Hunting for new lineages and mechanisms of life Nature Microbiology, Published online: 20 April 2026; doi:10.1038/s41564-026-02336-0The US Department of Energy’s Joint Genome Institute recently held the New Lineages of Life Symposium at the University of Nevada, Las Vegas. The symposium brought together researchers focused on diverse and varied ecosystems but united by their goal to discover and characterize microbial dark matter.

Out Now! Hunting for new lineages and mechanisms of life #MicroSky

Isolation of two species of Caldatribacterium (Atribacterota) and the importance of folate for their culturability
www.researchsquare.com/article/rs-6...

"~folate provided in vitamin solutions was inadvertently removed by filter sterilization according to standard media preparation protocols."

An enhanced domestication method for uncultured bacteria Abstract. When environmental bacteria transition to laboratory conditions, a process termed domestication, the shift from the native habitat to a culture m

Most bacteria remain uncultured with vast microbial ‘dark matter’ awaiting discovery.. to address this am excited to share EDEN - an enhanced domestication method to grow uncultured bacteria & new diversity. Using EDEN we isolate a new species active against MDR pathogens..

doi.org/10.1093/isme...

It is crazy that in 2026, major research findings published in high impact journals are still being built on a dichotomous view of p-values without any consideration of effect sizes or biological context! Just because you get p < 0.05 that doesn’t mean it is biologically significant....

Feels like this paper on protein-templated DNA synthesis by a natural enzyme warrants some comment.
So here's a 🧵. /1
www.science.org/doi/10.1126/...

1/8 🔥 New preprint dropped: Dynamic co-existence of bacteriophages and their hosts 🦠 in the Arabidopsis thaliana 🌱 phyllosphere
Work led by the indomitable @sheilaroitman.bsky.social‬
#plantscience #microbiome #holobiont
www.biorxiv.org/content/10.6...

High-density microdroplet cultivation reveals the essential role of microbial interactions in the growth of environmental microbes | mBio The overwhelming majority of environmental microbes remain uncultured, limiting our understanding of their physiology and ecological roles. Although microbial interactions have been predicted as one o...

High-density microdroplet cultivation reveals the essential role of microbial interactions in the growth of environmental microbes.🦠🧫
journals.asm.org/doi/10.1128/...

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:

merenlab.org/2026/04/15/u...

New publication out @natcomms.nature.com! We identify novel viruses that actively infect highly productive chemoautotrophs, and reveal key trophic interactions and virus-host dynamics that impact microbial carbon cycling in aphotic environments.

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

High-throughput characterization of Mycobacterium tuberculosis gene function across diverse conditions Limited-throughput genetics has slowed discovery of gene functions in Mycobacterium tuberculosis. This study develops a genome-wide barcoded transposon library and tests it across 95 environmental conditions, providing a rich resource of new gene functions, including metabolic and drug-resistance pathways.

High-throughput characterization of Mycobacterium tuberculosis gene function across diverse conditions | PLOS Biology journals.plos.org/plosbiology/article

PhD positions in hadal biogeochemistry & microbial ecology Application deadline: 4 May 2026 at 23:59 hours local Danish time

📣We have 5 PhD positions in hadal biogeochemistry and microbial ecology at the Danish Center for Hadal Research: lnkd.in/eJ6rp_Rk. 📣

Deadline: 4 May 2026

Please share widely!

fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/Candid...

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

An ocean-wide partnership: How #diatoms use a sulfated #polysaccharide to keep #bacteria close & friendly.

mpi-bremen.de/en/How-diato...

Out now #Microbiome by J. Krull @chandnisidhu.bsky.social J.-H. Hehemann C. J. Crawford et al.

@marumunibremen.bsky.social @unibremen.bsky.social
(C) M. Reich

Quite a few flowcells going beyond 200 gbp

Notice for users submitting MAGs to INSDC

Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen...

What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.

Multiple fully funded PhD/postdoc positions available: experimental evolution of tumour suppression, egalitarian & fraternal ETIs, jumbo phage ecology & genetics. Related EoIs welcome.

Email CV/statement of motivation written in own words. Open until filled.

Grateful for reposting 🙏

Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249

Given a discussion on another thread, thought it might be useful to start a separate thread on how users are achieving higher ONT yields—extraction kits, size selection, sample type, basic stats, etc.

Anyone welcome to chime in.

@acritschristoph.bsky.social
@kirk3gaard.bsky.social

gbdraw: a genome diagram generator for microbes and organelles www.biorxiv.org/content/10.64898/2026.04...

Energetics and Ecological Implications of Bacterial Electron Transport Chains This review synthesises vast knowledge on bacterial electron transport chains with an emphasis on the energetics and underlying design principles. It further explores the varied respiratory chain com...

I became curious about the PMF generation efficiency of alternative complex III (ACIII), after reading this paper.

Energetics and Ecological Implications of Bacterial Electron Transport Chains enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

The microbiome of marine mat-forming cyanobacteria—a microcosm of taxonomic novelty and phototrophic diversity academic.oup.com/ismecommun/a...

With a 135 complete, circular Pelagibacter genomes, we have answered some of the most outstanding questions about what is often considered the most abundant organism on the planet, with roughly 10 million times more individuals in the ocean than stars in the universe. Check out our preprint.

Actinomarina, resolved | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Pelagibacter, resolved Pelagibacter, the largest genus within the SAR11 clade, is the most abundant bacterium in the ocean, yet the vast majority of its species-level diversity remains uncharacterized at the genomic level. Here we present 135 complete Pelagibacter genomes -- the largest such collection assembled to date -- comprising 75 from Oxford Nanopore metagenomes of the San Francisco Estuary (SFE), 31 from a deeply sequenced station within the same transect, and 29 from public databases. These genomes define 52 species at 95% ANI, of which 44 (85%) are taxonomically novel. An expanded phylogeny incorporating 89 additional high-quality NCBI genomes confirms that our collection captures the phylogenetic backbone of the genus, with genomes from Hawaii, Namibia, and the Sargasso Sea nesting within SFE clades. The pangenome is open (14,862 singletons, 62%), driven by two distinct mechanisms. First, a universal hypervariable region (HVR) at a conserved chromosomal position (7-15% from dnaA) is present in all 135 genomes, anchored by tRNA genes at both boundaries (Phe/His and Arg). The HVR carries genome-specific surface polysaccharide biosynthesis genes with a GC age gradient -- highest GC at the tRNA boundaries, lowest in the center -- consistent with a two-ended phage insertion model. Only this HVR is positionally conserved across the genus; the three other hypervariable regions previously described in a single reference genome are not. Second, scattered genomic islands throughout the chromosome contribute the remaining singleton content, including chimeric islands with genes from four bacterial phyla. Biosynthetic pathway reconstruction reveals auxotrophies that are phylogenetically structured, not uniform: biotin, reduced sulfur, and glycine are genus-wide dependencies, while isoleucine, pantothenate, histidine, and glyoxylate cycle capacity vary across lineages with significant phylogenetic clustering. Structural annotation with ESMFold and Foldseek resolved 3,125 hypothetical proteins; 1,222 remain uncharacterized by any method, including a 47-amino-acid protein conserved in two-thirds of all genomes within a fixed operonic context -- independently predicted by two gene callers yet matching nothing in any database. A controlled depth comparison at one station demonstrates that standard metagenome sequencing systematically underestimates Pelagibacter diversity, with three species recovered only at elevated depth and the species count at that station more than doubling (9 vs 4). ### Competing Interest Statement The authors have declared no competing interest.

Pelagibacter, resolved | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Whenever I presented Phold, I was frequently asked "can you do the same beyond phages?" We ( @oschwengers.bsky.social @linsalrob.bsky.social @binomicalabs.org et al) finally did it with Baktfold github.com/gbouras13/ba... www.biorxiv.org/content/10.6...

Cultivation and genomic characterization of the first representative of the globally distributed marine UBA868 group www.biorxiv.org/content/10.6... #jcampubs 🌊

@paulturnerlab.bsky.social and I wrote a perspective on the need and recently developed approaches to study individual virus traits in the most numerous viruses on our planet (phages).

Let's move beyond measuring the mean #phagesky

www.nature.com/articles/s44...

#microsky #virology #microscopy

We tested the efficacy of semi-permeable capsules to capture protists from cultures and environmental samples using the Onyx from @atrandi.bsky.social. Tremendous effort from everyone in the lab and led by Marco Fantini and Nik Brask - check out the videos here: www.biorxiv.org/content/10.6...

Semi-permeable capsules enable parallel cultivation and live microscopic observations of microbial eukaryotes www.biorxiv.org/content/10.64898/2026.04...

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :

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

See the linked threads for more details!