Ryan Ziels

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.

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
☕🔥

Thanks for your contributions! We love your tool(s)!

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!

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.

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism www.nature.com/articles/s41... #jcampubs

Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.

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...

And here is the open-access link: rdcu.be/eL0JT

This was a massive collaborative effort, and wouldn’t be possible without support from @jgi.doe.gov, EMSL, and NSERC.

I’m 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! 🦠

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.

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! 🙏🦠⚡️🔥

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

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.

🖥️🧬 @axelvisel.bsky.social @danudwary.secondarymetabolism.com @simrouxvirus.bsky.social

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 the conversion of acetate into methane through obligate

Here’s one! doi.org/10.1038/s413...

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...

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...

Logo for the Sandpiper website

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 🧵

Thanks Phil! I submitted the new type genome / species name to SeqCode. Will this be automatically linked to GTDB once it’s 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

Assistant/Associate/Full Professor - Climate Equity and Environmental Justice - Rausser College of Natural Resources University of California, Berkeley is hiring. Apply now!

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

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

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...

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

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome

Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration journals.asm.org/doi/full/10.... #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

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!

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

~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...

It’s on my to-do list to visit! Are there things that a 3 year old would like?

Firefox FTW!

Do participants have to be from US institutions?

#IndigenousPeoplesDay is Monday. My challenge to non-Natives: dig into the history of the people who were displaced from your land, learn about the history of how they were displaced, find out where they are now, and support them financially or by protesting with them. Go beyond platitudes.

Shift in buoyant density of DNA in a SIP experiment, at least that’s what I see when looking at this 😜

How Google Alters Search Queries to Get at Your Wallet Testimony during Google’s antitrust case revealed that the company may be altering billions of queries a day to generate results that will get you to buy more stuff.

capitalism ruins everything

Release anvi'o v8, "marie" · merenlab/anvio We are happy to announce anvi'o v8 with the code name, "marie"! After about 4,200 changes that introduced over 36,000 new lines of code, this stable release of anvi'o represents significant advance...

🚨 #anvio v8 (marie) is out 🚨

This version includes new toys for integrated studies of microbial metabolism, genomic inversions, & phylogeography of proteins among many fixes and improvements.

Release notes:

github.com/merenlab/anv...

Installation page:

anvio.org/install