A. Murat Eren (Meren)
@merenbey.bsky.social
Professor of Ecosystem Data Science at @hifmb.bsky.social studying the ecology and evolution of microbes through high-resolution 'omics and #anvio
Reposted by A. Murat Eren (Meren)
HIFMB newsletter out now! 🦑
In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean.
That and more here: 241806.seu2.cleverreach.com/m/16677411
In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean.
That and more here: 241806.seu2.cleverreach.com/m/16677411
HIFMB News #2/2025
241806.seu2.cleverreach.com
December 16, 2025 at 12:12 PM
HIFMB newsletter out now! 🦑
In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean.
That and more here: 241806.seu2.cleverreach.com/m/16677411
In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean.
That and more here: 241806.seu2.cleverreach.com/m/16677411
New blog post for my microbiologist colleagues:
merenlab.org/2025/12/15/r...
In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.
merenlab.org/2025/12/15/r...
In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.
Lost and Found in Modern Microbiology: An Ethnography of Modern Microbiologists
A paper on how microbiologists navigate the tension between reductionism and complexity in their everyday practices, and my 2 cents on it.
merenlab.org
December 15, 2025 at 1:55 PM
New blog post for my microbiologist colleagues:
merenlab.org/2025/12/15/r...
In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.
merenlab.org/2025/12/15/r...
In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.
Reposted by A. Murat Eren (Meren)
More than a year ago researchers from @hifmb.de and @icbm-uol.bsky.social started to write about different perspectives on marine biodiversity change from natural and social science perspectives. This morphed into a review paper that was published online today link.springer.com/article/10.1... 🧪
Towards a broader perspective on marine biodiversity change - Marine Biodiversity
Biodiversity decline jeopardizes the foundation of natural ecosystems and human well-being, a concern that prompted major global agreements aiming to bend the curve towards a net positive biodiversity...
link.springer.com
December 12, 2025 at 3:19 PM
More than a year ago researchers from @hifmb.de and @icbm-uol.bsky.social started to write about different perspectives on marine biodiversity change from natural and social science perspectives. This morphed into a review paper that was published online today link.springer.com/article/10.1... 🧪
Reposted by A. Murat Eren (Meren)
📝 We need YOUR input!
We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series.
Please review our list and add any we've missed: tinyurl.com/4bmeenp9
We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series.
Please review our list and add any we've missed: tinyurl.com/4bmeenp9
Ocean_observatories_socials
tinyurl.com
December 8, 2025 at 3:39 PM
📝 We need YOUR input!
We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series.
Please review our list and add any we've missed: tinyurl.com/4bmeenp9
We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series.
Please review our list and add any we've missed: tinyurl.com/4bmeenp9
Reposted by A. Murat Eren (Meren)
What would a marine microbiome observing system meant to last decades look like? 🌊🦠
We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations.
merenlab.org/workshops/MM...
We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations.
merenlab.org/workshops/MM...
Marine Microbial Observatories for the Future: From Samples to Data to Legacy Using Integrated 'Omics Strategies
A workshop for the future
merenlab.org
December 8, 2025 at 3:39 PM
What would a marine microbiome observing system meant to last decades look like? 🌊🦠
We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations.
merenlab.org/workshops/MM...
We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations.
merenlab.org/workshops/MM...
Reposted by A. Murat Eren (Meren)
I am happy to share that our data descriptor on the Hawaiʻi Diel Sampling is now published! 🌊🦠https://www.nature.com/articles/s41597-025-06166-3
Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.
Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.
A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts - Scientific Data
Scientific Data - A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts
www.nature.com
December 5, 2025 at 3:17 PM
I am happy to share that our data descriptor on the Hawaiʻi Diel Sampling is now published! 🌊🦠https://www.nature.com/articles/s41597-025-06166-3
Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.
Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.
Our data descriptor that includes surface ocean metagenomes (with Illumina & PacBio), metatranscriptomes, and tRNAs transcripts from Hawaiʻi is now out:
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts - Scientific Data
Scientific Data - A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts
www.nature.com
December 5, 2025 at 9:03 AM
Our data descriptor that includes surface ocean metagenomes (with Illumina & PacBio), metatranscriptomes, and tRNAs transcripts from Hawaiʻi is now out:
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
www.nature.com/articles/s41...
Just so you don't have to wait for our own investigations to finish. More data are here:
merenlab.org/data/hads/
Reposted by A. Murat Eren (Meren)
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
www.nature.com
November 28, 2025 at 4:43 PM
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
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/pr...
