Ian Marshall
@ianpgm.bsky.social
Associate Professor at Department of Biology, Aarhus University, Denmark 🇩🇰 working on microbial genomics, bioinformatics, cable bacteria, and other sediment microorganisms. https://www.au.dk/en/ianpgm@bio.au.dk/ 🇦🇺
Reposted by Ian Marshall
ISME20 Abstract guidelines are now available — start preparing your abstract to be able to share your latest research with the global community of microbial ecologists at ISME20, held in New Zealand, August 2026.
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
December 29, 2025 at 10:42 AM
ISME20 Abstract guidelines are now available — start preparing your abstract to be able to share your latest research with the global community of microbial ecologists at ISME20, held in New Zealand, August 2026.
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
Tip for identifying LLM-generated text: most humans make subscripts using the subscript formatting tool in their word processor, LLMs use the unicode character for subscript 2 (unicodeplus.com/U+2082) so that formatting is better preserved when they copy and paste.
December 22, 2025 at 8:24 AM
Tip for identifying LLM-generated text: most humans make subscripts using the subscript formatting tool in their word processor, LLMs use the unicode character for subscript 2 (unicodeplus.com/U+2082) so that formatting is better preserved when they copy and paste.
Reposted by Ian Marshall
Landmark study in @Nature! 🇩🇰 The "Microflora Danica" project has created the first-ever national microbiome atlas. Led by Aalborg University, @fwf-at.bsky.social CoE Microplanet's Director @michiwagner4.bsky.social, and @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social analyzed nitrifiers.
December 4, 2025 at 10:17 AM
Landmark study in @Nature! 🇩🇰 The "Microflora Danica" project has created the first-ever national microbiome atlas. Led by Aalborg University, @fwf-at.bsky.social CoE Microplanet's Director @michiwagner4.bsky.social, and @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social analyzed nitrifiers.
Reposted by Ian Marshall
14 two-year postdocs for academics of any nationality who cannot continue their research due to US politics. Do share if you know of such.
Post-doc positions:
"Academic freedom is under pressure today. This requires rescue havens of free research. ... [we] invite early career researchers, whose work is restricted due to political pressure in the USA..."
uni-freiburg.de/frias/call-f...
"Academic freedom is under pressure today. This requires rescue havens of free research. ... [we] invite early career researchers, whose work is restricted due to political pressure in the USA..."
uni-freiburg.de/frias/call-f...
Call for Applications: Early Career Rescue Fellowship – Freiburg Institute for Advanced Studies
uni-freiburg.de
December 19, 2025 at 5:19 PM
14 two-year postdocs for academics of any nationality who cannot continue their research due to US politics. Do share if you know of such.
Reposted by Ian Marshall
A quick microbio present before the holidays 🎁 >150 years after their first description, filamentous "Crenothrix bacteria" are now in stable laboratory culture! In our pre-print, we probe the unique physiology & ecology of the "lacustrine" group of these enigmatic methane-oxidizing microbes... 1/2
Isolation of Crenothrix bacteria reveals the distinct ecophysiologies of filamentous methanotrophs and adaptations to redox stress
At the dawn of modern microbiology, Cohn observed abundant filamentous bacteria in drinking water wells that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metaboli...
doi.org
December 19, 2025 at 10:21 AM
A quick microbio present before the holidays 🎁 >150 years after their first description, filamentous "Crenothrix bacteria" are now in stable laboratory culture! In our pre-print, we probe the unique physiology & ecology of the "lacustrine" group of these enigmatic methane-oxidizing microbes... 1/2
Reading student writing in 2025 feels like I wished a monkey's paw for perfect grammar and spelling
December 19, 2025 at 8:38 AM
Reading student writing in 2025 feels like I wished a monkey's paw for perfect grammar and spelling
Reposted by Ian Marshall
@isme-microbes.bsky.social offers a great opportunity to publish uncultured microbes via #SeqCode using #genomes as type material. A fantastic step toward embracing the true diversity of microbes! But isolates are also welcome 🧫🔬🦠😁
@seqcode.bsky.social
@seqcode.bsky.social
ISME Communications is expanding its scope to include Taxonomy and Nomenclature, recognizing their essential role in microbial ecology.
