The changing roles of Escherichia coli Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

"The changing roles of Escherichia coli" -- a short essay by yours truly.

rdcu.be/eVtXT

Colanic acid–mediated phage resistance enhances virulence in high-risk global clone Escherichia coli ST410 Author summary Multidrug-resistant Escherichia coli ST410 has emerged as a high-risk global clone threatening both human and animal health. Phages offer promising alternatives to antibiotics, yet the ...

Super-interesting paper

'Colanic acid–mediated phage resistance enhances virulence in high-risk global clone Escherichia coli ST410'

journals.plos.org/plospathogen...

indeed, 𝘙𝘶𝘨𝘰𝘴𝘪𝘵𝘢𝘭𝘦𝘢 𝘰𝘳𝘺𝘻𝘢𝘦 looke like fusilli, which are notably better at holding on salsa di pomodoro than spaghetti... and as pasta addicts, we fell instantly in love with the shape of this newly described alphaproteo from the Rhizobiales 🤭
#MicroSky

Releases · tseemann/shovill ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill

💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...

Associations of dietary intake for gut microbiota with frailty risk and mortality in older adults - Journal of Translational Medicine Journal of Translational Medicine - The associations between a diet that associated with a healthy gut microbiota and the risk of frailty, as well as mortality in older adults with frailty, remains...

A diet enriched in microbiome-fermentable substrates (more fruits and veggies) was shown to be associated with lower frailty and lower mortality risk in an older cohort (N>6000; 65+ y/o), with inflammation markers significantly mediating the dietary effect. link.springer.com/article/10.1...

‘Fire amoeba’ survives in hotter conditions than any other complex cell The single-celled organism can grow at 63 °C, a record for eukaryotic life.

This single-celled amoeba can thrive at temperatures that kill all other known eukaryotic life

go.nature.com/4452LXP

Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - Nature Microbiology A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.

#NewResearch

A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated C. difficile infection in mice.

#MicroSky 🦠💊

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

I really like when viruses confer useful genes to their hosts, it makes the idea of integrative viral elements all the more understandable. Conference of genes and a 'selfish' element reminds me a lot of plasmids too, I wonder what came first the virus or the plasmid?

Nested Symbiosis in Extreme Environments YouTube video by Archaeal Adventures

New video on Nested Symbiosis in extreme environments out on my YouTube Channel. Give it a watch if you can, a great paper by @mkrupovic.bsky.social

Original Paper: doi.org/10.1038/s415...

youtu.be/OQR5obtf7-4

From the Aegean Bronze Age, Minoan clay vessels with black handpainted decoration.on a pale biscuity-coloured slip Top left - clay flask decorated in Minoan ‘Marine Style’’ with an octopus with tentacles writhing around the body of the vase. Additional motifs such as seaweed and rocks represent the seabed. From Palaikastro, 1500-1450 BC Top right - clay rhyton in the shape of a bull’s head. A rhyton is a type of pouring vessel used for filling cups or making liquid offerings. There is a pouring hole at the bull’s mouth. From Knossos Little Palace, 1450-1375 BC Bottom left - Nautilus vessel - clay rhyton depicting the seabed with nautili, corals and seaweed. From Phaistos Palace, 1500-1450 BC Bottom right - Basket shaped rhyton decorated with double-axe motif. There is a small pouring hole in one of the bottom corners. From Pseira, 1500-1450 BC

Marvellous Minoan clay vessels made by creative potters on the island of Crete during the Aegean Bronze Age around 3,500 years ago! 🤩

Heraklion Archaeological Museum 📷 by me

#Archaeology

Matters Microbial #108: Neanderthal Oral Health, Ancient Bacteria and DNA YouTube video by MicrobeTV

This week, Dr. Laura Weyrich, Associate Professor of Anthropology at Pennsylvania State University, joins the #QualityQuorum to discuss the paleo oral microbiome! We will learn if our ancestors had the same kind of resident microbes as we do.
@markowenmartin.bsky.social @lauraweyrich.bsky.social

Horizontal gene transfer of the functional archaellum machinery to Bacteria Motility in Archaea is driven by a nanomachinery called the archaellum. So far, archaella have been exclusively described for the archaeal domain; however, a recent study reported the presence of arch...

Would you expect that Bacteria use an archaellum for swimming? We didn't, but we found that some Chloroflexota do! Find the story here: www.biorxiv.org/content/10.1...

A little thread below 1/n

Excited to present my work at poster #82 at #EESMicrobiome today! Come round and talk RNA viruses with me

☀️ Good morning from Day 3 of #EESMicrobiome 🦠

☕🥨 Fuelled by coffee and pretzels, we’re starting strong with Session 4: Microbiome–host interactions in health and disease.

