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Reposted by Ben Valderrama

Silas Kieser @silask.bsky.social · Aug 29

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

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Reposted by Ben Valderrama

Ben Good @benjaminhgood.bsky.social · Aug 16

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

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Reposted by Ben Valderrama

Bork Group at EMBL Heidelberg @borklab.bsky.social · Aug 15

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!

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Reposted by Ben Valderrama

Climate, Ecology, War & More by Dr. Glen Barry, BigEarthData.ai @bigearthdata.bsky.social · Aug 9

The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations
->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

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Ben Valderrama @bvalderrama.bsky.social · Aug 13

Thank you so much!

Reposted by Ben Valderrama

Javier Santoyo @jsantoyo.bsky.social · Aug 13

The South American MicroBiome Archive (saMBA): enriching the microbiome field by studying neglected populations. #Microbiome #NegletecPopulations @natcomms.nature.com 🧬
www.nature.com/articles/s41...

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Ben Valderrama @bvalderrama.bsky.social · Aug 11

Thanks John for sharing the work. Also for the constant mentoring and support! It's deeply appreciated 🙌🔥

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Reposted by Ben Valderrama

John F. Cryan @jfcryan.bsky.social · Aug 11

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...

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Ben Valderrama @bvalderrama.bsky.social · Aug 11

For more information about our work, see the thread I shared when the preprint was released: bsky.app/profile/bval...

Ben Valderrama @bvalderrama.bsky.social · Apr 9

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
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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

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Ben Valderrama @bvalderrama.bsky.social · Aug 11

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 - 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

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Reposted by Ben Valderrama

Rich LeDuc (He/Him) @rich-leduc.bsky.social · Aug 9

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...

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

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Reposted by Ben Valderrama

María R. Aburto @maburto.bsky.social · Aug 6

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

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

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Ben Valderrama @bvalderrama.bsky.social · Jul 21

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

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

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Ben Valderrama @bvalderrama.bsky.social · Jul 7

A blog post about batch effects in bioinformatics and how to address them
--
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

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Reposted by Ben Valderrama

Nature Microbiology @natmicrobiol.nature.com · Jun 27

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

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Reposted by Ben Valderrama

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Jun 17

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.

Lior Pachter @lpachter.bsky.social · Jun 16

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

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Ben Valderrama @bvalderrama.bsky.social · Jun 11

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 😂.

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

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Reposted by Ben Valderrama

Rich Abdill @richabdill.com · May 19

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

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Reposted by Ben Valderrama

Mizrahi Lab @mizrahilab.bsky.social · Apr 21

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...

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

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Ben Valderrama @bvalderrama.bsky.social · Apr 14

How I finally found my confidence as a scientist

After three postdoc positions, this researcher now sees her skills and knowledge as valuable

www.science.org

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Reposted by Ben Valderrama

Svetlana Ugarcina Perovic @svetlanaup.bsky.social · Apr 11

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!

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

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Ben Valderrama @bvalderrama.bsky.social · Apr 9

Finally, I’d like to thank again everyone involved in this research: Paulina Calderón-Romero, Thomaz, @biothomaz.bsky.social, and of course to my supervisors: Aonghus Lavelle, Ger Clarke, and John @jfcryan.bsky.social. Also, thanks to the centre APC @apcmicrobiomeirel.bsky.social

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Ben Valderrama @bvalderrama.bsky.social · Apr 9

We show how semiautomated project screening can better represent regional biodiversities 🌎. The workflow is available for researchers building similar archives for other regions or body sites. The data generated is open, and new features are coming, so keep an eye on GitHub: shorturl.at/i9P1G (8/8)

GitHub - Benjamin-Valderrama/saMBA-pipeline: Workflow to build archives of 16s faecal microbiome samples from neglected populations.

Workflow to build archives of 16s faecal microbiome samples from neglected populations. - Benjamin-Valderrama/saMBA-pipeline

github.com

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Ben Valderrama @bvalderrama.bsky.social · Apr 9

We improved estimates of regional biodiversity and identified countries with the greatest potential to uncover more biodiversity in future sampling efforts—an analysis that’s the first of its kind and a critical guide for regions with limited research resources. (7/8).

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Ben Valderrama @bvalderrama.bsky.social · Apr 9

After analysing >30 projects—most not included in any compendium before—we show how saMBA expanded our understanding of the human gut microbiome with samples from nearly every country in the region 🌎. We also found that nearly a third were likely discarded due to past sample size restrictions (6/8).

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