levelled me up.
Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too.
www.nature.com/articles/s41...
Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too.
www.nature.com/articles/s41...
Reposted by Phil Hugenholtz
Discovery of the most intron-rich eukaryotic genome phys.org/news/2025-12...
New #ISEPpapers: Nuclear #genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis academic.oup.com/dnaresearch/...
#Protists #Algae #Microbes #Genomics
New #ISEPpapers: Nuclear #genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis academic.oup.com/dnaresearch/...
#Protists #Algae #Microbes #Genomics
December 21, 2025 at 6:01 PM
Discovery of the most intron-rich eukaryotic genome phys.org/news/2025-12...
New #ISEPpapers: Nuclear #genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis academic.oup.com/dnaresearch/...
#Protists #Algae #Microbes #Genomics
New #ISEPpapers: Nuclear #genome sequencing reveals the highly intron-rich architecture of the chlorarachniophyte alga Amorphochlora amoebiformis academic.oup.com/dnaresearch/...
#Protists #Algae #Microbes #Genomics
Reposted by Phil Hugenholtz
@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
December 20, 2025 at 11:34 PM
@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...
Reposted by Phil Hugenholtz
Wait, is this a new taxonomy??
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
December 13, 2025 at 4:24 PM
Wait, is this a new taxonomy??