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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...

🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10

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.

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...

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 ...

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...

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

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...

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 👇)

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.

#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

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...

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 🧵.

This was seen in totally different human populations (European and Asian), meaning that is unlikely driven by lifestyle common to elders.
Overall we do not know why this is happening, but might highlight a lineage that is better adapted to gut conditions later in life (2/2)

Sure June!
Ruminoccocus gravus is a common member of the gut microbiome. When we looked into the genetics of this bacterium, we saw that older individuals harbored bacteria of similar genetics makeup, while this was not observed in younger people. (1/2)

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 🧵 ⬇️

Big thanks to the researchers and participants behind the studies we used, the Curated curatedMetagenomicData team for making these datasets accessible, and Lifelines for providing cohort and phenotypic data. 🙏 (11/n)

Special thanks to Nicola for hosting me in his lab in @CIBIO @CIBIO_UniTrento—an inspiring few months of great science! Grateful to @embo.org EMBO for funding this experience. (10/n)

@jingyuan-fu.bsky.social bsky.social @daomingwang.bsky.social @vheidrich.bsky.social ch.bsky.social @mireiavallesc.bsky.social allesc.bsky.social @fackelmeister.bsky.social @kmci.bsky.social @umcgroningen.bsky.social (9/n)

This has been a fantastic collaboration between the Groningen Microbiome Hub team and @cibiocm.bsky.social. Huge thanks to all the amazing team members from both groups! (8/n)

While in this work we are unable to assess what is the cause of such associations, we highlight the intriguing links between bacterial strains and human phenotypes.
We provide a list of strain-phenotype associations and large phylogenies, hoping they’ll spark further interest in the community. (7/n)

C. aerofaciens phylogeny showed a melanoma-enriched clade across diverse studies.

Interestingly, individuals with prostate cancer also clustered here! (6/n)

The phylogeny of R. gnavus displayed a clade most commonly seen in older individuals. We observed this clade in both Asian and European studies, and found a distinct bile acid profile in those individuals harboring this R. gnavus clade. (5/n)

Human phenotypes also clustered with species phylogenies.
Association analysis revealed multiple phenotype–species links, including strong, reproducible associations between R. gnavus and age, and C. aerofaciens and melanoma. (4/n)

Phylogenies revealed geographic stratification 🌎.
Species with stronger stratification were less often shared across individuals, suggesting limited dispersal drives the observed geographic patterns. (3/n)

Strain-level genetic variation can shape host–microbe interactions 🦠🧬 .
We analyzed >32,000 public metagenomes, profiled species marker genes at single-nucleotide resolution with StrainPhlAn, and built ~600 species phylogenies. (2/n)

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…

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