Kaitlin Creamer

Our recent publication where the central question was: in soils, are there trademark characteristics of rapidly transcribed genes? And it was a resounding “it depends”. We found gene function, environmental stimulus, and phylogeny all impacted this relationship. More here:
peerj.com/articles/206...

Today in Nature Communications, a team of IGI researchers from The Banfield Lab and Pam Ronald's labs uncover a new way to reduce methane emissions from rice by influencing the activity of rice paddy soil #microbes. Read more: https://ow.ly/45j150Y3WsI

🚨 New pre-print alert!
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires

www.biorxiv.org/content/10.6...

Excited to share our discovery of archaeal circular, jumbo extrachromosomal elements (up to ~535 kb genomes). One related, 409-kb genome is integrated in CH4-eating Methanoperedens, representing the largest integrative element in Archaea so far! Curious about what they are doing? See the paper

A new preprint from The Banfield Lab looks at mobile genetic elements with single-cell precision. Read here: https://ow.ly/hFBX50Y0nQA

#microbiology

How Ocean Currents Shape the Marine Microbiome Ocean microbes keep the planet healthy by cycling nutrients and capturing carbon, but a detailed and precise map of where they live had never been made—until now.

Huge thanks to The Scientist for this feature that really captured the spirit of our research!

www.the-scientist.com/how-ocean-cu...

Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics Mobile genetic elements (MGEs), including plasmids and viruses, drive microbial evolution and ecosystem dynamics, yet their distribution, host range, and functions remain poorly understood, especially...

New preprint out: Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics
www.biorxiv.org/content/10.6...

@mingyan-igi.bsky.social

Postdoc - Microbiome - Innovative Genomics Institute University of California, Berkeley is hiring. Apply now!

🚨 Our Lab is HIRING! If you are interested in characterizing model microbiomes using genome-resolved methods, statistical/metabolic modeling, and/or machine learning please submit an application here: aprecruit.berkeley.edu/JPF05234

#postdoc #sciencejobs #biology #microbiome

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology Abstract. Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating th

Think you need large volumes for microbial experiments?
Our recent publication introduces HiMEx, a simple, scalable method for microbial ecology. academic.oup.com/ismecommun/a...
🦠 it provides an easy, efficient approach to capturing viral diversity, opening new opportunities for virome analysis.

Out now in Nature Communications, from IGI's Jill Banfield (The Banfield Lab) and collaborators: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

Read here: https://www.nature.com/articles/s41467-025-65646-7

Three scientists, smiling, sitting at a lab bench with tubes and lab notebooks, and other supplies in front of them.

This was a big team effort- couldn't have done it w/o help & support of co-first author Gabe; Paul, Alyssa & all previous Jensen lab Salinispora experts for inspiration.

Special thanks to then-undergrads Victoria & David: carefully culturing & sequencing hundreds of strains took massive effort! 8/8

Does deep sampling find new compounds? 💊 Yes.

Gabriel & Ebru linked many unknown gene clusters to molecules. We also identified fridamycin E & ikarugamycin for the first time in Salinispora cultures; even well-studied bacterial genera have hidden chemical potential!

Matrix of GCF distributions in S. arenicola. Columns indicate presence (blue) of 100 GCFs across 157 S. arenicola genomes (y-axis). The three matrices describe shared, global-specific, or microscale-specific GCFs. For each matrix, the columns are arranged from left to right according to GCF abundance. Annotated GCFs are indicated by compound names and highlighted according to confidence level. The first column of the y-axis is colored according to geographic origin and ordered by 99% ANI populations, which are numbered (microscale shown in bold red) and demarcated by gray horizontal lines. The second column delineates microscale (black) and global strains (white).

Where does this diversity come from? Horizontal gene transfer likely contributes.

We found 18 biosynthetic gene cluster families that were unique to a single strain. This supports the "plug-and-play" evolution of secondary metabolites, reported previously in Salinispora.

Non-metric multidimensional scaling (NMDS) plots of GCF distribution among microscale and global S. arenicola strains. Top: Each dot represents a genome colored by population. Bottom: Each dot represents a genome colored by the location of origin

Why 2 populations in 1 spot, & globally?

We compared microscale vs. global strains. Result: Pop 1 & Pop 5 were clearly separated by their biosynthetic gene cluster profiles.

