Ben Valderrama
@bvalderrama.bsky.social
Computational Biologis at APC microbiome Ireland 🇮🇪
Personal website: https://shorturl.at/meCEH
Microbiome-Gut-Brain axis | Gut permeability | Bioinformatics🦠🧬💻 | Stats
Personal website: https://shorturl.at/meCEH
Microbiome-Gut-Brain axis | Gut permeability | Bioinformatics🦠🧬💻 | Stats
Pinned
Ben Valderrama
@bvalderrama.bsky.social
· Aug 11
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations - Nature Communications
Here, Valderrama et al., introduced ‘saMBA’, the largest collection of uniformly analyzed microbiome data from South America, the worlds most biodiverse yet less characterized region. The article prop...
shorturl.at
I'm beyond excited to share that our last work is now published in Nature Communications.
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
Reposted by Ben Valderrama
🚀 TaxSEA v1.2 is now live in #Bioconductor release 3.22!
TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵
TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵
November 3, 2025 at 12:27 AM
🚀 TaxSEA v1.2 is now live in #Bioconductor release 3.22!
TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵
TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵
Reposted by Ben Valderrama
Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1
October 30, 2025 at 8:54 PM
Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1
Reposted by Ben Valderrama
New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.
August 29, 2025 at 10:06 AM
New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.
Reposted by Ben Valderrama
Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.
Prehistoric Global Migration of Vanishing Gut Microbes With Humans
The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...
www.biorxiv.org
August 16, 2025 at 6:25 PM
Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.
Reposted by Ben Valderrama
New preprint from lab: www.biorxiv.org/content/10.1... describing the Metalog database of manually annotated contextual data for >110k metagenomics samples around the globe metalog.embl.de
See the thread below from @biocs.bsky.social for more info!
See the thread below from @biocs.bsky.social for more info!
August 15, 2025 at 8:11 AM
New preprint from lab: www.biorxiv.org/content/10.1... describing the Metalog database of manually annotated contextual data for >110k metagenomics samples around the globe metalog.embl.de
See the thread below from @biocs.bsky.social for more info!
See the thread below from @biocs.bsky.social for more info!
Reposted by Ben Valderrama
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
->Nature | More info from EcoSearch
->Nature | More info from EcoSearch
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
The European Nucleotide Archive (ENA) was used as an interface to systematically search the INSDC. Two authors (BV and PCR) screened the databases independently to identify bioprojects including samples from the gut microbiome of South American individuals. For each South...
www.nature.com
August 9, 2025 at 9:38 PM
Reposted by Ben Valderrama
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations. #Microbiome #NegletecPopulations @natcomms.nature.com 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 13, 2025 at 9:15 AM
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations. #Microbiome #NegletecPopulations @natcomms.nature.com 🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ben Valderrama
Putting the Global South on the Microbiome research map -
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
August 11, 2025 at 5:24 PM
Putting the Global South on the Microbiome research map -
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in @natcomms.nature.com
"If microbiome science is to benefit everyone, it must include everyone."
www.nature.com/articles/s41...
I'm beyond excited to share that our last work is now published in Nature Communications.
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations - Nature Communications
Here, Valderrama et al., introduced ‘saMBA’, the largest collection of uniformly analyzed microbiome data from South America, the worlds most biodiverse yet less characterized region. The article prop...
shorturl.at
August 11, 2025 at 1:33 PM
I'm beyond excited to share that our last work is now published in Nature Communications.
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
📄: shorturl.at/wq9pr
Reposted by Ben Valderrama
Seems like we keep saying the same things over and over in #science. Every biomedical researcher should have a graduate course in #statistics.
My record is $100k USD lost because a post doc had bad (well, no) experimental design for a proteomics project.
www.nature.com/articles/s41...
My record is $100k USD lost because a post doc had bad (well, no) experimental design for a proteomics project.
www.nature.com/articles/s41...
How thoughtful experimental design can empower biologists in the omics era - Nature Communications
Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...
www.nature.com
August 9, 2025 at 11:34 AM
Seems like we keep saying the same things over and over in #science. Every biomedical researcher should have a graduate course in #statistics.
My record is $100k USD lost because a post doc had bad (well, no) experimental design for a proteomics project.
www.nature.com/articles/s41...
