Phil Hugenholtz
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xrefugee13.bsky.social
Phil Hugenholtz
@xrefugee13.bsky.social
760 followers 890 following 56 posts
Microbiologist
Posts Replies Media Videos
xrefugee13.bsky.social
@arc-tracker.bsky.social - any intel on CoE announcements?
November 28, 2025 at 12:33 AM
Reposted by Phil Hugenholtz
michiwagner4.bsky.social
📢 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
November 27, 2025 at 5:38 PM
Reposted by Phil Hugenholtz
linsalrob.bsky.social
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...
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–...
www.nature.com
November 26, 2025 at 9:55 PM
Reposted by Phil Hugenholtz
quantamagazine.bsky.social
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.
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.
www.quantamagazine.org
November 25, 2025 at 9:04 PM
Reposted by Phil Hugenholtz
archaeal.bsky.social
youtu.be/Jy_boPdY0zo?...
The Origins of Complex Life | Searching for the Asgards
YouTube video by Schmidt Ocean
youtu.be
November 26, 2025 at 8:29 PM
Reposted by Phil Hugenholtz
isog.bsky.social
www.sciencealert.com/newly-discov... 🧪 #endosymbiosis #mitochondria
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.
www.sciencealert.com
November 26, 2025 at 3:54 AM
Reposted by Phil Hugenholtz
fburki.bsky.social
www.nature.com/articles/s41...
#protistsonsky
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...
www.nature.com
November 25, 2025 at 11:21 AM
Reposted by Phil Hugenholtz
mkddueholm.bsky.social
High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...
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
academic.oup.com
November 25, 2025 at 8:56 AM
Reposted by Phil Hugenholtz
evgenii-protasov.bsky.social
Deep-branching eukaryotes and early events in protist evolution
#evolution #eukaryotes #protists
onlinelibrary.wiley.com/doi/10.1111/...
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...
onlinelibrary.wiley.com
November 23, 2025 at 11:09 AM
Reposted by Phil Hugenholtz
genomebiolevol.bsky.social
@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
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
doi.org
November 18, 2025 at 10:53 AM
Reposted by Phil Hugenholtz
jsantoyo.bsky.social
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...
November 18, 2025 at 11:30 AM
Reposted by Phil Hugenholtz
evgenii-protasov.bsky.social
Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge
#microbiology #bacteria
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
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...
enviromicro-journals.onlinelibrary.wiley.com
November 16, 2025 at 10:50 AM
Reposted by Phil Hugenholtz
jsantoyo.bsky.social
Synteny plot quality control with SyntenyQC. #SyntenyPlots #Grnomivd #Bioinformatics 🧬 🖥️
academic.oup.com/bioinformati...
November 15, 2025 at 11:49 AM
Reposted by Phil Hugenholtz
fmartin54.bsky.social
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/...
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...
nph.onlinelibrary.wiley.com
November 14, 2025 at 5:05 PM
Reposted by Phil Hugenholtz
jcamthrash.bsky.social
Augmenting microbial phylogenomic signal with tailored marker gene sets www.nature.com/articles/s41... #jcampubs
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 ...
www.nature.com
November 13, 2025 at 8:54 PM
Reposted by Phil Hugenholtz
taylorpriest.bsky.social
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
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...
www.nature.com
November 14, 2025 at 10:23 AM
Reposted by Phil Hugenholtz
michaeldeghelt.bsky.social
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 🔬
Redirecting
doi.org
November 13, 2025 at 12:17 PM
Reposted by Phil Hugenholtz
aroneys.bsky.social
“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
Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA
November 13, 2025 at 10:09 AM
Reposted by Phil Hugenholtz
evgenii-protasov.bsky.social
Half of microbial eukaryote literature focuses on only twelve human parasites
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
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
academic.oup.com
November 9, 2025 at 10:10 AM
Reposted by Phil Hugenholtz
sullivan-lab.bsky.social
🚨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 👇
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...
doi.org
November 7, 2025 at 4:36 PM
Reposted by Phil Hugenholtz
plosbiology.org
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
Schematic illustration of how extensive sampling allows better estimates of species geographic distributions and the detection of new species. Left: The currently inferred distribution of species based on known records (red, records illustrated using black dots) is substantially expanded to better approximate the true distribution (yellow) when using new eDNA sampling at a global extent. Right: These eDNA samples can also detect new species records (light blue fishes) within ocean grid cells, especially species that are small and rare. Illustration prepared with the assistance of GPT5.0.
November 3, 2025 at 10:12 AM
Reposted by Phil Hugenholtz
taylorpriest.bsky.social
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-...
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
academic.oup.com
November 3, 2025 at 9:01 AM
Reposted by Phil Hugenholtz
arc-tracker.bsky.social
#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...
Screenshot of ARC "network messages" webpage stating that Centres of Excellence outcomes are "postponed". Blue text on white background as a heading, above an image of concentric part circles, to make a sort-of whirlpool pattern, above black text on white background.
November 3, 2025 at 6:32 AM
Reposted by Phil Hugenholtz
proteinmechanic.bsky.social
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
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
November 3, 2025 at 4:21 AM
Reposted by Phil Hugenholtz
deemteam.bsky.social
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
November 2, 2025 at 5:52 PM