🧬CroCoDeEL is a new tool for detecting cross-sample contamination in metagenomic data.🐊🦠 The idea behind CroCoDeEL is simple and elegant. Imagine different cocktails poured into a row of glasses...🧵 www.nature.com/articles/s41... #Microbiome #Metagenomics #Contamination

We've known the gut-brain axis is a key underpinning of Parkinson's disease. Today, for the 1st time, a gut microbiome signature denoting risk found in healthy individuals with genetic predisposition nature.com/articles/s41...

Microbiome signature of Parkinson’s disease in healthy and genetically at-risk individuals - Nature Medicine

Microbiome analysis suggests that gut microbial changes in Parkinson’s disease evolve progressively from healthy individuals to genetically at-risk individuals to clinically affected patients, with th...

nature.com

Finally out! 🥂 link.springer.com/article/10.1... We used 3 different methods to profile fecal DNA and analysed how gut microbiome composition and human cell fractions define disease severity in IBD pediatric patients. Many thanks to my supervisor Moran Yassour and our collaborators 🧵⬇️

Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum - Microbiome

Background Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized ...

link.springer.com

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!

Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

nature.com

Sebastian Schmidt@tsbschm.bsky.social · 9mo ago

We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social www.biorxiv.org/content/10.1...

Early-life changes to the gut microbiome can affect social behaviour. A study published in @cp-iscience.bsky.social found certain diet ingredients helped restore that response and changed brain pathways linked to learning and development. buff.ly/YeQk7LV #GutBrainAxis #Microbiome Collaborators⬇

New APC paper in Nature Comms First author Cristina Cuesta-Marti and colleagues examine how eating unhealthy foods early in life leaves lasting brain and feeding changes but bacteria can help restore healthy eating. www.nature.com/articles/s41... #Microbiome #GutBrainAxis Tagging collaborators ⬇️

How does industrialization and lifestyle impact our interactions with gut microbiomes? And what is the consequence of these perturbations on our physiology? Discover findings from our new study addressing these questions: www.biorxiv.org/content/10.1... #microbiome #globalhealth #GMbC

🚀 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 👇 🧵

Orchestrating Microbiome Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.10.29.685036v1

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

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...

biorxiv.org

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!

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

biorxiv.org

Michael Kuhn@biocs.bsky.social · 12mo ago

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

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...

nature.com

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

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...

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

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...

nature.com

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...

thelancet.com

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

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

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

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 · last yr.

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

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

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

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...

biorxiv.org

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

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)

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...

biorxiv.org

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

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

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...

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...

nature.com