Benjamin Coltman
@bcoltman.bsky.social
Digging into the complexity of soil microbial communities
microbial ecology | synbio | microbiome
Postdoc @univie.ac.at @cemess.bsky.social @dome-vienna.bsky.social @microbesplanet.bsky.social
microbial ecology | synbio | microbiome
Postdoc @univie.ac.at @cemess.bsky.social @dome-vienna.bsky.social @microbesplanet.bsky.social
Reposted by Benjamin Coltman
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Benjamin Coltman
Last chance to turn it off.
On Monday, November 3rd, Microsoft will start using your LinkedIn data for AI training. And remember, you're opted in by default.
To toggle it off 👉 Account - Settings & Privacy > Data privacy > Data for Generative AI Improvement.
On Monday, November 3rd, Microsoft will start using your LinkedIn data for AI training. And remember, you're opted in by default.
To toggle it off 👉 Account - Settings & Privacy > Data privacy > Data for Generative AI Improvement.
October 31, 2025 at 1:37 PM
Last chance to turn it off.
On Monday, November 3rd, Microsoft will start using your LinkedIn data for AI training. And remember, you're opted in by default.
To toggle it off 👉 Account - Settings & Privacy > Data privacy > Data for Generative AI Improvement.
On Monday, November 3rd, Microsoft will start using your LinkedIn data for AI training. And remember, you're opted in by default.
To toggle it off 👉 Account - Settings & Privacy > Data privacy > Data for Generative AI Improvement.
Reposted by Benjamin Coltman
This week as part of the @pilzfestspiele.at - our group showed mycorrhizal fungal colonized roots, our culture collection, posters of results, and we had a massive turnout! People are becoming increasingly interested in fungi @cemess.bsky.social @ter-cemess.bsky.social
www.fungalecologylab.com
www.fungalecologylab.com
October 10, 2025 at 5:04 PM
This week as part of the @pilzfestspiele.at - our group showed mycorrhizal fungal colonized roots, our culture collection, posters of results, and we had a massive turnout! People are becoming increasingly interested in fungi @cemess.bsky.social @ter-cemess.bsky.social
www.fungalecologylab.com
www.fungalecologylab.com
Looks interesting @nmjgeerlings.bsky.social
1/
Tomorrow’s large scale cross-modality models will further unlock biology, but they need standardized inputs. With @sophia-maedler.bsky.social & @nik-as.bsky.social, we built #scPortrait, @scverse.bsky.social package to turn microscopy images into single-cell image datasets for multimodal modeling
Tomorrow’s large scale cross-modality models will further unlock biology, but they need standardized inputs. With @sophia-maedler.bsky.social & @nik-as.bsky.social, we built #scPortrait, @scverse.bsky.social package to turn microscopy images into single-cell image datasets for multimodal modeling
September 28, 2025 at 3:17 PM
Looks interesting @nmjgeerlings.bsky.social
Reposted by Benjamin Coltman
Paracetamol remains an important option to treat pain or fever in pregnant women.
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Use of paracetamol during pregnancy unchanged in the EU | European Medicines Agency (EMA)
Paracetamol medicines can be used in pregnancy, in accordance with official recommendations
www.ema.europa.eu
September 23, 2025 at 10:28 AM
Paracetamol remains an important option to treat pain or fever in pregnant women.
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
It’s great to be at #mbkceesme2025 so far, hearing about all things microbial! It’s always rewarding to present one’s work and hear the community’s feedback. Thanks for the support @isme-microbes.bsky.social
September 23, 2025 at 3:08 PM
It’s great to be at #mbkceesme2025 so far, hearing about all things microbial! It’s always rewarding to present one’s work and hear the community’s feedback. Thanks for the support @isme-microbes.bsky.social
Reposted by Benjamin Coltman
Interested in the design of defined microbial communities for fundamental research and applications? Hope this work & tool will help you 👇 As always @tcahitch.bsky.social has been a driving factor ⭐⭐⭐! github.com/ClavelLab/Mi...; academic.oup.com/ismej/advanc...
Validate User
academic.oup.com
September 18, 2025 at 12:11 PM
Interested in the design of defined microbial communities for fundamental research and applications? Hope this work & tool will help you 👇 As always @tcahitch.bsky.social has been a driving factor ⭐⭐⭐! github.com/ClavelLab/Mi...; academic.oup.com/ismej/advanc...
