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

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 🦠🧫

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...

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...

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

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 🧵.

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 🧵 ⬇️

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...

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)

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 💨

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.

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.

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.

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...

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....

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...

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:

Please add microbiome-related conferences for 2024 in this thread. Thanks.

Today marks the opening of the MicrobiomeHub @umcg. Im incredibly excited this unique opportunity to delve deeper into the #microbiome, #host-microbe interactions and eventually human health is now real. Onto much more groundbreaking health science! @GroMicrobiome @researchumcg

Happy to share in my first 'twit' that yesterday we celebrated the opening of the Groningen Microbiome Hub at the University Medical Center Groningen, where I had the opportunity to present the exciting strain work we have conducted with @cibiocm.bsky.social for the past year #microbiome