Bayesian inference captures metabolite–bacteria interactions in a microbial community Abstract. Macro-ecosystems, including the human gut, host a vast and diverse set of microbes that indirectly interact with each other through consuming and

Bayesian inference captures metabolite–bacteria interactions in a microbial community
#microbiology #MicroSky
@isme-microbes.bsky.social
doi.org/10.1093/isme...

The AI Rewrite Dilemma https://lh3.github.io/2026/04/17/the-ai-rewrite-dilemma

Fast prediction of protein flexibility | Bioinformatics | Oxford Academic academic.oup.com/bioinformatics/advance-a...

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...

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence - Nature Communications Bacterial persister cells exhibit a transient state of antibiotic tolerance and are commonly assumed to be metabolically ‘dormant’. In this Perspective, Orman et al. re-examine common assumptions and emphasize that persisters represent a range of metabolic states, driven by internal and external factors, which may explain the inconsistent expression of classic persister hallmarks.

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence | Nature Communications https://www.nature.com/articles/s41467-026-71427-7

Looks like a nice paper - "In addition, the growth of taxonomies containing many uncultured microorganisms, such as Verrucomicrobia, Planctomycetia, Acidobacteria, and Vicinimibacteria, was observed"

(minor note - 'Vicinimibacteria' is a typo, should be Vicinamibacteria)

Update time!!!

odd that they run VAMB but only the default... AVAMB and TaxVAMB perform way better

MegaHIT performance changes quite a bit if you select the right presets based on the sample

CheckM2 can go both ways in my exp with closed, polished MAGs (some barely >90%C and >=10%cont)

1/ Excited to share our preprint! 🥳

Degradation of aromatic compounds, including BTEX pollutants, requires highly endergonic aromatic ring reduction. Using #cryoEM and in situ #cryoET, we show how BCRII couples electron bifurcation modules in one giant redox machine

www.biorxiv.org/content/10.6...

The awesome virome logo of a phage above a strand of DNA

Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome

github.com/shandley/awe...

Immensely rewarding part of this work was working with Indigenous language experts and elders in the naming of our species of Asgard….’marumarumayae’ derived from the Malgana language from the people of Gathaagudu (#Shark Bay)

Phylogenomic mixture models outperform homogeneous and partitioned models Abstract. Significant advances have been made in resolving the tree of life, but many nodes remain debated. The last two decades saw the emergence of mixtu

Phylogenomic mixture models outperform homogeneous and partitioned models | Molecular Biology and Evolution | Oxford Academic academic.oup.com/mbe/advance-article/doi/...

Dear Nanopore folks, could you give an advice about an issue that my lab has with direct RNA sequencing on MinION. We're doing RNA004 sequencing of various samples and again and again, there's a staggering amount of reads with just repetitive AAG triplet. This happens for weird IVT RNA and […]

Selenocysteine-dependent Enzymes: Structure, Function and Selenium-derived Mechanism
#biochemistry #enzymes #selenocysteine
doi.org/10.1016/j.jm...

#Paper Our new study on #Asgard archaea is out in Nature Communications. We find a distinctive evolutionary pattern: widespread #HGT, but genome expansion mainly through gene duplication. An interesting window into the origins of #eukaryotic complexity.

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

One of biggest mysteries in biology: how did complex eukaryotic cells evolve from simple microbes? ~1.8 billion years ago, an archaeal cell likely merged with a bacterium to form the first eukaryotic cell, but can we ever find direct evidence of this transformative event? 🦠 🚶‍♂️

PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis | Nucleic Acids Research | Oxford Academic academic.oup.com/nar/article/54/3/gkaf150...

Asgard Archaea May Reveal How Complex Life Began - Ancient #stromatolites from #SharkBay have yielded the first visual evidence of an #AsgardArchaeon physically interacting with a bacterium via #nanotubes - www.disabled-world.com/disability/e...

From Asgard to Earth: Tiny tubes may reveal the moment complex life began Stromatolites—and their close relatives, microbial mats—could be mistaken for what seems like a bunch of old dark rocks.

New imaging reveals Asgard archaea and bacteria physically linked by nanotubes in stromatolites, offering insight into how complex life may have first emerged on Earth.

Paper finally out in @currentbiology.bsky.social !!

#ArchaeaSky

authors.elsevier.com/sd/article/S...

Eukaryotes didn't just arise from two partners. Phylogenomics of the LECA proteome reveals multiple waves of bacterial HGT, some predating mitochondrial endosymbiosis, plus a possible role for giant viruses.

www.biorxiv.org/content/10.1101/2024.10....

Deciphering microbial interactions using a label-free microbead sorting approach Abstract. Microorganisms form communities, and their interactions shape the function and stability of these communities. Understanding these interactions c

Deciphering microbial interactions using a label-free microbead sorting approach academic.oup.com/ismecommun/a... #jcampubs

You can now run a multiple sequence alignment directly on your SeqHub search results.

Once the alignment runs, conserved regions are mapped onto the 3D structure of your query protein. Explore results in SeqHub or download as an a3m file.

I saw this one today it might be of interest
bsky.app/profile/jcam...

New genetic codes in bacteria and archaea identified with a fast k-mer based algorithm www.biorxiv.org/content/10.6... #jcampubs

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...

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

Redox chemistry of early Earth and the origin of life - Communications Chemistry Redox reactions played an important role in shaping the conditions that enabled the emergence of life on the early Earth, but how these relate to specific environmental conditions and whether they led to heterotroph or autotroph organisms remains a matter of debate. In this Review, the authors summarize and discuss evidence reconciling dominant theories — from the redox nature of the Hadean atmosphere and the presence of conditions that could have supported both heterotrophs and chemoautotrophs, to the transport of organic compounds that could have led to the emergence of life in multiple local environments.

Redox chemistry of early Earth and the origin of life | Communications Chemistry https://www.nature.com/articles/s42004-026-01969-w

Cultivation and genomic characterization of the first representative of the globally distributed marine UBA868 group | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes journals.asm.org/doi/full/10.... #jcampubs

Bacterial extracellular vesicles as recyclable nutrient reservoirs | Nature Communications https://www.nature.com/articles/s41467-026-71463-3