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/pr...
anvi-report-circularity
An anvi'o program. Predict contig circularity from paired-end read alignments in a given BAM file.
anvio.org
November 28, 2025 at 9:11 AM
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/pr...
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/pr...
Reposted by A. Murat Eren (Meren)
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
Reposted by A. Murat Eren (Meren)
Out today in Science Magazine — First author Veronika Kivenson and PIs Jill Banfield (The Banfield Lab) and Alanna Schepartz team up to reveal a new genetic code in #archaea, with implications for #methane and #climate, and #bioengineering! Learn more: https://ow.ly/Kuem50Xurh0
November 20, 2025 at 7:20 PM
Out today in Science Magazine — First author Veronika Kivenson and PIs Jill Banfield (The Banfield Lab) and Alanna Schepartz team up to reveal a new genetic code in #archaea, with implications for #methane and #climate, and #bioengineering! Learn more: https://ow.ly/Kuem50Xurh0
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
November 20, 2025 at 6:42 PM
We have a date for the free-to-attend #anvio workshop and ECR Symposium for 2026, and we look forward to meeting you at the @hifmb.de in Oldenburg, Germany!
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
Please find more information on the venue, program, and the application form here, and spread the word 😇
anvio.org/workshops/20...
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.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
ECR connection: Meet Meren when you need to
A means for ECRs to get advice from a senior scientist outside of their support network
merenlab.org
November 16, 2025 at 4:56 PM
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.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Reposted by A. Murat Eren (Meren)
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com
rdcu.be/eLtCH
rdcu.be/eLtCH
November 2, 2025 at 5:52 PM
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com
rdcu.be/eLtCH
rdcu.be/eLtCH
Reposted by A. Murat Eren (Meren)
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:
anvio.org/tutorials/co...
anvio.org/tutorials/co...
Competitive metagenomic read recruitment explained
A tutorial on the nuts and bolts of competitive read recruitment
anvio.org
October 25, 2025 at 10:50 AM
I wrote a new tutorial on competitive metagenomic read recruitment (and profiling of the results with #anvio), for those of us nerds who would like to get their hands dirty with data:
anvio.org/tutorials/co...
anvio.org/tutorials/co...
Reposted by A. Murat Eren (Meren)
Evidence from 14 research funding programmes confirms that early winners tend to keep winning (Matthew effect). But the idea that an early setback makes you stronger later doesn’t replicate widely.
buff.ly/UEtcRd4
buff.ly/UEtcRd4
October 24, 2025 at 8:21 AM
Evidence from 14 research funding programmes confirms that early winners tend to keep winning (Matthew effect). But the idea that an early setback makes you stronger later doesn’t replicate widely.
buff.ly/UEtcRd4
buff.ly/UEtcRd4
Read the annual report from @elife.bsky.social:
elifesciences.org/inside-elife...
I welcome that eLife is no longer indexed by SCIE. And I admire that they have not backed away from their innovative model, which makes me even more motivated to send our best work to eLife.
elifesciences.org/inside-elife...
I welcome that eLife is no longer indexed by SCIE. And I admire that they have not backed away from their innovative model, which makes me even more motivated to send our best work to eLife.
Annual Report: 2024 in review
In 2024, eLife continued with its efforts to make peer review and publishing better for science and scientists.
elifesciences.org
October 23, 2025 at 1:37 PM
Read the annual report from @elife.bsky.social:
elifesciences.org/inside-elife...
I welcome that eLife is no longer indexed by SCIE. And I admire that they have not backed away from their innovative model, which makes me even more motivated to send our best work to eLife.
elifesciences.org/inside-elife...
I welcome that eLife is no longer indexed by SCIE. And I admire that they have not backed away from their innovative model, which makes me even more motivated to send our best work to eLife.
Please share this with anyone who may be interested in a post-doc in Germany:
jobs.awi.de/Vacancies/20...
This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
jobs.awi.de/Vacancies/20...
This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
October 22, 2025 at 10:36 AM
Please share this with anyone who may be interested in a post-doc in Germany:
jobs.awi.de/Vacancies/20...
This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
jobs.awi.de/Vacancies/20...
This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
Reposted by A. Murat Eren (Meren)
I'm delighted our paper is out: doi.org/10.1093/isme...
With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠
With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠
Habitat-specificity in SAR11 is associated with a few genes under high selection
Abstract. The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages
doi.org
October 20, 2025 at 7:40 PM
I'm delighted our paper is out: doi.org/10.1093/isme...
