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Francisco Zorrilla

@metagenomez.bsky.social

omics-driven and constraint-based modeling of microbial community metabolism 🧬 post-doc in the Sunagawa Lab, Institute of Microbiology, ETH Zürich

7 Posts326 Follower144 Folgt
Christian Kost@kostchristian.bsky.social · last mo.

Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb

Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology

Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

nature.com

Kiran R. Patil@kiranrpatil.bsky.social · 3mo ago

Interested in Genome-scale Metabolic Models for Gut microbes? Check out our latest preprint on automated model reconstruction. Carved by @ariannabasilecc.bsky.social, in teamwork with Aditi, @indraroux.bsky.social, @metagenomez.bsky.social, and @skamrad.bsky.social. www.biorxiv.org/content/10.6...

CarveMe-GutMicrobes: Automated Metabolic Model Reconstruction for Gut Microbial Species and Communities

Genome-scale metabolic models (GSMMs) are important aids towards system-level understanding of the metabolic physiology of the gut microbes and for rational microbiome engineering. While large-scale r...

biorxiv.org

Jim Shaw@jimshaw.bsky.social · last yr.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

Francisco Zorrilla@metagenomez.bsky.social · last yr.

🚨Applications open! ❄️Winter School 2026 (12–23 Jan, Lausanne) ➡️Advanced methods in microbial community analysis 🧬Hands-on training in 16S, metagenomics, metatranscriptomics, functional annotation & ML 📍Free course, apply now: nccr-microbiomes.ch/education/january-short-course/ #NCCR #Microbiomes

Zamin Iqbal@zaminiqbal.bsky.social · last yr.

"SSAlign, a protein structure retrieval tool that leverages protein language models to jointly encode sequence and structural information...On large-scale datasets such as AFDB50, SSAlign outpaces Foldseek by two to three orders of magnitude in search speed" www.biorxiv.org/content/10.1...

SSAlign: Ultrafast and Sensitive Protein Structure Search at Scale

The advent of highly accurate structure prediction techniques such as AlphaFold3 is driving an unprecedented expansion of protein structure databases. This rapid growth creates an urgent demand for novel search tools, as even the current fastest available methods like Foldseek face significant limitations in sensitivity and scalability when confronted with these massive repositories. To meet this challenge, we have developed SSAlign, a protein structure retrieval tool that leverages protein language models to jointly encode sequence and structural information, and adopts a two-stage alignment strategy optimized with multi-GPU and multi-process parallelization. On large-scale datasets such as AFDB50, SSAlign outpaces Foldseek by two to three orders of magnitude in search speed, offering unmatched scalability for high-throughput structural analysis. Compared to Foldseek, SSAlign retrieves substantially more high-quality matches on Swiss-Prot and achieves marked performance improvements on SCOPe40, with relative AUC increases of +20.2% at the family level and +33.3% at the superfamily level, demonstrating significantly enhanced sensitivity and recall. In sum, SSAlign achieves TM-align-comparable accuracy with Foldseek-surpassing speed and coverage, offering an efficient, sensitive, and scalable solution for large-scale structural biology and structure-based drug discovery. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 62172172 Hubei Provincial Natural Science Foundation of China, 2025AFB159 The Postdoctoral Fellowship Program of CPSF, GZC20240545

biorxiv.org

Ben Langmead@benlangmead.bsky.social · last yr.

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

Mumemto: efficient maximal matching across pangenomes - Genome Biology

Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple...

genomebiology.biomedcentral.com

Vikram Shivakumar@vikramshivakumar.bsky.social · 2y ago

Excited to share a preprint for (w/ @benlangmead.bsky.social) our new tool, Mumemto, on biorxiv! Mumemto finds multi-MUMs across pangenomes (i.e. mummer but for pangenomes). It can rapidly visualize synteny, identify misassemblies, and accelerate core genome and multiple alignment, highlighting SVs.

Sean Gibbons 🦠💩@gibbological.bsky.social · last yr.

Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...

Emergence and disruption of cooperativity in a denitrifying microbial community

Abstract. Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the em

academic.oup.com

Communications Biology@commsbio.nature.com · last yr.

Media optimization using machine learning increased flaviolin production in P. putida, generating counter-intuitive media recipes. doi.org/10.1038/s420...

Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida - Communications Biology

Media optimization using machine learning increased flaviolin production in Pseudomonas putida, generating counter-intuitive media recipes.

doi.org

Sean Gibbons 🦠💩@gibbological.bsky.social · last yr.

Microbial community-scale metabolic models (MCMMs) map gut microbiome composition & dietary context to functional outputs, at scale. Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com www.nature.com/articles/s41...

Moving from genome-scale to community-scale metabolic models for the human gut microbiome - Nature Microbiology

In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

nature.com

Christoph Kaleta@kaletalab.bsky.social · 2y ago

1/12 Thrilled to share our latest paper on host-microbiome-interactions in aging out in Nature Microbiology @naturemicrobiol.bsky.social, great work led by Lena Best @sci-witch.bsky.social with the Frahm lab within the ITN SmartAge. @crc1182.bsky.social @uni-kiel.de www.nature.com/articles/s41...

Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice - Nature Microbiology

A multi-omics approach reveals host–microbiome interactions in aging in mice.

nature.com

Cameron Thrash@jcamthrash.bsky.social · 2y ago

MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome microbiomejournal.biomedcentral.com/articles/10.... #jcampubs

MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome - Microbiome

Background The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown. Results We presen...

microbiomejournal.biomedcentral.com

Daniel Machado@dan1elmachado.bsky.social · 2y ago

Super excited to share the work of one of my first PhD students, Idun Burgos :) An extensively curated GEM for R. cellulolyticum, a promising microbial cell factory to digest lignocellulose. www.biorxiv.org/content/10.1...

Genome-scale metabolic modeling of Ruminiclostridium cellulolyticum: a microbial cell factory for valorization of lignocellulosic biomass

The development of sustainable biotechnological processes requires a transition from the traditional fermentation of refined substrates towards the valorization of waste materials such as lignocellulo...

biorxiv.org

Kiran R. Patil@kiranrpatil.bsky.social · 2y ago

Kudos to Ghada @kostchristian.bsky.social team and @metagenomez.bsky.social et al. for this mammoth effort! An important step forward towards understanding natural microbial communities and determinants of their fascinating diversity.

Christian Kost@kostchristian.bsky.social · 2y ago

New paper from my group and the group of @kiranrpatil.bsky.social: Obligate cross-feeding of metabolites is common in soil microbial communities By Ghada Yousif @metagenomez.bsky.social with @swagatika.bsky.social @isamirgiri.bsky.social Sharvari Harshe et al. www.biorxiv.org/content/10.1... 🧵👇

Christian Kost@kostchristian.bsky.social · 2y ago

New paper from my group and the group of @kiranrpatil.bsky.social: Obligate cross-feeding of metabolites is common in soil microbial communities By Ghada Yousif @metagenomez.bsky.social with @swagatika.bsky.social @isamirgiri.bsky.social Sharvari Harshe et al. www.biorxiv.org/content/10.1... 🧵👇

Obligate cross-feeding of metabolites is common in soil microbial communities

Many microorganisms are refractory to laboratory cultivation. One possible explanation, known as the great plate count anomaly, is metabolic dependencies among community members. However, systematic s...

biorxiv.org

Alexandre Almeida@alexmsalmeida.bsky.social · 2y ago

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

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...

nature.com