Phil Hugenholtz
@xrefugee13.bsky.social
📤 768
📥 900
📝 58
Microbiologist
reposted by
Phil Hugenholtz
Morten Kam Dahl Dueholm
about 9 hours ago
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...
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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...
https://www.biorxiv.org/content/10.64898/2025.12.21.693542v1
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Phil Hugenholtz
James McInerney
7 months ago
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...
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https://github.com/mol-evol/gcua1/25
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reposted by
Phil Hugenholtz
Peter Dougherty
7 days ago
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!
add a skeleton here at some point
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reposted by
Phil Hugenholtz
RRID Robot
11 days ago
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
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https://www.biorxiv.org/content/10.1101/2024.12.30.630741v2
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reposted by
Phil Hugenholtz
Ben Vezina
15 days ago
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...
add a skeleton here at some point
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reposted by
Phil Hugenholtz
ISEP
15 days ago
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
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reposted by
Phil Hugenholtz
Zamin Iqbal
16 days ago
@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...
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reposted by
Phil Hugenholtz
RuthLeyMicro
23 days ago
Wait, is this a new taxonomy??
add a skeleton here at some point
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reposted by
Phil Hugenholtz
ace-gtdb.bsky.social
25 days ago
GTDB is now cross-referenced from ENA genome assembly pages. Check it out:
www.ebi.ac.uk/ena/browser/...
. Thank you to
@ebi.embl.org
for support with setting up these links!
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ENA Browser
ENA Browser
https://www.ebi.ac.uk/ena/browser/view/GCA_000009045.1?show=xrefs
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reposted by
Phil Hugenholtz
ace-gtdb.bsky.social
25 days ago
The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at
gtdb.ecogenomic.org/tools/skani
. Find more information about
@jimshaw.bsky.social
fantastic tool at
www.nature.com/articles/s41...
.
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GTDB - skani calculator
An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.
https://gtdb.ecogenomic.org/tools/skani
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Phil Hugenholtz
ARC Tracker
25 days ago
More on ARC job cuts & restructure: ARC’s spending $374k on consultants for organisational “review” & “planning & development”. They’re also spending $765k on “risk management”. That’s $1.1 million on consultants being spent over 1 year. Un. Believable. Slow clap, ARC.
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reposted by
Phil Hugenholtz
Joint Genome Institute
26 days ago
The Metagenome Stability Diagram uses gene markers across ecosystems to understand how environmental conditions constrain metabolic activity in microbiomes. 🖥️🧬🦠
https://jgi.doe.gov/user-science/science-stories/data-discovery-tool-helps-identify-microbial-roles-within-metagenomes
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Data Discovery Tool Helps Identify Microbial Roles within Metagenomes | Joint Genome Institute
Protein annotations provide insights into environmental tendencies
https://jgi.doe.gov/user-science/science-stories/data-discovery-tool-helps-identify-microbial-roles-within-metagenomes
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3
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reposted by
Phil Hugenholtz
Karolin Luger
27 days ago
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the
#Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms -
www.annualreviews.org/content/jour...
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reposted by
Phil Hugenholtz
ARC Tracker
29 days ago
ARC says they’ll announce Centres of Excellence outcomes tomorrow (Tuesday 9th Dec). This is more than 2 months late, most likely due to the new security checking requirements for ARC grants. Centres of Excellence grants also need to have been approved by the Minister.
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reposted by
Phil Hugenholtz
Mizrahi Lab
about 1 month ago
Excited to share our new
@natecoevo.nature.com
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
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reposted by
Phil Hugenholtz
Dutchscientist (the real one)
about 1 month ago
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from
@bedec.bsky.social
. It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
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GitHub - bede/deacon: Fast DNA search and [host] depletion using minimizers
Fast DNA search and [host] depletion using minimizers - bede/deacon
https://github.com/bede/deacon
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reposted by
Phil Hugenholtz
Henry Gee
about 1 month ago
Eukaryogenesis was a billion year spree, but the acquisition of mitochondria happened when the party was winding down
www.nature.com/articles/s41...
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Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature
Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...
https://www.nature.com/articles/s41586-025-09808-z
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interesting side project picked up during development of gTranslate - discussed in the preprint
add a skeleton here at some point
about 1 month ago
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reposted by
Phil Hugenholtz
Lorenzo Pantolini
about 1 month ago
Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters. Pre-print:
www.biorxiv.org/content/10.1...
🧵👇(1/n)
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Rewriting protein alphabets with language models
Detecting remote homology with speed and sensitivity is crucial for tasks like function annotation and structure prediction. We introduce a novel approach using contrastive learning to convert protein...
https://www.biorxiv.org/content/10.1101/2025.11.27.690975v1
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reposted by
Phil Hugenholtz
bioRxiv Bioinfo
about 1 month ago
pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences
https://www.biorxiv.org/content/10.1101/2025.11.27.689987v1
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reposted by
Phil Hugenholtz
Arkadiy Garber
about 1 month ago
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
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metaTraits: a large-scale integration of microbial phenotypic trait information
Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1241/8343513
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reposted by
Phil Hugenholtz
Mart Krupovic
about 1 month ago
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses!
www.nature.com/articles/s41...
