Sergio Andreu-Sanchez
@seandreu.bsky.social
Postdoctoral researcher at @raeslab.org, former Groningen Microbiome Hub.
(meta)Genomics, bioinformatics
(meta)Genomics, bioinformatics
Pinned
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
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...
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
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 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
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
November 4, 2025 at 7:35 AM
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 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
Reposted by Sergio Andreu-Sanchez
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
October 28, 2025 at 7:51 AM
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
🦠🧫
🦠🧫
Reposted by Sergio Andreu-Sanchez
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 👇)
October 15, 2025 at 12:22 PM
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 👇)
Reposted by Sergio Andreu-Sanchez
#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 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.
www.nature.com
September 22, 2025 at 3:27 PM
#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 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...
Reposted by Sergio Andreu-Sanchez
Sergio Andreu Sanchez @seandreu.bsky.social (DSM-Firmenich): Understanding the role of the human gut microbiota in aging and health
#HumanMicrobiome
#NIME2025
#HumanMicrobiome
#NIME2025
October 7, 2025 at 1:34 PM
Sergio Andreu Sanchez @seandreu.bsky.social (DSM-Firmenich): Understanding the role of the human gut microbiota in aging and health
#HumanMicrobiome
#NIME2025
#HumanMicrobiome
#NIME2025
Reposted by Sergio Andreu-Sanchez
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...
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
September 17, 2025 at 5:41 PM
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...
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...
Reposted by Sergio Andreu-Sanchez
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
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by Sergio Andreu-Sanchez
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 ⬇️
🔗
www.biorxiv.org/content/10.1...
📦
saezlab.github.io/MetaProViz/
🧵 Thread ⬇️
August 25, 2025 at 7:07 AM
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 ⬇️
🔗
www.biorxiv.org/content/10.1...
📦
saezlab.github.io/MetaProViz/
🧵 Thread ⬇️
Reposted by Sergio Andreu-Sanchez
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 🧵.
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 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:10 PM
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 🧵.
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 🧵.
Reposted by Sergio Andreu-Sanchez
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]
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]
May 1, 2025 at 6:41 PM
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]
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]
Reposted by Sergio Andreu-Sanchez
🥁 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 🧵 ⬇️
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...
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
April 30, 2025 at 7:04 PM
🥁 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 🧵 ⬇️
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...
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
April 30, 2025 at 4:15 PM
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...
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!
I feel really lucky to have had the opportunity to work in such fantastic scientific environment.
Exciting things to come in the next chapter!
July 3, 2024 at 5:06 AM
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!
I feel really lucky to have had the opportunity to work in such fantastic scientific environment.
Exciting things to come in the next chapter!
Reposted by Sergio Andreu-Sanchez
What are some classic papers in phylogenetics?
Please repost
Please repost
May 27, 2024 at 5:00 AM
What are some classic papers in phylogenetics?
Please repost
Please repost
Reposted by Sergio Andreu-Sanchez
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)
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
May 7, 2024 at 7:23 PM
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)
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)
Reposted by Sergio Andreu-Sanchez
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:
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:
April 15, 2024 at 3:34 PM
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:
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:
Reposted by Sergio Andreu-Sanchez
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...
paper here: www.nature.com/articles/nat...
January 31, 2024 at 4:59 PM
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...
paper here: www.nature.com/articles/nat...
Reposted by Sergio Andreu-Sanchez
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 💨
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets https://www.biorxiv.org/content/10.1101/2024.01.30.577458v1
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets https://www.biorxiv.org/content/10.1101/2024.01.30.577458v1
Motivation: Since 2016, the number of microbial species with available reference genomes in NCBI has
www.biorxiv.org
February 1, 2024 at 1:26 PM
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 💨
Reposted by Sergio Andreu-Sanchez
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.
Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
February 1, 2024 at 7:02 PM
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.
Assemble, but for an unassembled read-based perspective in environmental microbiomes, SingleM is a strong option.
Reposted by Sergio Andreu-Sanchez
We are excited to present our latest preprint on breastmilk and infant gut microbiome! 1/n
tinyurl.com/4rcpsawm
@blekhman.bsky.social
tinyurl.com/4rcpsawm
@blekhman.bsky.social
January 29, 2024 at 1:32 PM
We are excited to present our latest preprint on breastmilk and infant gut microbiome! 1/n
tinyurl.com/4rcpsawm
@blekhman.bsky.social
tinyurl.com/4rcpsawm
@blekhman.bsky.social
Reposted by Sergio Andreu-Sanchez
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.
Highly-resolved within-species dynamics in the human facial skin microbiome https://www.biorxiv.org/content/10.1101/2024.01.10.575018v1
Highly-resolved within-species dynamics in the human facial skin microbiome https://www.biorxiv.org/content/10.1101/2024.01.10.575018v1
Human facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species, Cutibact
www.biorxiv.org
January 11, 2024 at 2:34 PM
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.
Reposted by Sergio Andreu-Sanchez
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.
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...
www.nature.com
January 3, 2024 at 11:17 PM
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.
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...
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...
www.nature.com
January 4, 2024 at 8:31 AM
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...
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...
Reposted by Sergio Andreu-Sanchez
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....
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
December 28, 2023 at 6:40 PM
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....
onlinelibrary.wiley.com/doi/full/10....
Reposted by Sergio Andreu-Sanchez
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...
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...
www.nature.com
December 28, 2023 at 3:58 AM
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...
www.nature.com/articles/s41...