My record is $100k USD lost because a post doc had bad (well, no) experimental design for a proteomics project.
www.nature.com/articles/s41...
Reposted by Ben Valderrama
So happy to see this excellent work out!
‘Gut microbiota regulates exercise-induced hormetic modulation of cognitive function’
Fantastic collaboration with @jltrejoneuro.bsky.social @cintadoelisa.bsky.social @jfcryan.bsky.social
www.thelancet.com/journals/ebi...
‘Gut microbiota regulates exercise-induced hormetic modulation of cognitive function’
Fantastic collaboration with @jltrejoneuro.bsky.social @cintadoelisa.bsky.social @jfcryan.bsky.social
www.thelancet.com/journals/ebi...
Gut microbiota regulates exercise-induced hormetic modulation of cognitive function
These findings suggest that the hormetic effects of physical exercise on cognitive
function and neurogenesis are mediated by corresponding changes in the gut microbiota,
highlighting a novel mechanist...
www.thelancet.com
August 6, 2025 at 10:03 AM
So happy to see this excellent work out!
‘Gut microbiota regulates exercise-induced hormetic modulation of cognitive function’
Fantastic collaboration with @jltrejoneuro.bsky.social @cintadoelisa.bsky.social @jfcryan.bsky.social
www.thelancet.com/journals/ebi...
‘Gut microbiota regulates exercise-induced hormetic modulation of cognitive function’
Fantastic collaboration with @jltrejoneuro.bsky.social @cintadoelisa.bsky.social @jfcryan.bsky.social
www.thelancet.com/journals/ebi...
I’ve been thinking about meta-analysis of microbiome data for a on-going collaboration when I noticed that, although they are fairly common in the literature, there is a lack of critical discussion on their limitations. This blog is my (unsolicited) contribution to the matter.
shorturl.at/mXSar
shorturl.at/mXSar
Common Limitations of Gut Microbiome Meta-Analyses Undermine their Credibility
Although microbiome meta-analyses are fairly common in the literature, there is a lack of critical discussion on their limitations. This post is my (unsolicited) contribution to that topic.
shorturl.at
July 21, 2025 at 2:24 PM
I’ve been thinking about meta-analysis of microbiome data for a on-going collaboration when I noticed that, although they are fairly common in the literature, there is a lack of critical discussion on their limitations. This blog is my (unsolicited) contribution to the matter.
shorturl.at/mXSar
shorturl.at/mXSar
A blog post about batch effects in bioinformatics and how to address them
--
By me 🤓
shorturl.at/cmF8z
--
By me 🤓
shorturl.at/cmF8z
When Good Science Goes Wrong: How Batch Effects Can Obscure Biology
...and how to successfully avoid it
open.substack.com
July 7, 2025 at 12:18 PM
A blog post about batch effects in bioinformatics and how to address them
--
By me 🤓
shorturl.at/cmF8z
--
By me 🤓
shorturl.at/cmF8z
Reposted by Ben Valderrama
It's #WorldMicrobiomeDay! 🦠
We are proud to be a part of this exciting research area through contributions by our amazing authors.
To celebrate this occasion, here are some of our favourite microbiome papers.
Do you have a favourite of yours? let us know in the replies.
#MicroSky #MicrobiomeSky
We are proud to be a part of this exciting research area through contributions by our amazing authors.
To celebrate this occasion, here are some of our favourite microbiome papers.
Do you have a favourite of yours? let us know in the replies.
#MicroSky #MicrobiomeSky
June 27, 2025 at 8:12 AM
It's #WorldMicrobiomeDay! 🦠
We are proud to be a part of this exciting research area through contributions by our amazing authors.
To celebrate this occasion, here are some of our favourite microbiome papers.
Do you have a favourite of yours? let us know in the replies.
#MicroSky #MicrobiomeSky
We are proud to be a part of this exciting research area through contributions by our amazing authors.
To celebrate this occasion, here are some of our favourite microbiome papers.
Do you have a favourite of yours? let us know in the replies.
#MicroSky #MicrobiomeSky
Reposted by Ben Valderrama
Apparently it is still possible in 2025 to publish a paper in Nature that *filters* for strong signals before applying un-corrected significance tests. Seeing mistakes like this pass peer review is demoralizing.