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Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
https://www.nature.com/articles/s41564-025-02190-6
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reposted by
Phil Hugenholtz
The Banfield Lab
about 1 month ago
Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses
www.nature.com/articles/s41...
@luisvalentin.bsky.social
@lingdong-shi.bsky.social
@martianmicrobe.bsky.social
@mschoelmerich.bsky.social
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Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications
Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...
https://www.nature.com/articles/s41467-025-65646-7
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reposted by
Phil Hugenholtz
Maria Dzunkova
about 1 month ago
Our institute
@i2sysbio.es
published news on our article published in
#ISME
Communications. We developed a
#bioinformatics
tool to demultiplex reads from
#Atrandi
microfluids platform
@atrandi.bsky.social
for microbial
#single-cell
genomics, great for detection of
#phages
&
#viruses
👩🔬🧬🧪🦠🧫🖥
#microsky
add a skeleton here at some point
1
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@arc-tracker.bsky.social
- any intel on CoE announcements?
about 1 month ago
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reposted by
Phil Hugenholtz
Michael Wagner
about 1 month ago
📢 New preprint on bioRxiv! We introduce V4-EXT, a revised 16S rRNA V4 primer set that dramatically improves detection of Patescibacteria and other undersampled lineages ✅ 938 samples ✅ More novel ASVs Primer choice matters 👀
www.biorxiv.org/content/10.1...
@ppjevac.bsky.social
#HuifengHu
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reposted by
Phil Hugenholtz
Rob Edwards
about 1 month ago
Long read Metagenomics,
#phage
and
#prophage
in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
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Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
https://www.nature.com/articles/s41586-025-09786-2
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reposted by
Phil Hugenholtz
Quanta Magazine
about 1 month ago
According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.
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A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
https://www.quantamagazine.org/a-cell-so-minimal-that-it-challenges-definitions-of-life-20251124/
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reposted by
Phil Hugenholtz
Brett Baker
about 1 month ago
youtu.be/Jy_boPdY0zo?...
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The Origins of Complex Life | Searching for the Asgards
YouTube video by Schmidt Ocean
https://youtu.be/Jy_boPdY0zo?si=2lPDaex4JgXV26gY
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reposted by
Phil Hugenholtz
Gene Doctor Gene
about 1 month ago
www.sciencealert.com/newly-discov...
🧪
#endosymbiosis
#mitochondria
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Newly Discovered Organism Could Represent a Whole New Branch in The Tree of Life
It's not every day that biologists announce an entirely new branch of life, and this one has been hiding under their noses for years.
https://www.sciencealert.com/newly-discovered-organism-could-represent-a-whole-new-branch-in-the-tree-of-life#
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reposted by
Phil Hugenholtz
Fabien Burki
about 1 month ago
www.nature.com/articles/s41...
#protistsonsky
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Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae - Nature Communications
Protist microbiomes are poorly understood. Here, the authors analysed single protist cells to profile their microbiomes and viromes showing that these tiny eukaryotes serve as environmental hubs for h...
https://www.nature.com/articles/s41467-025-65263-4
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reposted by
Phil Hugenholtz
Morten Kam Dahl Dueholm
about 1 month ago
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules.
academic.oup.com/ismecommun/a...
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High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules
Abstract. Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most m
https://academic.oup.com/ismecommun/article/5/1/ycaf117/8198090
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15
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reposted by
Phil Hugenholtz
Evgenii Protasov
about 1 month ago
Deep-branching eukaryotes and early events in protist evolution
#evolution
#eukaryotes
#protists
onlinelibrary.wiley.com/doi/10.1111/...
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Deep‐branching eukaryotes and early events in protist evolution
The first eukaryotes evolved from their archaean ancestors in the early Proterozoic, likely ca. 2000–1800 million years ago (Mya). Their macroscopic multicellular descendants, such as plants, heterok...
https://onlinelibrary.wiley.com/doi/10.1111/brv.70101
1
4
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reposted by
Phil Hugenholtz
Genome Biology and Evolution
about 2 months ago
@katharinasures.bsky.social
@probstlab.bsky.social
et al. analysed CRISPR-Cas systems of metagenome-assembled genomes from two subsurface environments, shedding new light on the diversity of CRISPR spacers in natural microbial communities. 🔗
doi.org/10.1093/gbe/evaf201
#genome
#evolution
#CRISPR
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Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments
Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities
https://doi.org/10.1093/gbe/evaf201
1
14
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reposted by
Phil Hugenholtz
Javier Santoyo
about 2 months ago
FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT).
#Kmers
#MaskedBWT
#Genomics
#Bioinformatics
@bioinfoadv.bsky.social
🧪🧬 🖥️
academic.oup.com/bioinformati...