Read more: isme-microbes.org/taxonomy-and...
#microbes #taxonomy
Read more: isme-microbes.org/taxonomy-and...
#microbes #taxonomy
December 16, 2025 at 10:00 AM
@isme-microbes.bsky.social offers a great opportunity to publish uncultured microbes via #SeqCode using #genomes as type material. A fantastic step toward embracing the true diversity of microbes! But isolates are also welcome 🧫🔬🦠😁
@seqcode.bsky.social
@seqcode.bsky.social
Reposted by Ian Marshall
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Thanks to @carlsbergfondet.dk for supporting my Carlsberg Semper Ardens Accelerate project on aerobic methanotrophic bacteria growing anaerobically! www.carlsbergfondet.dk/det-har-vi-s...
Anaerobic growth of aerobic methane-oxidising bacteria (AnGer-MOB) | Carlsbergfondet.dk
www.carlsbergfondet.dk
December 14, 2025 at 10:20 AM
Thanks to @carlsbergfondet.dk for supporting my Carlsberg Semper Ardens Accelerate project on aerobic methanotrophic bacteria growing anaerobically! www.carlsbergfondet.dk/det-har-vi-s...
Reposted by Ian Marshall
The Microflora Danica atlas of Danish environmental microbiomes www.nature.com/articles/s41... #jcampubs
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 11, 2025 at 6:23 AM
The Microflora Danica atlas of Danish environmental microbiomes www.nature.com/articles/s41... #jcampubs
Reposted by Ian Marshall
It’s exciting to see converging evidence across systems! 😀
Alongside the new work on gutless worms, our study shows that organosulfur cycling is also essential in lucinid holobionts. Lucinid host provides DMSP to its symbionts, sulphur-oxidising Thiodiazotropha and, a new member, Endozoicomonas.
Alongside the new work on gutless worms, our study shows that organosulfur cycling is also essential in lucinid holobionts. Lucinid host provides DMSP to its symbionts, sulphur-oxidising Thiodiazotropha and, a new member, Endozoicomonas.
December 8, 2025 at 9:31 AM
It’s exciting to see converging evidence across systems! 😀
Alongside the new work on gutless worms, our study shows that organosulfur cycling is also essential in lucinid holobionts. Lucinid host provides DMSP to its symbionts, sulphur-oxidising Thiodiazotropha and, a new member, Endozoicomonas.
Alongside the new work on gutless worms, our study shows that organosulfur cycling is also essential in lucinid holobionts. Lucinid host provides DMSP to its symbionts, sulphur-oxidising Thiodiazotropha and, a new member, Endozoicomonas.
Congratulations @louison-nicolas.bsky.social !
Respiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬
Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations!
doi.org/10.1093/isme...
Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations!
doi.org/10.1093/isme...
Validate User
doi.org
December 6, 2025 at 10:46 AM
Congratulations @louison-nicolas.bsky.social !
Reposted by Ian Marshall
Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea www.biorxiv.org/content/10.6... #jcampubs
December 4, 2025 at 2:18 PM
Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea www.biorxiv.org/content/10.6... #jcampubs
Reposted by Ian Marshall
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 3, 2025 at 8:50 PM
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ian Marshall
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
December 2, 2025 at 5:52 PM
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Reposted by Ian Marshall
🔬Looking for a student project? We’re looking for students!
👉If you are interested in pursuing a project within electromicrobiology and cable bacteria, then you should check out our student projects on our webside, packed with project ideas. (Link in comment)
👉If you are interested in pursuing a project within electromicrobiology and cable bacteria, then you should check out our student projects on our webside, packed with project ideas. (Link in comment)
November 24, 2025 at 9:29 AM
🔬Looking for a student project? We’re looking for students!
