Oldenburg, Germany
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Now this is out, I would like to tell you what I learned from this study about the human gut microbiome (and its place in noncommunicable diseases of complex etiology, such as Crohn's and ulcerative colitis).
Delighted to announce the publication of this work from my PhD! We show that metabolically independent microbes associated with human gut “dysbiosis” may not in fact be causal of disease, but instead selected for under stressful conditions. (1/4)
doi.org/10.1186/s13059-023-0…
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A preprint by Raïssa Meyer and Sarah Tucker et al that argues for a federated global observatory for the ocean microbiome with a roadmap to 2075:
doi.org/10.5281/zenodo.22957…
Also see microbial-observatories.org/; a new living catalogue for recent / ongoing large-scale observing efforts.
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If you heard about #anvio but never had a chance to figure out what it really is, please consider watching this 12-minute video by Iva Veseli:
piped.video/watch?v=fExu_euH…
It is a short and sweet introduction to what (and what not) to expect from anvi'o 😇
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What makes human guts and coral reefs similar? Here is a blog post with some thoughts on ecosystem stability, stress, and microbiome, following a fresh pre-print by Marko Terzin et al: merenlab.org/blog/coral-reef…
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A new blog post on a microbiome/cancer study that earns a second thought rather than just a nod or a shrug:
merenlab.org/blog/saccharomy…
And LET THE RECORD SHOW that this post COMPLETELY addresses the incorrect claim that Meren only complains about microbiome studies.
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HIFMB advertised 5 post-doc positions to work on social science / basic science interface, and here is a blog post to tell you why I care about this, and what it looks like:
merenlab.org/blog/HIPP-on-hu…
Please spread the word if you can.
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How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism:
merenlab.org/2026/04/15/unfa…
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"A data-conscious checklist for the reviewers of 'omics studies who champion open science", a Comment Iva Veseli and I wrote is now online at metaRxiv:
doi.org/10.31222/osf.io/2aef…
Please share it with your friends, colleagues, trainees, or editors of your favorite journals.
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A. Murat Eren (Meren) retweeted
Have you listened to the #MVIFconversations podcast?
There is a new episode where Christina and I talked to @merenbey about open source, mentoring, and believe me it's a GREAAAT one!!
#MVIFconversations podcast episode 3 with @merenbey is OUT!
▶️ Spotify: open.spotify.com/episode/1Ck…
▶️ Amazon Music: music.amazon.com/podcasts/81…
▶️ Apple Music: podcasts.apple.com/us/podcas…
▶️ YouTube podcast: piped.video/-qC3qSU884U?si=wPww…
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A. Murat Eren (Meren) retweeted
#MVIFconversations podcast episode 3 with @merenbey is OUT!
▶️ Spotify: open.spotify.com/episode/1Ck…
▶️ Amazon Music: music.amazon.com/podcasts/81…
▶️ Apple Music: podcasts.apple.com/us/podcas…
▶️ YouTube podcast: piped.video/-qC3qSU884U?si=wPww…
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We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Visit our web page:
anvio.org/
Read the release notes:
github.com/merenlab/anvio/re…
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The work @FlorianTrigodet nicely summarized in nitter.siddz.com/FlorianTrigodet/status… is now published in @NatureBiotech:
nature.com/articles/s41587-0…
With @archaeaologist and @BanfieldJill.
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, biorxiv.org/content/10.1101/… and tell you just a little bit about it in the following 🧵
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New blog post for my microbiologist colleagues:
merenlab.org/2025/12/15/redu…
In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.
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Our data descriptor that includes surface ocean metagenomes (with Illumina & PacBio), metatranscriptomes, and tRNAs transcripts is now out:
nature.com/articles/s41597-0…
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
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This was possible primarily thanks to Sarah Tucker, Jessika Fuessel, Kelle Freel, and others, and Mike Rappé's leadership that enabled a high-resolution sampling effort that covered two full days, which I had described in greater detail here:
merenlab.org/data/hads/
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Need to predict whether a given contig in your assembly was circular in the environment?
Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity:
anvio.org/help/main/programs…
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Here is an example report if you want to see what the output looks like:
anvio.org/help/main/artifact…
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We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026 in Oldenburg, Germany.
Please find more information on the venue, program, and the application form here, or spread the word 😇
anvio.org/workshops/2026-old…
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Just so you know, the previous iteration of the workshop went quite well (see more photos here: anvio.org/blog/oldenburg-25-…)
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.. and we were lucky to receive a generally positive feedback from the attendees (read more of the survey results here: anvio.org/blog/oldenburg-25-…). We strive to do better, come and be the judge of it yourself!
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Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Blog post explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/ECR-…
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