Ryan Ziels
@ryanziels.bsky.social
Associate Professor of Environmental Engineering | UBC | Engineer | Microbiologist | Surfer of mountains & waves
https://emberrlab.civil.ubc.ca/
https://emberrlab.civil.ubc.ca/
Reposted by Ryan Ziels
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
โ๐ฅ
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
โ๐ฅ
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 22, 2025 at 6:55 PM
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
โ๐ฅ
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
โ๐ฅ
Thanks for your contributions! We love your tool(s)!
October 23, 2025 at 5:31 PM
Thanks for your contributions! We love your tool(s)!
Reposted by Ryan Ziels
Very excited to finally have my thesis work out in the world! Hopefully it just got easier to understand the role of specific microbes in complex communities, even when they are really rare!
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 11:15 PM
Very excited to finally have my thesis work out in the world! Hopefully it just got easier to understand the role of specific microbes in complex communities, even when they are really rare!
Reposted by Ryan Ziels
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism www.nature.com/articles/s41... #jcampubs
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 22, 2025 at 4:38 AM
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism www.nature.com/articles/s41... #jcampubs
Reposted by Ryan Ziels
Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.
Iโm very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! ๐ฆ
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
October 21, 2025 at 6:25 PM
Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.
And here is the open-access link: rdcu.be/eL0JT
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism
Nature Microbiology - An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion...
rdcu.be
October 21, 2025 at 5:52 PM
And here is the open-access link: rdcu.be/eL0JT
This was a massive collaborative effort, and wouldnโt be possible without support from @jgi.doe.gov, EMSL, and NSERC.
October 21, 2025 at 5:10 PM
This was a massive collaborative effort, and wouldnโt be possible without support from @jgi.doe.gov, EMSL, and NSERC.
Iโm very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! ๐ฆ
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 5:08 PM
Iโm very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! ๐ฆ
Reposted by Ryan Ziels
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 1:38 PM
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Excited for this opportunity to work with excellent research scientists at EMSL and the @jgi.doe.gov to study the microbes driving clean biofuel production! ๐๐ฆ โก๏ธ๐ฅ
Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.
๐ฅ๏ธ๐งฌ @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
๐ฅ๏ธ๐งฌ @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
Six join FICUS program in 2026 | Joint Genome Institute
Pictured from left to right are: [above] Allegra Aron, Jana Pilatova and Ryan Ziels; [below] Andrew Vander Yacht, Itamar Shabtai and Victoria Orphan The JGI is excited to welcom
jgi.doe.gov
September 18, 2025 at 1:23 AM
Excited for this opportunity to work with excellent research scientists at EMSL and the @jgi.doe.gov to study the microbes driving clean biofuel production! ๐๐ฆ โก๏ธ๐ฅ
Reposted by Ryan Ziels
Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.
๐ฅ๏ธ๐งฌ @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
๐ฅ๏ธ๐งฌ @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
Six join FICUS program in 2026 | Joint Genome Institute
Pictured from left to right are: [above] Allegra Aron, Jana Pilatova and Ryan Ziels; [below] Andrew Vander Yacht, Itamar Shabtai and Victoria Orphan The JGI is excited to welcom
jgi.doe.gov
September 16, 2025 at 3:26 PM
Welcome the six researchers accepted to the FICUS program for FY26! Focus areas for projects include biofuels, biomaterials & bioproducts; hydrobiogeochemistry; & novel applications of molecular techniques.
๐ฅ๏ธ๐งฌ @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
๐ฅ๏ธ๐งฌ @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social
Hereโs one! doi.org/10.1038/s413...
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
AbstractIn many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating theย conversion of acetate into methane through obligate
doi.org
August 13, 2025 at 4:41 AM
Hereโs one! doi.org/10.1038/s413...
Reposted by Ryan Ziels
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome
Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed...
www.biorxiv.org
July 29, 2025 at 2:18 AM
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!
www.biorxiv.org/content/10.1...
