A Bayesian approach to differential prevalence analysis with applications in microbiome studies ("DiPPER") arxiv.org/abs/2602.05938

BiomeGPT: A foundation model for the human gut microbiome https://www.biorxiv.org/content/10.64898/2026.01.05.697599v1

How I recovered from a collaboration gone wrong www.science.org/content/arti...

@antagomir.bsky.social 🙌

With a huge inflow of tweeps to the skies, let us hope the skies will continue to support a spectrum of opinions rather than the division by extremes 🕊

1/ 🚨 New preprint alert! 🚨 We’re thrilled to share our latest work exploring microbiome & genomic #Bifidobacterium co-evolutionary & functional signatures across diverse animal hosts. This has been a long time coming, & huge credit to Magda for her incredible hard work as first author! 🐾✨👇

Fascinating Insights here 👇 50% of all bacteriology papers focus on just 10 species, a disproportionate emphasis on pathogens. Narrow focus hinders the development of novel health promoting microbes. #microbiome www.biorxiv.org/content/10.1...

Starting the new year with a new pre-print from the Hall Lab @halllab.bsky.social looking at the impact of empirical antibiotics on gut microbiome and resistome of both probiotic and non-probiotic supplemented VLBW preterm infants: www.biorxiv.org/content/10.1... #resistome #amr #microbiome #preterm

If you are a microbial ecologist, add this to your must-read library

Spatial heterogeneity influences phage-host co-existence dynamics and phage resistance development in Vibrio anguillarum https://www.biorxiv.org/content/10.1101/2024.12.28.630609v1

"Functional and evolutionary significance of unknown genes from uncultivated taxa", a publication from the lab of @jhcepas.bsky.social (2023), highlights what can be achieved by integrating GMGC and other gene catalogs to hunt for novel gene families in 150k genomes www.nature.com/artic...

SCARAP: scalable cross-species comparative genomics of prokaryotes https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae735/7921419 🧬🖥️🧪 https://github.com/swittouck/scarap

Ecological factors that drive microbial communities in culturally diverse fermented foods https://www.biorxiv.org/content/10.1101/2024.08.20.608727v1

NEW from Willem M. De Vos's lab, HELMi team and our lab: longitudinal metagenomic analyses on infant gut microbiota seeding dynamics just published! 👏 THANKS to Leonard Dubois, Mireia Valles Colomer and all co-authors, the study participants, and the funding agencies! www.cell.com/cell-host-mi...

The dysbiosisR package is a collection of functions to calculate six dysbiosis measures from microbiota profiling data. microsud.github.io/dysbiosisR/a...

Quantifying the daily harvest of fermentation products from the human gut microbiota https://www.biorxiv.org/content/10.1101/2024.01.05.573977v1

Prof. Marten Scheffer explains the concept of 'sickness of rarity' in ecosystems. We had an opportunity to collaborate & demonstrate its presence in human gut microbiota(HGM). This has implications for understanding occasional pathobiont blooms in HGM. www.wur.nl/en/research-...

A tiny fraction of all species forms most of nature: Rarity as a sticky state doi.org/10.1073/pnas...

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment https://www.biorxiv.org/content/10.1101/2023.12.30.573720v1

Exposure and resistance to lantibiotics impact microbiota composition and function https://www.biorxiv.org/content/10.1101/2023.12.30.573728v1

Automate Microbiome Analysis Using Quarto At the beginning of 2023, I created a blog post on how to automate basic and routine microbiome data analysis tasks in R using Quarto. Here is a tutorial for #Microbiome #blueskiers microsud.github.io/quarto_micro...

Our recent paper is out now in Aging Cell. pre-vaccination immune sytem configuration associate with antibody responses to influenza vaccination and contain signatures that improve our understanding of immune aging and post-vaccination immune subset kinetics. onlinelibrary.wiley.com/doi/full/10....

Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions www.frontiersin.org/articles/10.... #jcampubs

A catalogue of small proteins from the global microbiome https://www.biorxiv.org/content/10.1101/2023.12.27.573469v1

Job Alert! We are looking for a Principal Bioinformatics Research Scientist with extensive experience in large-scale microbial genomics to create and direct our new Microbial Computational Genomics and Bioinformatics Lab @StJudeResearch stjude.wd1.myworkdayjobs.com/stjude/job/M...

