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Reposted by Sergio Andreu-Sanchez

Ákos T Kovács @evolvedbiofilm.bsky.social · 1d

Sergio Andreu Sanchez @seandreu.bsky.social (DSM-Firmenich): Understanding the role of the human gut microbiota in aging and health

#HumanMicrobiome

#NIME2025

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Reposted by Sergio Andreu-Sanchez

Justin Silverman @inschool4life.bsky.social · 21d

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...

www.biorxiv.org

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Reposted by Sergio Andreu-Sanchez

Jim Shaw @jimshaw.bsky.social · Sep 7

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

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

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

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Reposted by Sergio Andreu-Sanchez

Saez-Rodriguez Group @saezlab.bsky.social · Aug 25

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 ⬇️

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Reposted by Sergio Andreu-Sanchez

Sebastian Schmidt @tsbschm.bsky.social · Jun 27

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 · Jun 27

A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1

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Sergio Andreu-Sanchez @seandreu.bsky.social · May 5

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · May 5

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)

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Reposted by Sergio Andreu-Sanchez

Tami Lieberman @contaminatedsci.bsky.social · May 1

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]

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Reposted by Sergio Andreu-Sanchez

Segata Lab @cibiocm.bsky.social · Apr 30

🥁 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 · Apr 30

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…

www.sciencedirect.com

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

@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)

allesc.bsky.social

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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

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

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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)

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Sergio Andreu-Sanchez @seandreu.bsky.social · Apr 30

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…

www.sciencedirect.com

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Sergio Andreu-Sanchez @seandreu.bsky.social · Jul 3

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!

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Reposted by Sergio Andreu-Sanchez

Rob Lanfear @roblanfear.bsky.social · May 27

What are some classic papers in phylogenetics?

Please repost

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Reposted by Sergio Andreu-Sanchez

Alex Crits-Christoph @acritschristoph.bsky.social · May 7

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

www.biorxiv.org

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Reposted by Sergio Andreu-Sanchez

Alex Crits-Christoph @acritschristoph.bsky.social · Apr 15

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:

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Reposted by Sergio Andreu-Sanchez

Luis E. Valentin-Alvarado @luisvalentin.bsky.social · Jan 31

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...

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