With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠
With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠
Reposted by A. Murat Eren (Meren)
A new review study shows the invisible transport pathways for #iron through #hydrothermal plumes.
More on Iron’s Irony here ➡️ www.marum.de/en/Iron-sIro...
@icbm-uol.bsky.social #ConstructorUniversity @geomarkiel.bsky.social @awi.de @marumunibremen.bsky.social
More on Iron’s Irony here ➡️ www.marum.de/en/Iron-sIro...
@icbm-uol.bsky.social #ConstructorUniversity @geomarkiel.bsky.social @awi.de @marumunibremen.bsky.social
October 20, 2025 at 11:51 AM
A new review study shows the invisible transport pathways for #iron through #hydrothermal plumes.
More on Iron’s Irony here ➡️ www.marum.de/en/Iron-sIro...
@icbm-uol.bsky.social #ConstructorUniversity @geomarkiel.bsky.social @awi.de @marumunibremen.bsky.social
More on Iron’s Irony here ➡️ www.marum.de/en/Iron-sIro...
@icbm-uol.bsky.social #ConstructorUniversity @geomarkiel.bsky.social @awi.de @marumunibremen.bsky.social
One of the things I find hardest to get used to in science is seeing how scientists can completely mischaracterize approaches developed by others just to justify their own. Here is a fresh example in which the highlighted statements are 100% objectively wrong about what PlasX or MobMess does
October 10, 2025 at 8:03 AM
One of the things I find hardest to get used to in science is seeing how scientists can completely mischaracterize approaches developed by others just to justify their own. Here is a fresh example in which the highlighted statements are 100% objectively wrong about what PlasX or MobMess does
TL;DR: "I use AI myself to do things that would have required expertise and training I didn't have, such as making sense of my blood work or writing faster & better, but do not like to see that it is being used for things for which I have expertise and training".
theoatmeal.com/comics/ai_ar...
theoatmeal.com/comics/ai_ar...
A cartoonist's review of AI art - The Oatmeal
This is a comic about AI art.
theoatmeal.com
October 9, 2025 at 6:56 AM
TL;DR: "I use AI myself to do things that would have required expertise and training I didn't have, such as making sense of my blood work or writing faster & better, but do not like to see that it is being used for things for which I have expertise and training".
theoatmeal.com/comics/ai_ar...
theoatmeal.com/comics/ai_ar...
Reposted by A. Murat Eren (Meren)
🪸🧪 We’re hiring! Join our ERC-funded group at the @hifmb.de in Oldenburg, Germany to explore the cellular origins of photosymbiosis:
𝟏 𝐏𝐨𝐬𝐭𝐝𝐨𝐜 + 𝟐 𝐏𝐡𝐃𝐬 𝐩𝐨𝐬𝐢𝐭𝐢𝐨𝐧𝐬.
Deadlines: Oct 29 & Nov 5. Links below.
Questions: nils.raedecker@hifmb.de
#Photosymbiosis #HIFMB #ERC #AcademicJobs
𝟏 𝐏𝐨𝐬𝐭𝐝𝐨𝐜 + 𝟐 𝐏𝐡𝐃𝐬 𝐩𝐨𝐬𝐢𝐭𝐢𝐨𝐧𝐬.
Deadlines: Oct 29 & Nov 5. Links below.
Questions: nils.raedecker@hifmb.de
#Photosymbiosis #HIFMB #ERC #AcademicJobs
October 6, 2025 at 12:27 PM
🪸🧪 We’re hiring! Join our ERC-funded group at the @hifmb.de in Oldenburg, Germany to explore the cellular origins of photosymbiosis:
𝟏 𝐏𝐨𝐬𝐭𝐝𝐨𝐜 + 𝟐 𝐏𝐡𝐃𝐬 𝐩𝐨𝐬𝐢𝐭𝐢𝐨𝐧𝐬.
Deadlines: Oct 29 & Nov 5. Links below.
Questions: nils.raedecker@hifmb.de
#Photosymbiosis #HIFMB #ERC #AcademicJobs
𝟏 𝐏𝐨𝐬𝐭𝐝𝐨𝐜 + 𝟐 𝐏𝐡𝐃𝐬 𝐩𝐨𝐬𝐢𝐭𝐢𝐨𝐧𝐬.
Deadlines: Oct 29 & Nov 5. Links below.
Questions: nils.raedecker@hifmb.de
#Photosymbiosis #HIFMB #ERC #AcademicJobs