David Seki

Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦

Key takeaways:
🔹 Host ancestry + diet shape Bif evolution
🔹 Mammals enriched for carb-busting enzymes
🔹 Untapped diversity in non-human hosts = new probiotic potential

Supervised learning in DNA neural networks - Nature DNA molecules can be programmed to autonomously carry out supervised learning in vitro, with the system learning to perform pattern classification from molecular examples of inputs and desired responses.

Nature research paper: Supervised learning in DNA neural networks

go.nature.com/4mOb9lH

Microbial iron oxide respiration coupled to sulfide oxidation - Nature Genomic and biochemical analyses of prokaryotic sulfur metabolism identify diverse microorganisms with the capacity to oxidize sulfide using iron(iii).

📢 New paper in @nature.com

Microbes rock 🎸🤘 with sulfide and iron minerals

I am very excited to share our recent study, which describes a previously unknown microbial energy metabolism ⚡⚡⚡🦠🧫⚡⚡⚡

🆕 Microbial iron oxide respiration coupled to sulfide oxidation - MISO

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

A novel bacterial protein family that catalyses nitrous oxide reduction - Nature Cultivation of tropical soil microorganisms combined with physiological experiments and bioinformatics analyses identify a family of clade III lactonase-type nitrous oxide reductases with low sequence...

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

#microsky

mRNA vaccines for HIV trigger strong immune response in people Results from early-stage trial show that 80% of participants who received one of two HIV vaccine candidates produced antibodies against viral proteins.

Two vaccine candidates using mRNA technology elicit a potent immune response against HIV

go.nature.com/4ov7WZI

This is figure 1, which shows the methodological pipeline.

An analysis in Nature Ecology & Evolution shows that near-national-scale losses of bird diversity greatly exceed losses recorded at the local scale in Colombia, suggesting that extrapolations from local studies will severely underestimate biodiversity losses. go.nature.com/3HbRv3s 🧪

My thanks go out to the many people that have been involved over the years! @halllab.bsky.social, John Penders & Nils van Best, @raymondkiu.bsky.social & Magda & Antia, @lucyicm.bsky.social & @cassiebakshani.bsky.social, @ptchiv.bsky.social, @envsysmicro.at

❤️

Finally, we demonstrate experimentally that E. coli supplies cysteine to auxotrophic B. bifidum, enabling cooperative degradation of 2'-fucosyllactose (the predominant HMO), thereby promoting mutual benefits.

We developed new computational approaches that deepened our understanding of early-life microbiota dynamics 👍

Then, evolutionary-guided genome analysis revealed that the co-existence of Bifidobacterium & E. coli is driven by shared selective pressures, promoting cooperation in HMO degradation 🤝

In this longitudinal cohort of initially exclusively breastfed & term-born infants - E. coli strains persist in individuals and co-exist with dominant Bifidobacterium.

Excited to finally share results from my first post-doc @halllab.bsky.social 🫡

E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.

www.biorxiv.org/content/10.1...

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium - Nature Microbiology Genomic and functional analyses of healthcare-associated vancomycin-resistant Enterococcus faecium reveal that bacteriocin T8 is enriched in emergent lineages and provides a competitive advantage in v...

Excited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social

Silhouettes of infant, mouse, chick, and bacteria.

Interested in the influence of the infant microbiome on health? Quickly interrogating non-model organisms using omic approaches?

A new publication, describing genome-scale resources in bifidobacteria, is now available online: doi.org/10.1016/j.ce...

#microbiome #microsky

Highly multiplexed spatial transcriptomics in bacteria Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org
Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/...
#microsky #microbial #microbiology #genomics
#transcriptomic 🦠🧫

Excited to share our opinion piece with the KC Huang Lab.
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social

Host metabolism balances microbial regulation of bile acid signalling - Nature A family of host-derived bile acid–methylcysteamine conjugates functions as FXR antagonists, forming part of a microbiota-dependent metabolic network that regulates FXR-dependent physiology.

Host metabolism balances microbial regulation of bile acid signalling | @nature.com

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

Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts Animal hosts harbour divergent microbiota, including various Bifidobacterium species and strains, yet their evolutionary relationships, and functional adaptions remain understudied. By integrating tax...

1/ 🚨 New preprint alert! 🚨 We’re thrilled to share our latest work exploring microbiome & genomic #Bifidobacterium co-evolutionary & functional signatures across diverse animal hosts. This has been a long time coming, & huge credit to Magda for her incredible hard work as first author! 🐾✨👇

Yes please <3

Decoding Early Life Microbiota and Host Interactions at University of Birmingham on FindAPhD.com PhD Project - Decoding Early Life Microbiota and Host Interactions at University of Birmingham, listed on FindAPhD.com

🚨 PhD Opportunity @halllab.bsky.social!
🔬 Decoding Early Life Microbiota & Host Interactions
🧬 Ideal for those with bioinformatics/microbiome experience
🌍 Open to international candidates (MSCA mobility rules apply).
📅 Deadline: 18th Dec
🌐 Apply now: www.findaphd.com/phds/project...