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reply to: Reply to: False positives in the study of memory-related gene expression
In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…
liorpachter.wordpress.com
June 17, 2025 at 7:25 AM
Apparently it is still possible in 2025 to publish a paper in Nature that *filters* for strong signals before applying un-corrected significance tests. Seeing mistakes like this pass peer review is demoralizing.
I started a blog: "The Middle Author's Syndrome" and I've just wrote my first post: bvalderrama.substack.com/p/my-first-r....
It's about a new side research project I just started. We will see if and how these experiments (the blog and the project) develop over time 😂.
It's about a new side research project I just started. We will see if and how these experiments (the blog and the project) develop over time 😂.
My First Research Project Conducted in the Open
TL;DR I’ll start a biobliometrics analysis on the Microbiome-Gut-Brain axis field.
bvalderrama.substack.com
June 11, 2025 at 2:23 PM
I started a blog: "The Middle Author's Syndrome" and I've just wrote my first post: bvalderrama.substack.com/p/my-first-r....
It's about a new side research project I just started. We will see if and how these experiments (the blog and the project) develop over time 😂.
It's about a new side research project I just started. We will see if and how these experiments (the blog and the project) develop over time 😂.
Reposted by Ben Valderrama
We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky
Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and N...
arxiv.org
May 19, 2025 at 7:40 PM
We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky
Reposted by Ben Valderrama
Another step for microbiome research!🔬 New study introduces saMBA, a gut microbiome archive from South America. Understanding the full picture of gut microbiome biodiversity is crucial & saMBA is helping us get there!
@bvalderrama.bsky.social @jfcryan.bsky.social
www.biorxiv.org/content/10.1...
@bvalderrama.bsky.social @jfcryan.bsky.social
www.biorxiv.org/content/10.1...
The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations
The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to whi...
www.biorxiv.org
April 21, 2025 at 11:57 AM
Another step for microbiome research!🔬 New study introduces saMBA, a gut microbiome archive from South America. Understanding the full picture of gut microbiome biodiversity is crucial & saMBA is helping us get there!
@bvalderrama.bsky.social @jfcryan.bsky.social
www.biorxiv.org/content/10.1...
@bvalderrama.bsky.social @jfcryan.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Ben Valderrama
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/04/10/a...
• The South American MicroBiome Archive / @bvalderrama.bsky.social
• coverM / @aroneys.bsky.social
• #OpenSourceDiaries / Anita Ihuman
• invitation for the next week @microbiomevif.bsky.social
& more.
Happy Friday!
• The South American MicroBiome Archive / @bvalderrama.bsky.social
• coverM / @aroneys.bsky.social
• #OpenSourceDiaries / Anita Ihuman
• invitation for the next week @microbiomevif.bsky.social
& more.
Happy Friday!
April 11, 2025
Happy Friday and see you next week at MVIF! Gut microbiome The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of negle…
microbiomedigest.com
April 11, 2025 at 7:25 AM
New #MicrobiomeDigest is OUT microbiomedigest.com/2025/04/10/a...
• The South American MicroBiome Archive / @bvalderrama.bsky.social
• coverM / @aroneys.bsky.social
• #OpenSourceDiaries / Anita Ihuman
• invitation for the next week @microbiomevif.bsky.social
& more.
Happy Friday!
• The South American MicroBiome Archive / @bvalderrama.bsky.social
• coverM / @aroneys.bsky.social
• #OpenSourceDiaries / Anita Ihuman
• invitation for the next week @microbiomevif.bsky.social
& more.
Happy Friday!
Excited to share our preprint on the South American MicroBiome Archive (saMBA)! 🌎🦠.
We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.
📄: shorturl.at/Lmvp5
🧵: What did we find—and why? Find out 👇
#microbiome #gut-microbiome
(1/8)
We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.
📄: shorturl.at/Lmvp5
🧵: What did we find—and why? Find out 👇
#microbiome #gut-microbiome
(1/8)
The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations
The composition and function of the human gut microbiome has been linked to multiple health outcomes across all world regions, often with region-specific associations. Unfortunately, the extent to whi...
www.biorxiv.org
April 9, 2025 at 12:50 PM
Excited to share our preprint on the South American MicroBiome Archive (saMBA)! 🌎🦠.
We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.