Reposted by Benjamin Coltman
Branched-chain amino acid assimilation promotes mixotrophy of ammonia-oxidizing archaeal sponge symbionts www.biorxiv.org/content/10.1... #jcampubs
September 10, 2025 at 4:21 PM
Branched-chain amino acid assimilation promotes mixotrophy of ammonia-oxidizing archaeal sponge symbionts www.biorxiv.org/content/10.1... #jcampubs
Reposted by Benjamin Coltman
Holy cow - hyperspectral detection of bacteria at long distance.... "The bacteria were detectable outdoors under ambient light from up to 90 m in a single 4,000-m2 hyperspectral image taken using fixed and unmanned aerial vehicle-mounted cameras." 🤯
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Hyperspectral reporters for long-distance and wide-area detection of gene expression in living bacteria - Nature Biotechnology
Hyperspectral reporter genes allow imaging of ground bacteria from aerial vehicles
www.nature.com
September 11, 2025 at 4:21 PM
Holy cow - hyperspectral detection of bacteria at long distance.... "The bacteria were detectable outdoors under ambient light from up to 90 m in a single 4,000-m2 hyperspectral image taken using fixed and unmanned aerial vehicle-mounted cameras." 🤯
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Jan Erisman closed the 28th European Nitrogen Cycle Meeting with a raw reminder: the nitrogen cycle is out of sync!
Still, the meeting was full of inspiring research on all things N and some promising paths to reduce our impact!
Big questions remain… #ENC28
univie.eventsair.com/enc2025/
Still, the meeting was full of inspiring research on all things N and some promising paths to reduce our impact!
Big questions remain… #ENC28
univie.eventsair.com/enc2025/
September 11, 2025 at 4:00 PM
Jan Erisman closed the 28th European Nitrogen Cycle Meeting with a raw reminder: the nitrogen cycle is out of sync!
Still, the meeting was full of inspiring research on all things N and some promising paths to reduce our impact!
Big questions remain… #ENC28
univie.eventsair.com/enc2025/
Still, the meeting was full of inspiring research on all things N and some promising paths to reduce our impact!
Big questions remain… #ENC28
univie.eventsair.com/enc2025/
Reposted by Benjamin Coltman
“I don’t want asylum seekers to live on my street” is genuinely a wild thing to say as a notionally progressive politician
Oh nothing, just the actual Prime Minister telling people they’re entirely correct to drive asylum seekers out of their communities
September 1, 2025 at 1:56 PM
“I don’t want asylum seekers to live on my street” is genuinely a wild thing to say as a notionally progressive politician
Reposted by Benjamin Coltman
The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4
rdcu.be/eCbj4
Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology
The microbial composition of metagenomes is identified in seconds by profiling against large databases.
go.nature.com
August 27, 2025 at 1:14 AM
The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4
rdcu.be/eCbj4
Reposted by Benjamin Coltman
Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates https://www.biorxiv.org/content/10.1101/2025.08.23.671898v1
August 24, 2025 at 4:08 AM
Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates https://www.biorxiv.org/content/10.1101/2025.08.23.671898v1
Reposted by Benjamin Coltman
Out now!
🍫🦠A defined microbial community reproduces attributes of fine flavour #chocolate fermentation
By Gabriel Castrillo, David Salt & co
#microsky #microbiomesky 🧪
Read it here: www.nature.com/articles/s41...
🍫🦠A defined microbial community reproduces attributes of fine flavour #chocolate fermentation
By Gabriel Castrillo, David Salt & co
#microsky #microbiomesky 🧪
Read it here: www.nature.com/articles/s41...
A defined microbial community reproduces attributes of fine flavour chocolate fermentation - Nature Microbiology
An in-depth microbiological and metagenomic analysis of Colombian farm and fermentation facilities resulted in the design of a defined microbial community that can reproduce the flavour of fine chocol...
www.nature.com
August 18, 2025 at 3:35 PM
Out now!
🍫🦠A defined microbial community reproduces attributes of fine flavour #chocolate fermentation
By Gabriel Castrillo, David Salt & co
#microsky #microbiomesky 🧪
Read it here: www.nature.com/articles/s41...
🍫🦠A defined microbial community reproduces attributes of fine flavour #chocolate fermentation
By Gabriel Castrillo, David Salt & co
#microsky #microbiomesky 🧪
Read it here: www.nature.com/articles/s41...
