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.

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!

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. #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

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...

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...

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

A blog post about batch effects in bioinformatics and how to address them -- By me 🤓 shorturl.at/cmF8z

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.

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 😂.

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

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...

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!

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)

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

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...

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...

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.

A glycan atlas of the mammalian intestine through ontogeny and inflammation https://www.biorxiv.org/content/10.1101/2025.03.06.641959v1

ICYMI: New online! AI-enabled ‘endo-histo-omics’: breaking down intestinal barriers in IBD

We're once again hosting the Human #Microbiome conference at @embl.org, organized by Ami Bhatt, Nicola Segata, Mani Arumugam and Peer Bork! We always have a great lineup of speakers, so register now and think about an abstract to submit (abstract submission deadline in June)

The latest from the StatDivLab -- guidance for your #microbiome data analysis with a focus on the #statistics. Planning, deciding, modeling, justifying, communicating, visualizing... "Papers Need Friends" blog post coming shortly.

Happy to share the publication of (what will be) the first chapter of my PhD thesis: 'From in silico screening to in vivo validation in zebrafish – a framework for reeling in the right psychobiotics' 📃: shorturl.at/ZMh9p #microbiome #probiotics

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:

Are you interested in microbial proteins? 🦠🔬 Join our NFDI4Microbiota Coffee Talk on Feb 24, 2:30 PM CET! Thomas Hitch (RWTH Aachen) will present a method that increases protein detection, revealing hidden groups in the gut microbiome. More info here: tinyurl.com/mudhdnra

Hi, we have an open PhD position in our lab starting winter 2025. Join the great MolMed PhD program at a vibrant research institution and help us understand probiotic engraftment. More info at www.dienerlab.com/posts/phd2025/ . Application through the MedUni portal: phd-recruiting.medunigraz.at

"Furthermore, we analyzed tissue-specific glycosylation patterns in mice and demonstrated that a defined gut microbiota substantially remodels the mouse brain glycoproteome, shedding light on the link between the gut microbiome and brain protein functions." www.nature.com/articles/s41...

Come join us! 🚨 PhD opportunity 🚨doing bioinformatics on the microbiome-gut-brain axis at APC microbiome ireland Applications open until March 14th More info: shorturl.at/BpLNb 👈

Microbiome conferences in 2025

Excited share that our @romefoundation.bsky.social Working Team's manuscript 📄 on Overlap in Disorders of Gut-Brain Interaction #DGBI is now published in @natrevgastrohep.bsky.social! Grateful for this amazing journey with global experts. Read here: nature.com/articles/s41... #DGBI #GISky #GutSky

Our paper out @CellCellPress: Structure guided discovery of viral proteins that inhibit host immunity Congrats Erez Yirmiya, Azita Leavitt, Gil Amitai, our collaborators at the Kranzusch lab, and coauthors A 🧵 1/10 www.cell.com/cell/abstrac...

Here we show that transmitting the Microbiome can transfer a host trait, independently of selection on the host genome. In mice, with selection for low activity levels. Correlates with levels of lactobacilli and indolelactate: transferring these alone also reduces activity.

"Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease" Another very interesting paper from the Elinav Lab.

A data-driven causal inference approach suggests that Eggerthella and Hungatella are causal contributors to Major Depressive Disorder in humans (N=1,269) goto.now/AMfYs 🚨 microbiome gut brain axis

🚨 New review in @natrevgastrohep.bsky.social: Should you take probiotics with antibiotics? www.nature.com/articles/s41... Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵

This week I presented my work on the characterization of gut microbiomes across southamerican populations at the annual meeting of the Irish Society of Comp. Bio. Our work won an award & loads of very good feedback 🥳. Sadly, I had to crop the pic but (hopefully) we will drop a preprint soon

Pulled together this starter pack for Microbiota-Gut-Brain Axis Research. 🧠🦠🥼 Hope it is helpful for the people joining in here and nucleating a community. May have missed people, please leave a reply and I can then add to the pack. Cheers. go.bsky.app/PZhXP7R

Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index www.biorxiv.org/content/10.1...

Scenario A: One researcher gets their hands on a large dataset. Brainstorms 100 hypotheses, runs analyses for each one, only publishes the significant ones. Scenario B: Public dataset. 100 researchers download it, each tests 1 hypothesis. Only the significant ones get published. Which is better?

Online in Science co-lead with Frances Spragge! We looked at why microbiome diversity protects against pathogens. It's down to a simple principle of collective nutrient overlap, which can predict protective communities against a given pathogen! 🧵👇 www.science.org/doi/10.1126/...

This amazing paper led by @jccvila.bsky.social shows that microbial community assembly in different carbon sources can be predicted by the conservation of metabolism. Carbon sources that get metabolized more similarly also lead to more similar communities. www.biorxiv.org/content/10.1...