Taylor priest

A new era for #ONT amplicon sequencing?
We show that #ONT #amplicon sequencing now achieves accuracy sufficient for #ASV resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on #ONT and #PacBio. @nanoporetech.com www.biorxiv.org/content/10.6...

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

Great to see this amazing resource finally published !

MicrobeAtlas - 2.4 million SSU rRNA gene sequence datasets systematically analysed against an extensive full length reference database enabling tracking of OTUs at global scales!

www.cell.com/cell/fulltex...

Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity - Nature Reconstructing microbial genomes from 820 reef-building corals collected at 99 reefs across 32 islands throughout the Pacific Ocean highlights the importance of conserving coral reefs as vital reservo...

We are thrilled to announce the newest study from our lab (and great collaborators) is out now in @nature.com

We show that #coral #microbes are untapped "biosynthetic reservoirs", full of unique
natural products.

doi.org/10.1038/s415...

Very happy to be able to contribute to this great research out now in @nature - where we reveal that coral associated microbes are rich biosynthetic reservoirs !

Microbial Cohorts: Bringing Ecological Meaning to the Modularity Concept of Co-Occurrence Networks Abstract. Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to i

Microbial Cohorts: Bringing Ecological Meaning to the Modularity Concept of Co-Occurrence Networks

academic.oup.com/ismecommun/a...

The paradox of immune systems conservation between prokaryotes and eukaryotes Nature Reviews Microbiology, Published online: 05 February 2026; doi:10.1038/s41579-026-01284-0The 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 Argonautes and antiviral STAND NTPases, became central to eukaryotic innate immunity. In this Comment, we hypothesize that the cause of this paradox is the drastic reduction of horizontal gene transfer rate in eukaryotes.

ICYMI: New online! The paradox of immune systems conservation between prokaryotes and eukaryotes

Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

AlphaGenome is out! Input 1 Mb DNA -> predict gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chromatin contact maps, ..., up to single-base-pair resolution! Trained on human and mouse data 🧪🧬🖥️🦠✨
www.nature.com/articles/s41...

Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

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And a very worthwhile mention ;) globDB is an extensive database so you would get even better coverage than using GTDB as a reference !

Good point. Of course this approach would exclude reads without genes. I have used this approach for PacBio HiFi reads before and it works well, but there you rarely get any reads shorter than 1 kbp. I imagine with Nanopore this is only a minor fraction of the reads though, right?

True, it could definitely be used to get compositional insights. I am not convinced by the accuracy of the relative proportions from it though.

Plasmid mutation rates scale with copy number | PNAS Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...

New paper out in PNAS!!! 🎉

Do more plasmid copies mean faster evolution?

🧵 Dive into the story

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

Application of Nanopore sequencing to intact caspid-packaged DNA reveals that bacterial DNA encapsulation is widespread in the human gut #microbiome

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

Could also do whole read alignments using minimap2 to e.g. GTDB genomes and the LCA if multiple hits found

I don't believe there is a 'best practice'. In the past I've used a protein+LCA based approach. LCA helps to give taxonomic insights even when there aren't high identity matches. Can use GTDB or any other genomes database as a ref (have to build a non-redundant protein catalogue from it)

Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria Abstract. The genetic material of bacteria and archaea is organized into various structures and set-ups, attesting that genome architecture is dynamic in t

Genomic rearrangements occur at varying rates across Archaea and Bacteria, but are typically enriched near the ori region. While gene synteny is widely conserved, some species show highly flexible genomic layouts. #Microevo #evolution #genomics

academic.oup.com/gbe/advance-...

Community conservatism is widespread across microbial phyla and environments - Nature Ecology & Evolution This study reveals that closely related microorganisms tend to inhabit similar communities across all major environments and phyla. The authors term this phenomenon ‘community conservatism’, extending...

A nice study showing that community conservatism is common in microbial communities across different environments
#microecoevo #microbes

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

Bacteriophages mobilize bacterial defense systems via lateral transduction Bacteriophages and PICIs spread bacterial defenses via lateral transduction, shaping microbial immunity and pathogen evolution.

Bacteriophages mobilize bacterial defense systems via lateral transduction

#phage #virus #microecoevo

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

Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research?

Then come and join our group !

Great paper! Well done to everyone involved 👏

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊

Subsurface oxygen maxima in oligotrophic oceans are catalyzed by the viral shunt - www.nature.com/articles/s41...

Identifying Fundamental Gaps in Functional Metagenomics: A Step Towards Unlocking Microbiome Research Potential www.biorxiv.org/content/10.6... #jcampubs

microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats https://www.biorxiv.org/content/10.64898/2026.01.12.698811v1

Seasonal patterns of DOM molecules are linked to microbial functions in the oligotrophic ocean | mSystems Marine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth’s climate. DOM dynamics are largely regulated by a complex web of chemical-microbial inte...

Microbes and DOM molecules both exhibit strong seasonality, with the largest majority of recurrent signals occuring in summer

journals.asm.org/doi/10.1128/...

A breakthrough from 60 years ago: “General nature of the genetic code for proteins” (1961) In 1961, Francis Crick and Sydney Brenner, together with two Cambridge colleagues, published an article in Nature that used simple genetic experiments to demonstrate that the genetic code was almost ...

Don’t forget that the 1961 triplet code paper only became elegant when it was written! The experiments were all a bit of a mess... I suspect the same was true of the other classic papers!

Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean Abstract. Urea is an important alternative nitrogen source to ammonium for nitrification in oligotrophic oceans, yet its role in substrate-driven nitrous o

Urea-driven nitrification contributes up to 40% of the total N2O produced through nitrification processes in the oligotrophic oceans

academic.oup.com/ismej/articl...

The microbial keystone concept is a very cool topic in microbiome ecology. This review summarises mechanisms, prediction methods and implications, with "keystoneness" being highly context/time dependent + new methods approaches suggested. Very nice read!
www.nature.com/articles/s41...

Two articles published in concert in Nature Microbiology indicate that lytic phages may be prevalent and persistent in isolated microbes - www.nature.com/articles/s41... & www.nature.com/articles/s41...