Benchmarking A Novel Quantitative PCR-based Microbiome Profiling Platform Against Sequencing-based Methods https://www.biorxiv.org/content/10.1101/2023.12.27.573468v1

I'm happy 😀 to announce I have a PhD position on the mathematical 🧮 modelling 💻 of microbial 🦠 evolution! I'm looking forward to working with an enthousiastic candidate on this project, please contact me with any questions! #JobAlert Please retweet! vacatures.uva.nl/UvA/job/PhD-...

Bacteroidia and Clostridia perform a progressive cascade of polysaccharide degradation along the hindgut of the herbivorous fish Kyphosus sydneyanus https://www.biorxiv.org/content/10.1101/2023.12.23.570891v1

📢 App Version 1.60 is rolling out now (1/5) We have a new logo! 🦋  Bluesky is emerging from its cocoon of clouds to transform into a social butterfly. Read more about why we chose this logo here: blueskyweb.xyz/blog/12-21-2...

This is a super cool piece of work - Olivia Kosterlitz & Benjamin Kerr et al Evolutionary “Crowdsourcing”: Alignment of Fitness Landscapes Allows for Cross-species Adaptation of a Horizontally Transferred Gene academic.oup.com/mbe/article/... #MicroSky #EvoSky

New paper: of 5000 PhDs awarded at large Dutch uni, men were about twice as likely to receive a cum laude degree even if they had same supervisor. Difference most severe with all male PhD committees & reduces with more female members. www.nature.com/articles/s41...

We are looking for a colleague! Assistant/associate professor machine learning in bioinformatics at Wageningen University www.wur.nl/en/vacancy/a...

If you are applying for a PhD in the US, can I suggest you consider Australia🦘? Great science and many of the advantages of the US: English-speaking, easy-going, multi-cultural But the coffee is better, no school shootings, and if—God forbid—you ever need an ambulance, that won't bankrupt you

Reactivity of complex communities can be more important than stability @NatureComms by Yuguang Yang, @coytelab.bsky.social, Kevin R. Foster & Aming Li www.nature.com/articles/s41...

Wishing everyone a Happy and prosperous Diwali! Let us celebrate our cultural identities, spread peace and love 🕊 ❤️

A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. #microbiome #preprint www.biorxiv.org/content/10.1...

Tidyverse has really disappointed with lack of stability 😞

Phylogenetic diversity of the carbon monoxide-utilizing prokaryotes and their divergent carbon monoxide metabolisms in the human gut microbiome https://www.biorxiv.org/content/10.1101/2023.10.23.563559v1

Reading: www.biorxiv.org/content/10.1...

𝗙𝘂𝗻𝗰𝘁𝗶𝗼𝗻𝗮𝗹 𝗖𝗼𝗻𝗳𝗶𝗴𝘂𝗿𝗮𝘁𝗶𝗼𝗻𝘀 𝗼𝗳 𝘁𝗵𝗲 𝗚𝘂𝘁 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲 𝗹𝗶𝗻𝗸𝗲𝗱 𝘁𝗼 𝗗𝗶𝗲𝘁, 𝗗𝘆𝘀𝗯𝗶𝗼𝘀𝗶𝘀, 𝗮𝗻𝗱 𝗛𝗲𝗮𝗹𝘁𝗵 Authors use meta-omics data to identify four distinct functional configurations of the gut microbiome. microbiomejournal.biomedcentral.com/articles/10....

Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life: a randomized controlled interventional trial with infant formula https://www.biorxiv.org/content/10.1101/2023.10.19.563092v1

JOIN our lab in a nice little city –Trento🇮🇹– surrounded by mountains & lakes. Are you a COMPUTATIONAL BIOLOGIST and interested in doing microbiome science with a supportive team of dry-lab & wet-lab scientists? Feel free to contact [email protected] 1/3

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...

Mechanism of 2-Fucosyllactose degradation by Human-Associated Akkermansia https://www.biorxiv.org/content/10.1101/2023.10.17.562767v1

A microbiologist and this museum ❤️ 📍Amsterdam

Extensions of Survey for another few days so we can include the Bluesky and mastodon participants that were not polled earlier.

Nobel prize in physiology or medicine awarded to Katalin Karikó and Drew Weissman! 🥳

Clinical Lab Scientist (CLS) position open at Student Health at @ucdavis. Come work in a fancy lab with a great student population! careerspub.universityofcalifornia.edu/psp/ucdavis/...

Disrupted Ecology and H. parainfluenzae Distinguish the Gut Microbiota of an Ethnic Minority Predisposed to Type 2 Diabetes Mellitus https://www.biorxiv.org/content/10.1101/2023.10.01.560393v1