Specialized metabolism likely acts as an ecotype-defining trait, helping distinct populations coexist in the same sediment.

S. arenicola gene cluster family (GCF) network. Network shows nodes representing a BGC and each cluster of nodes a GCF. GCFs are categorized as shared (present in both data sets), global (global-specific), or microscale (microscale-specific) and color-coded by biosynthetic class. Text GCF annotations are provided for experimentally validated Salinispora products or MIBiG BGC matches.

Turns out, specialized metabolite potential plays a huge part.

From 96 "microscale" strains, we captured 67% of the entire S. arenicola global biosynthetic diversity (60 of 89 gene cluster families)!

We even found 11 GCFs that were unique to the microscale plot..

Close-up of 16 Salinispora colonies grown on agar plates. Colony morphologies range from “popcorn-like” to displaying circular concentric growth, with some showing extensive vertical growth on the agar surface. Colony pigmentation varies from pale yellow to deep orange.

The answer: Nope.

They were not clonal. They resolved into 2 distinct S. arenicola populations co-existing inches apart! (We also isolated 2 other species).

Huge shoutout to Victoria who led the isolation of these strains: check out these beautiful Salinispora colonies from each sub-quadrat 👇

Our new paper on Salinispora is out in @asm.org #AppEnvMicro! @scrippsocean.bsky.social

Ever wonder if an actinomycete living in 1m² ocean sediment is just one big clonal colony?

We sequenced 99 Salinispora strains from a single Fiji reef plot to find out. 🧵1/8 doi.org/10.1128/aem....

Taxonomic and biosynthetic diversity of the marine actinomycete Salinispora across spatial scales journals.asm.org/doi/full/10.... #jcampubs

illustration of petri dishes growing microbes

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

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...

Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

www.nature.com/articles/s41...

@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...

Headshots of Veronika, Jill, and Alanna

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

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1

Multi-omics analysis reveals important role for microbial-derived metabolites from Botryllus schlosseri in metal interactions | mSystems Given the importance of marine invertebrates and their microbial communities in marine ecosystems, we sought to characterize the largely unknown microbial associates, metal sequestration, and metabolite production of the marine colonial tunicate, Botryllus schlosseri, a model organism for cellular and developmental studies. Using an integrated multidisciplinary approach, we identified significant correlations between metals, metabolites, and bacterial taxa. B. schlosseri tissue was highly enriched in metals compared to seawater, and B. schlosseri microbiome beta-diversity was significantly different from seawater. We also introduced the concept of the pan-metabolome to classify metabolites based on their presence or absence across complex samples and found microbial metabolites in both the core and flexible metabolome. These findings offer insights into B. schlosseri’s biological and chemical interactions with microorganisms and their environment, bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.

Congrats to Dulce Guillén Matus for her newest manuscript out today! A collaborative manuscript on the microbes, metals, and metabolites of Botryllus schlosseri, a marine tunicate! doi.org/10.1128/msys...

strongest earthquake I’ve felt ever living in California, jolted me out of sleep with plenty of shaking felt on the 4th floor in Emeryville..! 4.6, epicenter in Berkeley?

Decades-Old Barrels of Industrial Waste Still Impacting Ocean Floor Off LA In 2020, haunting images of corroded metal barrels in the deep ocean off Los Angeles leapt into the public consciousness. Initially linked to the toxic pesticide DDT, some barrels were encircled by gh...

🌊 Remember the barrels found off the coast of LA? New research from Scripps Oceanography found that 'halos' around some of the barrels came from caustic alkaline waste leaking from the barrels. https://scripps.ucsd.edu/news/decades-old-barrels-industrial-waste-still-impacting-ocean-floor-la

Study Reveals how Deep Ocean Currents Shape Microbial Life across South Pacific A groundbreaking study in the journal Science, has unveiled how deep ocean currents—known as global overturning circulation—play a pivotal role in shaping the diversity and function of microbial life ...

🌊 ↪️↩️ Deep ocean currents play a pivotal role in shaping the diversity and function of microbial life across the South Pacific Ocean, according to a groundbreaking study led by @jcvi.org and Scripps Oceanography scientists. More on the study published by @science.org. ⬇️

Congrats @andrejakust.bsky.social and team!!! Capturing the complex microbiome of Cyanobacteria, allowing for ecologically-relevant studies in the lab! 🦠🔬