📄: shorturl.at/Lmvp5
🧵: What did we find—and why? Find out 👇
#microbiome #gut-microbiome
(1/8)
We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.
📄: shorturl.at/Lmvp5
🧵: What did we find—and why? Find out 👇
#microbiome #gut-microbiome
(1/8)
Reposted by Ben Valderrama
First paper from my PD at @apcmicrobiomeirel.bsky.social out! 🥳
Do you want to know how acute stress enhances synaptic plasticity?
Our latest study shows that the gut microbiota is essential.
@jfcryan.bsky.social @kjdoriordan.bsky.social
sciencedirect.com/science/article/pii/S0028390825001406?s=08
Do you want to know how acute stress enhances synaptic plasticity?
Our latest study shows that the gut microbiota is essential.
@jfcryan.bsky.social @kjdoriordan.bsky.social
sciencedirect.com/science/article/pii/S0028390825001406?s=08
Acute stress enhances synaptic plasticity in male mice via a microbiota-dependent mechanism
Acute stress can enhance or impair synaptic plasticity depending on the nature, duration, and type of stress exposure as well as the brain region exam…
sciencedirect.com
April 5, 2025 at 3:13 PM
First paper from my PD at @apcmicrobiomeirel.bsky.social out! 🥳
Do you want to know how acute stress enhances synaptic plasticity?
Our latest study shows that the gut microbiota is essential.
@jfcryan.bsky.social @kjdoriordan.bsky.social
sciencedirect.com/science/article/pii/S0028390825001406?s=08
Do you want to know how acute stress enhances synaptic plasticity?
Our latest study shows that the gut microbiota is essential.
@jfcryan.bsky.social @kjdoriordan.bsky.social
sciencedirect.com/science/article/pii/S0028390825001406?s=08
Reposted by Ben Valderrama
Happy to share DEBIAS-M, our new method for domain adaptation and bias correction in #microbiome data.🧬🖥️
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models - Nature Microbiology
DEBIAS-M corrects technical variability in microbiome data in a manner both interpretable and suitable for machine learning. In extensive benchmarks, DEBIAS-M facilitates robust analyses that generali...
www.nature.com
March 27, 2025 at 4:01 PM
Happy to share DEBIAS-M, our new method for domain adaptation and bias correction in #microbiome data.🧬🖥️
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Microbiome data is very variable, with substantial study- and batch-effects. DEBIAS-M corrects these, enabling robust and generalizable analyses.
A quick thread:
www.nature.com/articles/s41...
Reposted by Ben Valderrama
Brain, bacteria, and behaviour (PhD-level) summer course, The Netherlands, July 11-15 - also featuring R/Bioconductor & microbiome data science:
www.radboudumc.nl/en/agenda/20...
www.radboudumc.nl/en/agenda/20...
Brain, bacteria, and behaviour summer course - Understanding the gut brain axis
Looking for information about Brain, bacteria, and behaviour summer course? Read more about this Radboudumc agenda item
www.radboudumc.nl
March 24, 2025 at 10:41 PM
Brain, bacteria, and behaviour (PhD-level) summer course, The Netherlands, July 11-15 - also featuring R/Bioconductor & microbiome data science:
www.radboudumc.nl/en/agenda/20...
www.radboudumc.nl/en/agenda/20...
Are you thinking about applying ML to analyze your microbiome data but unsure how or where to start?
Worry no more! Our book chapter has you covered:
shorturl.at/8kvX1
It’s an online intro to deploying ML on real microbiome data with code, result interpretation, tips, and challenges at the end.
Worry no more! Our book chapter has you covered:
shorturl.at/8kvX1
It’s an online intro to deploying ML on real microbiome data with code, result interpretation, tips, and challenges at the end.
24 Machine learning – Orchestrating Microbiome Analysis
shorturl.at
March 24, 2025 at 10:18 AM
Are you thinking about applying ML to analyze your microbiome data but unsure how or where to start?
Worry no more! Our book chapter has you covered:
shorturl.at/8kvX1
It’s an online intro to deploying ML on real microbiome data with code, result interpretation, tips, and challenges at the end.
Worry no more! Our book chapter has you covered:
shorturl.at/8kvX1
It’s an online intro to deploying ML on real microbiome data with code, result interpretation, tips, and challenges at the end.