Taylor priest

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?

doi.org/10.1093/narg...

Landmark study in @Nature! 🇩🇰 The "Microflora Danica" project has created the first-ever national microbiome atlas. Led by Aalborg University, @fwf-at.bsky.social CoE Microplanet's Director @michiwagner4.bsky.social, and @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social analyzed nitrifiers.

Rare microbial relict sheds light on an ancient eukaryotic supergroup - Nature The discovery of an unusual protist named Solarion arienae, which has a mitochondrial genome with some intriguing features, provides insight into the early radiation of eukaryotic groups.

#NatMicroPicks

A new protist with remnants of ancient mitochondrial DNA 🧬🦠

The eukaryotic tree of life grows with the addition Solarion arienae - a unique and peculiar protist species

#MicroSky

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

📢 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

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

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...

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

Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes - Nature Microbiology Environmental micro-compartment genomics provides efficient and high-throughput single-particle DNA sequencing that captures overlooked members of microbial communities.

Very cool study - a new approach for single cell genomics that captures a wealth of #virus diversity in only 300 nanolitres of #ocean water, including viruses that use non-canonical bases

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

#microsky

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...

🚨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 👇

Glad to see this 🙌 Great job!

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.

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

The final dataset is smaller than the newest mOTUs (version 4) - and of course is a compilation, so doesn't have systematically produced MAGs. However, I think they have done a nice job at integrating and connecting genes to genomes to biomass etc. And the website is very user friendly!

From what I can tell, they pulled SPIRE, mOTUs (version 3) and some other MAG datasets and then additionally processed 14,000 SRA metagenomes (not sure why those 14,000 and it isn't clear in the paper)

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

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

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-...

The evolutionary and ecological consequences of cooperation | The American Naturalist: Vol 0, No ja

The evolutionary and ecological consequences of cooperation

-in American Naturalist by @stuwest.bsky.social, @annadewar.bsky.social, @ryosukeiritani.bsky.social, Laurence Belcher, and @asgriffin.bsky.social

www.journals.uchicago.edu/doi/abs/10.1...

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎

www.pnas.org/doi/10.1073/...

Postdoc vacancy: Microbial dormancy in the cryosphere
@erc.europa.eu #ERC_SIESTA
📢 PLEASE RT

🧬 Single cell microbial activity measurements, flow cytometry, cell sorting, omics, ecological interpretation

☀️ Marseille, France
‼️ Apply ASAP & before 7 Nov
Link: emploi.cnrs.fr/Offres/CDD/U...

Completely agree!

The challenge with assessing host specificity in a lab is, 1) not natural conditions
2) limited number of hosts tested (from strain to taxon level). So I think lab experiments can't provide conclusive evidence about host range. But they're crucial for mechanistic understanding of interactions

Nitrogen fixation under declining Arctic sea ice - Communications Earth & Environment Nitrogen fixation occurs under Arctic sea ice and is positively correlated with primary production, according to analyses of transects across the marginal ice zone and in the Central Arctic Ocean.

Phytoplankton blooms at the marginal ice zone in the central Arctic support elevated nitrogen fixation by non-cyanobacterial diazotrophs - www.nature.com/articles/s43...

Habitat-specificity in SAR11 is associated with a few genes under high selection Abstract. The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages

I'm delighted our paper is out: doi.org/10.1093/isme...
With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠

Habitat-specificity in SAR11 is associated with a few genes under high selection Abstract. The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages

The ecological and phylogenetic partitioning of coastal and offshore SAR11 is underpinned by a handful of distinct metabolic traits under high selective pressure - academic.oup.com/ismej/advanc...

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions

Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues.
@mkrupovic.bsky.social
@yifanzhou.bsky.social
@deemteam.bsky.social

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

Thank you @omicscode.bsky.social !

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...

Australian tropical rainforest trees switch in world first from carbon sink to emissions source Researchers say carbon emissions change in Queensland tropical rainforests may have global climate implications

This is not good. Positive feedbacks adding to warming....
www.theguardian.com/environment/...

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Phages communicate across species to shape microbial ecosystems Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...

Our latest work reveals that arbitrium phages cross-communicate across species! These tiny viruses “listen” to signals from others, coordinating lysis-lysogeny decisions across species.
Original idea from @albertomarina.bsky.social and, as usual, he was right.
www.biorxiv.org/content/10.1...

Bacteria in hot springs can move against fast water flow without flagella. Instead, they use pili like grappling hooks to crawl upstream, revealing a surprising survival strategy in extreme environments.
isme-microbes.org/hot-spring-b...
#microbes #bacterialmotility #extremophiles #hotsprings