Christoph Kaleta

Our work with Lena Takayasu and @dwmckellar.bsky.social in Iwijn De Vlaminck's lab is now out in @natmicrobiol.nature.com ! 🎉

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution

rdcu.be/e7i7o

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution Nature Microbiology, Published online: 06 March 2026; doi:10.1038/s41564-026-02286-7Bulk polyadenylation improves the capture of microbial RNA, enabling host–microorganism interactions to be visualized at a high resolution when combined with commercially available spatial transcriptomics platforms.

Out Now! Spatial transcriptomics maps host–gut microbiome biogeography at high resolution #MicroSky

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉

How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...

I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...

V. interesting work from @gibbological.bsky.social et al showing that metabolic modeling can predict probiotic engraftment & SCFA production across human intervention trials w/ ~75-80% accuracy. Great argument for model-informed personalised probiotic interventions.
journals.plos.org/plosbiology/...

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health Silva et al. perform a global analysis of over 11,000 gut microbiomes and reveal that uncultured bacteria are key markers of gut health. The uncultured genus CAG-170 is strongly linked to low gut dysb...

#NatMicroPicks

A microbial signature of health! 🦠⚕️

A large meta-analysis highlights the importance of previously unknown and uncultured gut bacteria in maintaining human health

#MicroSky

www.cell.com/cell-host-mi...

Here is a robust biochemical & functional difference between young and old mammalian cells:

- The fraction of new amino acids incorporated into proteins.

The difference is consistent, quantitative, cell-type specific, and deeply intriguing.

What aging mechanisms cause it ?

1/

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself.

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

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

A nice demonstration of how cross-feeding shapes small microbial community compositions

From Segré lab @dsegre.bsky.social

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

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

3 recent trials in Nature Medicine test FMT as an ICI add-on (renal+lung cancers). Early efficacy signals + mechanistic hints that taxa/function shifts may matter more than donor similarity + toxicity effects mixed.
Promising, but prob need larger trials and more standardisation. Links to studies 👇

What causes tipping points in complex microbial ecosystems? Check this @pnas.org paper by @thilogross.bsky.social showing that cross-feeding networks create strong interdependencies & small structural changes can trigger abrupt collapses. @akhilesh-nandan.bsky.social www.pnas.org/doi/epdf/10....

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The 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 Arg...

The immune systems paradox

Some widespread prokaryotic immune systems are absent in eukaryotes, whereas relatively rare ones became central to eukaryotic innate immunity

@audeber.bsky.social & E. Koonin hypothesize the answer is #HGT

shareable link: rdcu.be/e2EmD

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

Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut | mSystems To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversi...

Comparative genomics of Bifidobacterium adolescentis (n=1.6k genomes, mostly MAGs from 44 countries) for adult-gut adaptation signatures: 203 soft-core host-interaction genes (incl adhesion/pili) +7 clades w/ some geographic structure + co-occur w/ butyrate producers
journals.asm.org/doi/full/10....

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing

Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function Nature Microbiology, Published online: 05 February 2026; doi:10.1038/s41564-026-02259-wA covariate-aware analysis reveals that microbiome changes in the gut of patients with chronic kidney disease are better explained by intestinal transit time than by kidney function.

Out Now! Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function #MicroSky

Scientists discover brain network that may cause Parkinson’s disease An “extraordinary” brain network discovery shows that Parkinson’s disease may not be a movement disorder after all

An “extraordinary” brain network discovery shows that Parkinson’s disease may not be a movement disorder after all

Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer

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

From the paper: Deeply divergent Treponema pallidum lineage in the Americas and implications for pathogen evolution. We identified and reconstructed a ~5500-year-old 1.7× T. pallidum genome (TE1-3) from a Middle Holocene individual at Tequendama I rock shelter in Colombia. Phylogenomic analysis reveals that TE1-3 is an early-branching sister lineage to all extant T. pallidum subspecies, with divergence dating to ~13,700 years ago (95% HPD: 6768 to 20,592 cal yr B.P.) and coinciding with early human migration and ecological shifts in the Americas. Despite its antiquity, TE1-3 possesses the T. pallidum virulence-associated genes, suggesting conserved pathogenic capacity. TE1-3 provides the earliest molecular evidence of T. pallidum in the Americas to date, bridging a multimillennial gap between skeletal signs and genomic data and offering a rare glimpse into the long-term evolution of treponemal pathogens.

A 5500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia

"This genome falls outside of known T. pallidum lineages today, but it has many genetic hallmarks associated with virulence in modern pathogens of these subspecies"

Science
pubmed.ncbi.nlm.nih.gov/41570125/

#MicroSky

Mega-journal Heliyon retracts hundreds of papers after internal audit Heliyon has published fewer papers and ramped up its retractions since a major indexing service put the journal on hold and the publisher launched an audit of all papers published in the journal si…

Mega-journal Heliyon retracts hundreds of papers after internal audit 

@retractionwatch.com
retractionwatch.com/2026/02/03/m...

B cells drive CD4 T cell immunosenescence and age-associated health decline B cells promote CD4 T cell aging and decline in health-span parameters through intercellular communication and nutrient sensing.

What drives immunosenescence—the degradation of function our immune system with aging that increases the risk of age-related diseases?
Today's report: B cells are identified as the bad actors because they induce T cell (CD4) dysfunction and inflammaging
science.org/doi/10.1126/...

🆕 @science.org
Revising the heritability of lifespan, from 25% to ~50%, by correcting for extrinsic factors
science.org/doi/10.1126/...

Intriguing work showing that essential amino acids in metazoans have considerable higher biosynthetic costs, potentially explaining the loss of their biosynthetic pathways: rdcu.be/e09J7

Genomic features associated with sustained mammalian transmission of avian influenza A viruses Nature Microbiology, Published online: 27 January 2026; doi:10.1038/s41564-025-02257-4Reduced GC-related content in the influenza A virus genome may be a necessary condition for sustained mammalian transmission and should be included in risk assessment tools for pandemic influenza.

Out Now! Genomic features associated with sustained mammalian transmission of avian influenza A viruses #MicroSky

Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation Nature Microbiology, Published online: 26 January 2026; doi:10.1038/s41564-025-02241-yLarge-scale computational and in vitro analyses identify commensal type III secretion systems and substrates in the human gut microbiome that can interact with human proteins to modulate immune pathways.

Out Now! Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation #MicroSky

Single gene found to influence gut bacteria balance and IBD susceptibility Two recent studies from the University of California, Riverside, published in the same issue of Gut Microbes highlight the role of a gene called PTPN2 in protecting the gut from harmful bacteria…

Single #gene found to influence #gut #bacteria balance and #IBD susceptibility ...

| #PTPN2 | #infection | #microbiome | #microbes | Via @sciencex.bsky.social

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

#NatMicroPicks Baby-to-baby strain transmission shapes the developing gut microbiome - out now in Nature! 👶🦠👶

#microsky #microbiome @nature.com @cibiocm.bsky.social

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

Microbiota utilization of intestinal amino acids modulates cancer progression and anticancer immunity Qiao et al. identify gut microbes and amino acid-metabolizing genes that influence tumor burden. A Bacteroides asparaginase, bo-ansB, modulates host tumor responses to dietary asparagine (Asn) by depl...

#NatMicroPicks

bacterial amino acid metabolism affects cancer progression 🦠🦀🐁

Bacteroides asparaginase lowers intestinal asparagine levels and drives colorectal tumor progression

#MicroSky

www.cell.com/cell-host-mi...