Sergio Andreu-Sanchez
@seandreu.bsky.social
Postdoctoral researcher at @raeslab.org, former Groningen Microbiome Hub. (meta)Genomics, bioinformatics
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10
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...
doi.org
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
embl.org
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
nature.com
Had a blast discussing science with Matt David on the Saving Sapiens podcast. We talk gut microbiome and the findings of our work earlier this year on strain variation linked to host's geography and health, now live on Youtube! Full episode: lnkd.in/gUwY36zU Paper link: lnkd.in/gNRtqhMF
This link will take you to a page that’s not on LinkedIn
lnkd.in
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO 🦠🧫
Selection and transmission of the gut microbiome alone can shift mammalian behavior
Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...
rdcu.be
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
#NewResearch Nasal colonisation by S. aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain #MicroSky #Depression www.nature.com/articles/s41...
Nasal Staphylococcus aureus carriage promotes depressive behaviour in mice via sex hormone degradation - Nature Microbiology
Nasal colonization by Staphylococcus aureus is linked with depression in a human cohort and shown in a mouse model to cause decreased serotonin and dopamine in the brain.
nature.com
Sergio Andreu Sanchez @seandreu.bsky.social (DSM-Firmenich): Understanding the role of the human gut microbiota in aging and health #HumanMicrobiome #NIME2025
New Paper! Machine learning models that attempt to predict microbial load collapse outside of their training context with an R2<0! In contrast, our Bayesian Partially Identified Models embrace uncertainty in unmeasured microbial load and consistently outpreform. www.biorxiv.org/content/10.1...
Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis
Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, of...
biorxiv.org
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 · 11mo agoHigh-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
We present our MetaProViz #Rpackage for #metabolomics analysis & prior knowledge integration to generate mechanistic hypotheses on how metabolic changes affect metabolite classes, pathways & environment interaction 🔗 www.biorxiv.org/content/10.1... 📦 saezlab.github.io/MetaProViz/ 🧵 Thread ⬇️
The team's first preprint is out! Led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last yr.A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]
🥁 New publication Our latest study in collab w/ the Groningen Microbiome Hub team is OUT! We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. And more! For more details 🧵 ⬇️
Sergio Andreu-Sanchez@seandreu.bsky.social · last yr.Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...
Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...
Global genetic structure of human gut microbiome species is related to geographic location and host health
The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…
sciencedirect.com
After 4,5 years, working besides great colleagues and mentors, last week I received my PhD degree at @unigroningen.bsky.social I feel really lucky to have had the opportunity to work in such fantastic scientific environment. Exciting things to come in the next chapter!
What are some classic papers in phylogenetics? Please repost
Fairy: fast approximate coverage for multi-sample metagenomic binning www.biorxiv.org/content/10.1... From @jimshaw.bsky.social Finally the answer for those routinely running 40,000 bowtie2 metagenome mappings per project (niche but real)
Fairy: fast approximate coverage for multi-sample metagenomic binning
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
biorxiv.org
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies- from Heng Li genomebiology.biomedcentral.com/articles/10.... They make this nice plot of the rank abundance curve showing which OTUs assemble into MAGs vs those that do not from the sheep's gut:
Nearly 20 years ago, Jill Banfield, Gene Tyson & team transformed #microbiology with their seminal paper on genome-resolved metagenomics. Their innovative approach in reconstructing microbial genomes opened new frontiers in understanding ecosystem dynamics! paper here: www.nature.com/articles/nat...
10 years on, @bkille.bsky.social @treangen.bsky.social and co. have refreshed Parsnp with a version 2! Build a core genome multi-alignment for 100k SARS genomes or 1k Mtb genomes in under an hour 💨
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 3y agoParsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets https://www.biorxiv.org/content/10.1101/2024.01.30.577458v1
SingleM finally has a preprint associated with it!! I've juxtaposed two of their figures - that is a heck of a benchmark. Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3y agoSingleM and Sandpiper: Robust microbial taxonomic profiles from metagenomic data https://www.biorxiv.org/content/10.1101/2024.01.30.578060v1
We are excited to present our latest preprint on breastmilk and infant gut microbiome! 1/n tinyurl.com/4rcpsawm @blekhman.bsky.social
Pleased that grad student Jacob Baker's tour de force analysis of intraspecies dynamics in the skin microbiome -- including >4,000 isolates of 2 species from 8 families carefully clustered into lineages and analyzed is now up.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3y agoHighly-resolved within-species dynamics in the human facial skin microbiome https://www.biorxiv.org/content/10.1101/2024.01.10.575018v1
Host genetic regulation of human gut microbial structural variation www.nature.com/articles/s41... Very nice study on the GalNAc utilization gene cluster in Faecalibacterium prausnitzii, associated with ABO genotype.
Host genetic regulation of human gut microbial structural variation - Nature
A meta-analysis of associations between human genetic variation and gut microbial structural variations shows that ABO genotype differentially affects the presence of Faecalibacterium prausnitzii...
nature.com
Latest work from the Groningen Microbiome Hub! F. prausnitzii's metabolic capabilities are selected by host's blood type. Great work from colleagues Daoming, Dasha, Lei and many others! www.nature.com/articles/s41...
Host genetic regulation of human gut microbial structural variation - Nature
A meta-analysis of associations between human genetic variation and gut microbial structural variations shows that ABO genotype differentially affects the presence of Faecalibacterium prausnitzii...
nature.com
Our recent paper is out now in Aging Cell. pre-vaccination immune sytem configuration associate with antibody responses to influenza vaccination and contain signatures that improve our understanding of immune aging and post-vaccination immune subset kinetics. onlinelibrary.wiley.com/doi/full/10....
Pre‐vaccination immunotypes reveal weak and robust antibody responders to influenza vaccination
Aging Cell is an open access geroscience journal addressing the biology of aging, from molecular mechanisms of aging to age-related disease.
onlinelibrary.wiley.com
Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients - samples over a ten year period www.nature.com/articles/s41...
Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long...
The diversity of ESBL-producing Klebsiella pneumoniae species complex and ESBL-Escherichia coli within patients is low and colonization with the same strain may persist for long periods. Authors utili...
nature.com
We're coming to the end of 2023, and I wanted to do a roundup of a few of my favorite microbiome papers of the year. So, in no particular order, here it goes: