iiinova — where your digital self keeps evolving

Jelle Slager @jslager.bsky.social · 03/05/2025

Our paper is now out in Gut Microbes! www.tandfonline.com/doi/full/10.... See the 🧵 below for an explainer 👇

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Robert Armstrong @robarmstrong.bsky.social · 08/04/2025

you can't spell "tariffs" without "FFS"

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Jelle Slager @jslager.bsky.social · 04/04/2025

Just out! Our manuscript (led by Pauline Lanting and @robertwarmerdam.bsky.social) on the generation of pharmacogenetic passports from low-cost GSA oligonucleotide array data.

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Max Kozlov @maxkozlov.bsky.social · 07/03/2025

DOGE is directly involved in the NIH grant terminations. Metadata on one of the grant termination letters says that someone named Joshua Hanley authored it. Hanley is listed on an alleged list of DOGE employees leaked yesterday.

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Jelle Slager @jslager.bsky.social · 07/01/2025

Finally: our work wouldn't be possible without the dedication of all the participants (patients ánd healthy individuals) that contribute bodily materials (in this case: stool samples 💩) and that fill out several questionnaires covering many different topics. So: a big thanks 🙏! (14/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

Functional follow-up studies will now have to address the infamous chicken-egg conundrum: which observed patterns are merely the consequence of the disease or the diet, and which were actually pre-existent and could play a role in disease onset or progression? (13/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

Subsequently, we found that the disappearing E. rectale subspecies is characterised by a lack of motility genes and the presence of many glycosyltransferases, which corresponds perfectly to the European subspecies as described by Karcher et al. (DOI: 10.1186/s13059-020-02042-y). (12/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

Lastly, we focused on observations in the bacterium Eubacterium rectale (now known as Agathobacter rectalis): besides increased interindividual variation among tCeD patients (see skeet 9/15), we also saw a cluster of strains (subspecies) being nearly absent in patients. (11/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

In line with this, we find that a protein domain, implicated in DNA repair and associated with within-species mutation rates, was underrepresented in tCeD patients. Perhaps faster evolution (accelerated by reactive oxygen species) benefits bacterial survival during inflammation? (10/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

Using the nucleotide-level resolution of MGS, we could also look into sub-species variation and found that several species also show an increased number of mutations in their core genome in patients, relative to controls. We speculate that inflammation may lead to elevated mutation rates. (9/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

Interestingly, while we expected the microbiomes of tCeD patients to share a certain signature, we instead saw that they have less similar microbiome compositions (i.e. higher BC dissimilarity) than random pairs of control individuals. The same was seen for IBD, but not for IBS patients. (8/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

We show that duration of GFD positively correlates (Spearman's Rho) with most of the overabundant species, suggesting a significant contribution of the diet to the observed patterns. (7/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

We found several bacteria previously associated with CeD (including several Bacteroides species), but also identified novel associations, such as Roseburia hominis and Eggerthella lenta. (6/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

First of all, as expected, there is little overlap between the microbial patterns observed in IBD, IBS, and coeliac disease, arguing against a general signature of intestinal problems. (5/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

Microbial DNA from all stool samples was sequenced using Metagenomic Shotgun Sequencing (MGS), allowing high-resolution analysis of microbiome composition. Now, let's dive in! 👇(4/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

We also selected several IBD and IBS patients from Lifelines, with controls. As virtually all CeD patients will adhere to a gluten-free diet (GFD) after having received diagnosis, the only available treatment, our study will find the combined effects of the disease and GFD. (3/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

To set the scene: we combined data from our own Celiac Disease Northern Netherlands cohort (CeDNN; currently unpublished) with data from the population cohort Lifelines (www.lifelines.nl) to end up with stool samples of 152 CeD patients and 760 matched controls. (2/15)

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Jelle Slager @jslager.bsky.social · 07/01/2025

We proudly present our preprint (i.e. not peer-reviewed yet!) on the gut microbiome of treated coeliac disease (tCeD) patients: www.biorxiv.org/content/10.1101/202… w/ Hanna Simpson, @irisjonkers.bsky.social, Sebo Withoff and many others. An explanatory thread 🧵 (1/15)

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ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 22/11/2024

Conversation with the brilliant contemporary microbiologist and molecular biologist—HHMI and MacArthur Fellow Bonnie Bassler of Princeton University Pioneer in the chemical signaling mechanisms that bacteria use to communicate with each other known as “quorum sensing” www.hhmi.org/news/tapping...

hhmi.org

Tapping into Bacterial Conversations | HHMI

Over the course of 30 years, HHMI Investigator Bonnie Bassler has helped usher in a new branch of science centered on quorum sensing, the process by which bacteria communicate with one another and orc...

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Jelle Slager @jslager.bsky.social · 21/11/2024

Not E. coli, but FWIW: we resequenced S. pneumoniae D39 (several passages down the line from the Avery strain) and found differences with the original. Some of those may have been incorrect in the original assembly, others true differences. academic.oup.com/nar/article/... See table 1, fig. 3, S1

academic.oup.com

Deep genome annotation of the opportunistic human pathogen Streptococcus pneumoniae D39

Abstract. A precise understanding of the genomic organization into transcriptional units and their regulation is essential for our comprehension of opportu

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De Speld @speld.nl · 19/11/2024

We hakken de knoop door: De Speld vertrekt van Bluesky en gaat definitief naar X. ‘Sfeer van constructieve, opbouwende dialoog druist in tegen alles waar wij voor staan’

x.com

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Asaf Levy @asaflevylab.bsky.social · 19/11/2024

We found something interesting in the evolution of plant microbiota. It is under review and we published the preprint today. Avi Bograd from my lab analyzed the genomes of 38,912 bacteria and identified a clear depletion of all MGE types in plant-associated bacteria vs. non-plant associated bacteria

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Jelle Slager @jslager.bsky.social · 19/11/2024

My son just classified his fart as a spelling-fart, as it sounded exactly like his spelling-notebook landing on his table. Does that count? 😅

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Altmetric @altmetric.com · 18/11/2024

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics

docs.bsky.app

Action Intent Links | Bluesky

Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...

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Reposted by Jelle Slager

Elisabeth Bik @elisabethbik.bsky.social · 18/11/2024

Absolutely thrilled to have won the @einsteinberlin.bsky.social Individual #EinsteinFoundationAward. Big congrats to PubPeer and @helenajambor.bsky.social for winning in their categories.

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Jan-Willem Veening @veeninglab.com · 14/11/2024

Now that Ricky is also here, we can safely close shop on the other side 😂

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Oliver Schwengers @oschwengers.bsky.social · 18/11/2024

🦠🧬💻 Bakta v1.10 - largest update so far: Highlights: - user-provided HMMs: --hmms - output file recovery from JSON files: bakta_io - export of inference metrics: inference.tsv - bypass overlap filters: --skip-filter - improved genome plots github.com/oschwengers/... 👇 (1/11)

github.com

Release v1.10 - Novel in & novel out · oschwengers/bakta

This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements. Compatible database scheme version: 5 Important Si...

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Jelle Slager @jslager.bsky.social · 05/01/2024

5 books or more from one author - my 10. Richard Dawkins J.K. Rowling Brandon Sanderson Ken Follett Raymond E. Feist Douglas Adams Carlos Ruiz Zafon Agatha Christie Roald Dahl Herman Koch

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Danna Gifford @dannagifford.bsky.social · 02/11/2023

📣 Paper: We show that mutators can drive the evolution of multi-resistance to antibiotics, in cases where purely wild type populations can't This came out earlier this year while the other place was imploding But it's a story I'm proud of for many reasons... 1/n journals.plos.org/plosgenetics...

journals.plos.org

Mutators can drive the evolution of multi-resistance to antibiotics

Author summary The global rise in antimicrobial resistance means we urgently need new approaches that halt its spread. Combination therapy, using multiple antibiotics as one treatment, proposes to do ...

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Jelle Slager @jslager.bsky.social · 19/10/2023

I'll start my time here with a question for experienced blueskyers: is there a way to block ELO from popping into your head everytime you go on this app?

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