Made from plastic, it's fantastic

Genetic tooling for a microbe that degrades PET plastic

TL;DR (bioRxiv)

1. Toolkit for genetic engineering of Ideonella sakaiensis (aka Piscinibacter sakaiensis)

2. Whole-genome, barcoded mutant library for high-throughput functional genomics

3. Mutants with improved DNA delivery

4. Uncovered genetic pathways for PET degradation, bioplastic production, and biofilm formation

5. PRISM videos available to distribute expertise to work with this microbe

6. We can do great science together—with dedicated experts at Cultivarium and across the academic ecosystem.

The story behind the paper

At Cultivarium, our mission is to speed up experimentation and engineering across the tree of life. Most of biology runs on a few model organisms, but the world’s problems—in this example plastic waste—often demand novel biology outside of that small circle.

This story, now available on bioRxiv, starts with one such outsider: Ideonella sakaiensis (aka Piscinibacter sakaiensis), a bacterium discovered 9 years ago in a Japanese recycling facility. When scientists first found it, Ideonella did something almost magical—it could eat plastic bottles. Specifically, it could degrade and metabolize polyethylene terephthalate (PET), one of the most common and persistent plastics on Earth.

Since then, Ideonella has become a symbol of hope in the fight against plastic waste. But there’s been one major problem: nobody could easily engineer it. Without tools to modify its DNA, the field turned to workarounds—expressing its plastic-degrading enzymes (PETase and MHETase) in E. coli or Pseudomonas. At the international Metabolic Engineering Conference in 2025, one speaker bluntly summarized the state of the field:

“Because Ideonella is not engineerable, we decided to engineer E. coli to degrade PET.”

This caught our attention because this is exactly the problem that Cultivarium was built to solve.

A hot collaboration from a cold email

In June 2023, shortly after we released our POSSUM, a scalable toolkit for identifying functional plasmids across microbes, Victoria Sajtovich from the Max Planck Institute for Terrestrial Microbiology (Marburg, Germany) reached out. She had been studying Ideonella and wondered if we could work together to find a replicating plasmid.

We were intrigued. We had tried growing two “identical” Ideonella strains from two different culture collections (NITE in Japan and DSMZ in Germany) and found, to our surprise, that they grew differently. Same name, different biology.

Victoria traveled to Cultivarium and spent a week in the lab with our team. She showed us how to culture Ideonella and we showed her how to run POSSUM experiments. We ran the experiment over a few focused days and after a weekend sequencing run, we found a working plasmid and selectable marker. What might have taken a researcher in a lab a year of searching took only a few days of hands-on work.

That moment was a tangible proof point of our ambition at Cultivarium: tools to compress the time to biological discovery by orders of magnitude.

From plasmids to a genome-wide mutant library

Once Ideonella was transformable, we went further. Using a transposon system, we created a genome-wide, randomly barcoded mutant library of 353,908 uniquely trackable strains. With sequencing, each mutant can be tracked even when all of them are mixed together, enabling pooled functional screens where we can measure the effect of each gene in different conditions.

Together with Felipe-Andres Piedra at Baylor College of Medicine, who developed a sensitive PET degradation assay (bioRxiv, AEM), we used this library to profile Ideonella’s genetic response to growing directly on PET. In high-throughput experiments spanning several weeks, we tracked biofilm and planktonic populations as they colonized and consumed PET films.

The results revealed the genes that matter most: those involved in PET metabolism, transport, and a surprising connection to PHB (a biodegradable bioplastic) biosynthesis. We also found mutants that improved degradation by forming denser biofilms—especially those lacking pilT, a gene that normally controls the bacterium’s pili retraction. These mutants stuck better to PET and degraded it faster.

Making laboratory strains that are easier to engineer

We didn’t stop at understanding degradation. Using the same mutant library, we ran a second screen to identify variants more amenable to DNA delivery. That effort surfaced a set of genes—especially those involved in the bacterium’s surface S-layer and restriction-modification systems—that, when disrupted, allowed plasmid DNA to enter more efficiently. These more transformable mutants could help researchers probe the genome and test DNA constructs to study and engineer Ideonella far more easily.

Sharing the knowledge, not just the results

Every experiment we ran carried lessons—about subtle media differences, strain variation, and the small details that determine success or failure. Those lessons inspired Cultivarium Lab Lore, an effort to source hard-won tacit knowledge of working with non-model microbes from scientists in the form of digital post-it notes that scientists can discuss, akin to Reddit.

These efforts also motivated PRISM, our platform for AI-transcribed and error-checked audio+video recordings of protocols (site). You can now watch and learn Ideonella PET-growth methods directly from Felipe’s lab through PRISM here. Sharing these multimodal protocols that scientists can study, without relying only on a Methods written in prose or bottlenecked by traveling to a specific lab, is how we make progress reproducible and accelerate the next wave of discovery.

The bigger picture

By developing the first functional plasmid, a transposon system, and a genome-wide barcoded library, we’ve turned Ideonella from an icon of curiosity into an engineerable chassis for studying PET biochemistry, ecology, and synthetic biology. This means researchers can now explore its metabolism in detail, optimize plastic degradation, or even redirect its carbon flow toward useful molecules.

We’d like to make these materials broadly available to the scientific ecosystem. Molecular assets will be distributed via Addgene and the mutant library through Cultivarium, for as long as we have the supply. We’d love to see a distributed network form to propagate these assets robustly throughout the community.

This is just the beginning. Ideonella is the first in a series of organism-centric vignettes that we’ll be sharing, each highlighting Cultivarium’s tooling to study and engineer remarkable microbes in record time.

If you want to go deeper on your organism of interest, reach out. We can work with you, whether in academic or industry, to unlock the genetic potential of the biosphere. Together, we can make the extraordinary accessible.