Yannis Ntekas

The Autism-Microbiome Hypothesis Is Falling Apart Why this new review paper should be required reading for every microbiome researcher

I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field

open.substack.com/pub/blekhman...

Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology Profiling host RNA shed in feces reveals disease states in the gut.

Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠
www.nature.com/articles/s41...

Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology Profiling host RNA shed in feces reveals disease states in the gut.

Another banger from the @harriswang.bsky.social Lab this month!

“Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut” www.nature.com/articles/s41...

Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide - Nature Computational drug discovery is used to identify a 12-mer peptide derived from BRINP2 with potent anti-obesity effects that are independent of leptin, glucagon-like peptide 1 receptor and melanocortin...

Exciting discovery by Svensson lab and collaborators @stanfordmedicine.bsky.social, computational discovery of 2500 new bioactive peptides, including 12-mer named BRP that reduces food intake leading to weight loss w/o nausea in mice!

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

Contributions from: Jeffrey Moffitt, @drmingyaoli.bsky.social, Qing Nie, Kazumasa Kanemaru, Sarah Teichmann, Daniel Dar, @ltkagohara.bsky.social, Shalev Itzkovitz, Roser Vento-Tormo, @fertiglab.bsky.social, @fabiantheis.bsky.social

Mitosis?

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues https://www.biorxiv.org/content/10.1101/2024.12.03.626516v1 The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from m

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues https://www.biorxiv.org/content/10.1101/2024.12.03.626516v1

New research from the Xavier lab at Broad reveals the gut's adaptability and immune-driven control in specific regions. A spatial map of the mouse intestines highlights its resilience to perturbations like inflammation, with implications for understanding diet, food allergies, and IBD in humans 🧬🦠

Thank you Micha! 🙏

We believe our approach marks a paradigm shift in microbiome science, integrating spatial context to uncover how the host interacts with the microbiome at relevant scales. Reach out if you want to try it yourselves

Finally, we explore a vignette of host-microbe interaction in a tumor-bearing tissue section, revealing microbial invasion into the host, possibly because misplaced mucus-producing cells leave the tissue unprotected, enabling generalized host-microbe interaction.

What excites me most: the achieved micron resolution lets us measure colony sizes for individual taxa, potentially linking them to their in vivo growth rates.
The cherry on top? We can identify colocalizing taxa and capture not just rRNA but also microbial genes!

Regarding the host, we retrieve both coding and non-coding signatures along the crypt-villus axis.
We observe high and diverse expression at villus tips, high % unspliced molecules near crypts, and high non-coding RNA percentages closer to the gut wall

Combining in situ polyadenylation with the StereoSeq platform, we reconstruct detailed maps of both cell types and microbial taxa at micron resolution, unlocking unprecedented insights into host-microbe interaction

Using Visium with in situ polyadenylation we explore microbial niches across the transverse and longitudinal axes of the GI

We first tested whether in situ polyadenylation enhances recovery of microbiome-derived RNA at low spatial resolution.
Applying our method across murine gut sections, we observed up to a 100-fold enrichment in microbial RNA while preserving host gene expression.

Building on previous work from @dwmckellar.bsky.social
, we combine a single enzymatic step of in situ polyadenylation with commercial spatial transcriptomics platforms—Visium and StereoSeq—to map host gene expression and microbiome in mouse gut tissue sections

Previous methods to map the interface, like imaging-based HiPR-FISH from our lab and sequencing-based with modified arrays like those developed by the Vickovic and Giacomello labs, capture target microbes but limit unbiased discovery or produce low-resolution maps.
Here we address these challenges.

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing Inter–microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few tools are available to measure these interactions. Here, we report a metho...

Spatial structure shapes the host-microbiome interactome.

Our new method to map the host-microbiome interface at high-resolution, now on bioRxiv!

Co-led with Lena Takayasu & @dwmckellar.bsky.social collab between the De Vlaminck and Brito labs

doi.org/10.1101/2024...

A thread⬇️