bvalderrama.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

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

submitted 15 days ago • 1 comment

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...

submitted 43 days ago • 0 comments

submitted 50 days ago • 0 comments

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!

submitted 54 days ago • 0 comments

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)

submitted 55 days ago • 1 comment

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

submitted 59 days ago • 0 comments

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...

submitted 68 days ago • 2 comments

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...

submitted 71 days ago • 0 comments

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.

submitted 72 days ago • 1 comment

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

submitted 85 days ago • 0 comments

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

submitted 86 days ago • 0 comments

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)

submitted 97 days ago • 0 comments

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.

submitted 102 days ago • 1 comment

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

submitted 105 days ago • 1 comment

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:

submitted 106 days ago • 1 comment

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

submitted 111 days ago • 0 comments

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

submitted 112 days ago • 0 comments

"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...

submitted 113 days ago • 0 comments

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 👈

submitted 113 days ago • 0 comments

Microbiome conferences in 2025

submitted 118 days ago • 0 comments

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

submitted 127 days ago • 1 comment

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...

submitted 131 days ago • 1 comment

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.

submitted 131 days ago • 0 comments

www.nature.com/articles/s41...

submitted 131 days ago • 0 comments

"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.

submitted 134 days ago • 0 comments

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

submitted 171 days ago • 0 comments

🚨 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/🧵

submitted 172 days ago • 1 comment

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

submitted 179 days ago • 4 comments

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

submitted 193 days ago • 23 comments

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...

submitted 200 days ago • 2 comments

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/...

submitted 536 days ago • 1 comment

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...

submitted 582 days ago • 0 comments

Disease-specific loss of microbial cross-feeding interactions in the human gut www.nature.com/articles/s41... #jcampubs

submitted 592 days ago • 0 comments

Happy to share our latest preprint -- we built an integrated compendium of all publicly available human gut microbiome 16S data (~168,000 samples) and used it to explore patterns of microbiome variation around the world www.biorxiv.org/content/10.1...

submitted 595 days ago • 2 comments

Exciting new preprint and resource for microbiome research. Authors assembled >160,000 publicly available 16S data from human gut microbiome samples, processed them with a single pipeline and then combined into the largest unified microbiome dataset to date. Here the website: microbeatlas.org

submitted 601 days ago • 0 comments