👉If you are interested in pursuing a project within electromicrobiology and cable bacteria, then you should check out our student projects on our webside, packed with project ideas. (Link in comment)
👉If you are interested in pursuing a project within electromicrobiology and cable bacteria, then you should check out our student projects on our webside, packed with project ideas. (Link in comment)
Just in time for me to cite in something I've been using GlobDB for
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 22, 2025 at 9:32 AM
Just in time for me to cite in something I've been using GlobDB for
Reposted by Ian Marshall
I feel this. A big part of my professional growth over the last few years has been the realization that I will not live to carry out the vast majority of my ideas. As a result, I'm much more open with sharing them than ever before.
Science is like this too 🧪
I am not aware of a single author who has a shortage of book ideas. Words, yes. Ways to make the ideas become a book, yes. But I've never met an author who doesn't have ideas just raining down all the damn time.
November 19, 2025 at 1:46 PM
I feel this. A big part of my professional growth over the last few years has been the realization that I will not live to carry out the vast majority of my ideas. As a result, I'm much more open with sharing them than ever before.
Reposted by Ian Marshall
An underrated cause of of the anxiety epidemic is that you can never see the f***ing filesystem anymore
November 13, 2025 at 11:23 PM
An underrated cause of of the anxiety epidemic is that you can never see the f***ing filesystem anymore
I think I use a weird dialect of R resulting from both pre- and post-tidyverse learning...
November 13, 2025 at 9:03 AM
I think I use a weird dialect of R resulting from both pre- and post-tidyverse learning...
Reposted by Ian Marshall
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
November 10, 2025 at 9:32 AM
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
This is fantastic, I laughed for about 3 minutes...
November 7, 2025 at 9:50 AM
This is fantastic, I laughed for about 3 minutes...
Reposted by Ian Marshall
Insights on adaptive strategies and evolution of cable bacteria in saline lakes
#microbiology #bacteria #CableBacteria
aslopubs.onlinelibrary.wiley.com/doi/10.1002/...
#microbiology #bacteria #CableBacteria
aslopubs.onlinelibrary.wiley.com/doi/10.1002/...
November 7, 2025 at 9:22 AM
Insights on adaptive strategies and evolution of cable bacteria in saline lakes
#microbiology #bacteria #CableBacteria
aslopubs.onlinelibrary.wiley.com/doi/10.1002/...
#microbiology #bacteria #CableBacteria
aslopubs.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Ian Marshall
'Hi it's me, Microsoft Outlook, the world's leading email client! You received an email with a meeting invite and a detailed agenda, and now you RSVPd? Let me just delete that email for you buddy :) I've hidden the agenda in your calendar, where evil Search won't find it. you don't need the mail :)'
November 3, 2025 at 10:56 AM
'Hi it's me, Microsoft Outlook, the world's leading email client! You received an email with a meeting invite and a detailed agenda, and now you RSVPd? Let me just delete that email for you buddy :) I've hidden the agenda in your calendar, where evil Search won't find it. you don't need the mail :)'
Me: Hey outlook, I need to send a reply to this email.
Outlook: Sure, start writing!
Me: Hey I need to follow up, let me write another reply.
Outlook: Sure thing. But you just want to write to yourself, right?
Outlook: Sure, start writing!
Me: Hey I need to follow up, let me write another reply.
Outlook: Sure thing. But you just want to write to yourself, right?
October 31, 2025 at 7:53 AM
Me: Hey outlook, I need to send a reply to this email.
Outlook: Sure, start writing!
Me: Hey I need to follow up, let me write another reply.
Outlook: Sure thing. But you just want to write to yourself, right?
Outlook: Sure, start writing!
Me: Hey I need to follow up, let me write another reply.
Outlook: Sure thing. But you just want to write to yourself, right?