Reposted by Benjamin Coltman
🚨4yr Technical Assistant Position on #Microbial Activities in #Marine #N-Cycling🦠🧪👩🎓🔬
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
RECLESS_TA_molecular_UniVie.pdf
u:cloud - Ihre Daten, auf Wolken gebettet.
ucloud.univie.ac.at
August 4, 2025 at 10:50 AM
🚨4yr Technical Assistant Position on #Microbial Activities in #Marine #N-Cycling🦠🧪👩🎓🔬
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Reposted by Benjamin Coltman
🚨3-yr Postdoc Position on #SingleCell Activities in #Marine #N-Cycling🦠🧪👩🎓🔬
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
RECLESS_Postdoc_single_cell_UniVie.pdf
u:cloud - Ihre Daten, auf Wolken gebettet.
ucloud.univie.ac.at
August 4, 2025 at 10:48 AM
🚨3-yr Postdoc Position on #SingleCell Activities in #Marine #N-Cycling🦠🧪👩🎓🔬
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Join me @univie.ac.at @dome-vienna.bsky.social
Part of our ERC Synergy #RECLESS looking at microbes in marine oxygen minimum zones
Apply by Oct 15, start March 2026!
-> ucloud.univie.ac.at/index.php/s/...
Reposted by Benjamin Coltman
Great podcast recording with Nicole Geerlings for #MattersMicrobial about weird and wonderful cable bacteria! I truly enjoyed the session. Releasing next week. @nmjgeerlings.bsky.social
July 18, 2025 at 2:47 AM
Great podcast recording with Nicole Geerlings for #MattersMicrobial about weird and wonderful cable bacteria! I truly enjoyed the session. Releasing next week. @nmjgeerlings.bsky.social
@juergenzanghellini.bsky.social kicked off the 10th Metabolic Pathway Analysis conference yesterday, hosted @univie.ac.at. A nice use of EFMs but despite Jürgen’s years of attempts, I’m still not convinced that the best ice cream is found at Schwedenplatz
July 29, 2025 at 6:31 AM
@juergenzanghellini.bsky.social kicked off the 10th Metabolic Pathway Analysis conference yesterday, hosted @univie.ac.at. A nice use of EFMs but despite Jürgen’s years of attempts, I’m still not convinced that the best ice cream is found at Schwedenplatz
Reposted by Benjamin Coltman
Today wrapped up our 4th summer school on Economic Principles in Cell Biology organized by @economic-cell.bsky.social at the beautiful @univie.ac.at 🤩
Huge thanks to all the students, teachers and @cecamevents.bsky.social for the support! ✨️
See you next year!
Huge thanks to all the students, teachers and @cecamevents.bsky.social for the support! ✨️
See you next year!
July 26, 2025 at 5:14 PM
Today wrapped up our 4th summer school on Economic Principles in Cell Biology organized by @economic-cell.bsky.social at the beautiful @univie.ac.at 🤩
Huge thanks to all the students, teachers and @cecamevents.bsky.social for the support! ✨️
See you next year!
Huge thanks to all the students, teachers and @cecamevents.bsky.social for the support! ✨️
See you next year!
Reposted by Benjamin Coltman
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
An awesome resource for probing who, where and how often specific microbes are found!
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - @benjwoodcroft.bsky.social go.nature.com/3IwOxHh
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology
Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.
go.nature.com
July 16, 2025 at 8:57 PM
An awesome resource for probing who, where and how often specific microbes are found!
Reposted by Benjamin Coltman
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
Reposted by Benjamin Coltman
Job vacancy as senior scientist on #fluorescent #microscopy (incl confocal and high resolution) open at University of Vienna!
Apply until June 15: jobs.univie.ac.at/job/Senior-S...
Apply until June 15: jobs.univie.ac.at/job/Senior-S...
Senior Scientist
Senior Scientist
jobs.univie.ac.at
June 4, 2025 at 4:36 PM
Job vacancy as senior scientist on #fluorescent #microscopy (incl confocal and high resolution) open at University of Vienna!
Apply until June 15: jobs.univie.ac.at/job/Senior-S...
Apply until June 15: jobs.univie.ac.at/job/Senior-S...
Reposted by Benjamin Coltman
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
May 22, 2025 at 12:42 PM
NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.
Reposted by Benjamin Coltman
We are launching the Austrian Microbiome Research Awards 2025! 🇦🇹🔬
Calling all Austrian microbiome researchers to submit your best MSc/PhD thesis or research paper by June 7, more info: microplanet.at
@fwf-at.bsky.social @univie.ac.at
Calling all Austrian microbiome researchers to submit your best MSc/PhD thesis or research paper by June 7, more info: microplanet.at
@fwf-at.bsky.social @univie.ac.at
May 15, 2025 at 8:24 AM
We are launching the Austrian Microbiome Research Awards 2025! 🇦🇹🔬
Calling all Austrian microbiome researchers to submit your best MSc/PhD thesis or research paper by June 7, more info: microplanet.at
@fwf-at.bsky.social @univie.ac.at
Calling all Austrian microbiome researchers to submit your best MSc/PhD thesis or research paper by June 7, more info: microplanet.at
@fwf-at.bsky.social @univie.ac.at