0
3
1
reposted by
Phil Hugenholtz
Evgenii Protasov
about 2 months ago
Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge
#microbiology
#bacteria
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
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Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge
Candidatus Saccharimonadia is ubiquitously found in activated sludge processes, but its ecophysiological characteristics remain poorly understood. Metagenome analysis of Ca. Saccharimonadia in size-f...
https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1758-2229.70231
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reposted by
Phil Hugenholtz
Javier Santoyo
about 2 months ago
Synteny plot quality control with SyntenyQC.
#SyntenyPlots
#Grnomivd
#Bioinformatics
🧬 🖥️
academic.oup.com/bioinformati...
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reposted by
Phil Hugenholtz
Francis M. Martin
about 2 months ago
We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View.
nph.onlinelibrary.wiley.com/doi/10.1002/...
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Demystifying fungal systematics: A gateway to fungal literacy and societal/ecological relevance through familiar species
Fungal systematics can feel overwhelming given the vast species diversity within this kingdom, with numerous subgroups at every taxonomic rank. This often creates a disconnect between the undertsnidn...
https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.70119
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reposted by
Phil Hugenholtz
Cameron Thrash
about 2 months ago
Augmenting microbial phylogenomic signal with tailored marker gene sets
www.nature.com/articles/s41...
#jcampubs
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Augmenting microbial phylogenomic signal with tailored marker gene sets - Nature Communications
Marker genes used in microbial phylogenomics are limited to fixed gene sets selected from complete genomes. TMarSel is a flexible yet robust method for selecting any number of markers from genomes or ...
https://www.nature.com/articles/s41467-025-64881-2
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reposted by
Phil Hugenholtz
Taylor priest
about 2 months ago
The core genomic backbone of bacteria is not necessarily resilient to gene flow! A new study shows that introgression impacts, on average, 2% of the core genes of species -
www.nature.com/articles/s41...
#microevo
#microeco
#evolution
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Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy - Nature Communications
It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...
https://www.nature.com/articles/s41467-025-64947-1
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reposted by
Phil Hugenholtz
Michael Deghelt
about 2 months ago
The diderm cell envelope is not a stack of layers but a unified scaffold of Inner Membrane–Peptidoglycan–Outer Membrane. We discuss how tethering the OM to the PG in E. coli preserves integrity — and extend the concept across diderm bacteria. Curr Opin Microbiol:
doi.org/10.1016/j.mi...
#microsky
🔬
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Redirecting
https://doi.org/10.1016/j.mib.2025.102681
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reposted by
Phil Hugenholtz
Samuel Aroney
about 2 months ago
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social
@rhysnewell.bsky.social
🧵1/6
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reposted by
Phil Hugenholtz
Evgenii Protasov
about 2 months ago
Half of microbial eukaryote literature focuses on only twelve human parasites
#microbiology
#protists
#eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
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Half of microbial eukaryote literature focuses on only 12 human parasites
Abstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc
https://academic.oup.com/ismej/article/19/1/wraf219/8276779
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reposted by
Phil Hugenholtz
Sullivan Lab at OSU
about 2 months ago
🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint:
doi.org/10.1101/2025...
Improvements details below 👇
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Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
https://doi.org/10.1101/2025.11.06.686974
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reposted by
Phil Hugenholtz
PLOS Biology
2 months ago
Scientists still have a very limited understanding of
#marine
#biodiversity
. Jonathan Belmaker explores a new
@plosbiology.org
study that uses unprecedented global environmental DNA
#eDNA
sampling to reveal the extent of our ignorance 🧪 Paper:
plos.io/47yRnEk
Primer:
plos.io/3XeJ2kl
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reposted by
Phil Hugenholtz
Taylor priest
2 months ago
GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website
academic.oup.com/nar/advance-...
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gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research
Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1115/8307362?login=true
1
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reposted by
Phil Hugenholtz
ARC Tracker
2 months ago
#CentresOfExcellence
#CE26
ARC has "postponed" announcement of Centres of Excellence outcomes! It says "due diligence checks" are still being carried out on some applications.
www.arc.gov.au/news-publica...
1
17
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reposted by
Phil Hugenholtz
Ashar Malik
2 months ago
We have had some amazing abstracts submitted to the free
@official-smbe.bsky.social
APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting.
biosig.lab.uq.edu.au/strphy26/sneakpeek/
.
#StrPhy26
@strphy.bsky.social
#Evolution
#Science
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APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
https://biosig.lab.uq.edu.au/strphy26/sneakpeek/
0
5
5
reposted by
Phil Hugenholtz
DEEMteam_Orsay
2 months ago
This paper has been a must! Great collaboration with
@mkrupovic.bsky.social
and
@yifanzhou.bsky.social
, a N&V by a legend of halophilic archaea
tinyurl.com/yc3dcv72
, and one picture of one of our expeditions to Dallol making the cover of the November issue of
@natmicrobiol.nature.com
rdcu.be/eLtCH
1
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reposted by
Phil Hugenholtz
Sebastian Schmidt
2 months ago
Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in
@narjournal.bsky.social
academic.oup.com/nar/advance-...
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Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1118/8307355
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