Reposted by Ryan Ziels
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 ๐งต
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 ๐งต
Thanks Phil! I submitted the new type genome / species name to SeqCode. Will this be automatically linked to GTDB once itโs validated?
July 16, 2025 at 7:59 PM
Thanks Phil! I submitted the new type genome / species name to SeqCode. Will this be automatically linked to GTDB once itโs validated?
Are you interested in microbes that are rare but active? We combined BONCAT with SIP and metaproteomics to improve the recovery of labeled proteins from such microbes. In this case, it illuminated a new anaerobic syntrophic acetate-oxidizing bacterium.
tinyurl.com/a8j29dsr
#microbiomesky #microsky
tinyurl.com/a8j29dsr
#microbiomesky #microsky
Activity-targeted metaproteomics enhances the ecophysiological characterization of cryptic syntrophic metabolisms
Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular me...
tinyurl.com
July 16, 2025 at 3:49 PM
Are you interested in microbes that are rare but active? We combined BONCAT with SIP and metaproteomics to improve the recovery of labeled proteins from such microbes. In this case, it illuminated a new anaerobic syntrophic acetate-oxidizing bacterium.
tinyurl.com/a8j29dsr
#microbiomesky #microsky
tinyurl.com/a8j29dsr
#microbiomesky #microsky
Reposted by Ryan Ziels
UC-Berkeley has an open-rank faculty position in our incredible Climate Equity and Environmental Justice (CEEJ) research cluster. It is an extraordinary interdisciplinary group working across multiple colleges and departments at the university! More information here: aprecruit.berkeley.edu/JPF04842
Assistant/Associate/Full Professor - Climate Equity and Environmental Justice - Rausser College of Natural Resources
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
July 12, 2025 at 12:02 AM
UC-Berkeley has an open-rank faculty position in our incredible Climate Equity and Environmental Justice (CEEJ) research cluster. It is an extraordinary interdisciplinary group working across multiple colleges and departments at the university! More information here: aprecruit.berkeley.edu/JPF04842
Reposted by Ryan Ziels
Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...
Emergence and disruption of cooperativity in a denitrifying microbial community
Abstract. Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the em
academic.oup.com
June 13, 2025 at 9:09 PM
Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...
Reposted by Ryan Ziels
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform
Abstract. Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms
academic.oup.com
November 15, 2024 at 5:00 PM
High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome
Reposted by Ryan Ziels
Refinement of the โCandidatus Accumulibacterโ genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration journals.asm.org/doi/full/10.... #jcampubs
February 29, 2024 at 2:33 PM
Refinement of the โCandidatus Accumulibacterโ genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration journals.asm.org/doi/full/10.... #jcampubs
Reposted by Ryan Ziels
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium www.nature.com/articles/s41... #jcampubs
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing c...
The ISME Journal - Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
www.nature.com
October 26, 2023 at 1:31 PM
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium www.nature.com/articles/s41... #jcampubs
This was a huge effort led by @lizilla93.bsky.social in collaboration with EMSL, and many others. Very glad to see it out!
October 25, 2023 at 4:35 PM
This was a huge effort led by @lizilla93.bsky.social in collaboration with EMSL, and many others. Very glad to see it out!
~70% of CH4 in anoxic ecosystems comes from acetate, but what microbes are catalyzing its oxidation, and how? We shed some new light on this question using long-term enrichments along with metabolic modeling informed by SIP-metaproteogenomics. #MicrobiomeSky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing c...
The ISME Journal - Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium
www.nature.com
October 25, 2023 at 4:33 PM
~70% of CH4 in anoxic ecosystems comes from acetate, but what microbes are catalyzing its oxidation, and how? We shed some new light on this question using long-term enrichments along with metabolic modeling informed by SIP-metaproteogenomics. #MicrobiomeSky
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Itโs on my to-do list to visit! Are there things that a 3 year old would like?
October 7, 2023 at 8:12 PM
Itโs on my to-do list to visit! Are there things that a 3 year old would like?