🎤 'Understanding gut-to-host communication to prevent cardiovascular disease' by @fzmarques.bsky.social (Monash University)

Welcome to the EMBO | EMBL Symposium ‘The human microbiome’ 🦠🙌🏼
With a growing crowd on site, it is time for the opening remarks – #EESMicrobiome Day 1, let’s go! 🤩

Happy to see this paper finally out in @pnas.org!

#phage #microbiology #MicroSky #VirEvol 🦠 🧫 🔬

Gift link: www.pnas.org/eprint/YYDZ9...

A mammoth toothache: bacterial community discovered in mouth of ancient mammal Genetic-sequencing techniques have uncovered the oldest host-associated microbial DNA ever recorded — inside samples of teeth and bones from woolly and steppe mammoths.

This study describes the oldest microbial DNA ever sequenced

go.nature.com/4nfIzcU

Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease The involvement of the intestinal microbiome in the pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC), is well-established. Bacteria interact with immune cells at sites o...

Interesting paper.

Authors ruled out contamination; are not claiming 'blood microbiome', but rather 'DNA remnants'

'Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease'

www.tandfonline.com/doi/full/10....

Our body is a mosaic of fungi. Some scientists think they could be influencing our brain The fungi within our bodies may have a much greater effect on our health than we've long given them credit for.

New BBC article on fungal infections in which we are quoted:
www.bbc.co.uk/future/artic...

A cartoon depiction of the Asgard archaeon Skadiarchaeum sp., named after the Norse goddess of skiing and hunting, Skadi.

In a couple of days, my grad student Stavros Trimmer will present his new Asgard archaea culture at the GRC Archaea. He named it Skadiarchaeum after Skadi, the Norse goddess of skiing and hunting. Cartoon of Skadi based on cryoET, which was performed together with with @florianwollweber.bsky.social

Superbugs could kill millions more and cost $2tn a year by 2050, models show Exclusive: Research on burden of antibiotic resistance for 122 countries predicts dire economic and health outcomes

Meanwhile the news.

To learn more about antibiotic-resistant superbugs visit our educational website or come to our pop-up shop in Cardiff.

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

Experimental evolution in an era of molecular manipulation Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00867-6In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the underlying genetics and forces that shape phenotypic evolution.

New online! Experimental evolution in an era of molecular manipulation

A caged drug enables precision delivery “GlycoCaging” uses gut bacteria to activate drugs for inflammatory bowel disease

“GlycoCaging” uses gut bacteria to activate drugs for inflammatory bowel disease.

Learn more in a new #SciencePerspective: scim.ag/4ltfMk8

Study design to capture the dynamic nature of early microbiome and brain development. (A) Study design; participants (N = 194) were seen up to three times over the first 18 months of life. Stool samples and EEG data were collected, generating microbial functional profiles (stool) and VEP waveforms (EEG) used in subsequent analyses. Analyses included generalized linear models (GLM) and feature set enrichment analysis (FSEA). (B) Longitudinal sampling of study participants; density plots (top) for stool and EEG collection show the ages represented in each visit. The scatter plot (bottom) shows individual participant visits. Dotted lines connect separate visits for the same participant. When stool and EEG data were collected for the same visit (purple) but not on the same day, the dot represents the median age of collection, and vertical bars in blue and red represent stool and EEG collections, respectively.

Leveraging longitudinal data from 194 infants across the first 18 months of life, researchers show that microbial genes encoding neuroactive compounds are associated with visual cortical neurodevelopment. Read the article in #mBio: asm.social/2uo

Model for the interaction between P. aeruginosa and K. pneumoniae. These bacteria can co-exist in nutrient-replete conditions. Under iron-limiting conditions, siderophore synthesis is induced in both bacteria. Iron limitation can also turn on the synthesis of biosurfactants, rhamnolipids, in P. aeruginosa, allowing it to push away K. pneumoniae.

#MicrobiologyMonday: Pseudomonas aeruginosa releases a surfactant that displaces Klebsiella pneumoniae from solid surfaces. By pushing K. pneumoniae away, the detergent allows P. aeruginosa to better compete for limited iron. Learn more in #mBio: asm.social/2sH

Half way through the IMI Summer school 2025 starts with a fantastic Q&A panel with our own UoB students and Postdocs and @wvschaik.bsky.social giving a great talk on AMR & Phages 🦠🦠

How does your diet impact the microbiome? Let's find out...🦠🦠

Some exciting results from the IMI Summer school experiments 🧪🧫🔬

great training for grant applications