Kombucha-inspired microbial mixture lets scientists create ‘living materials’

Imperial and MIT researchers have made smart living materials by engineering microbes to detect and react to their environment.

The materials, known as engineered living materials (ELMs), could be used to detect and filter contaminants in water, in packaging to detect and alert to damage using fluorescence, and act as ‘living photographs’ which display pictures projected onto them.

Our new system moves us forward by creating materials that are scalable and therefore more likely to be useful in the real world Charlie Gilbert Department of Bioengineering

These ELMs are made by a mutually beneficial (symbiotic) combination of yeast and bacteria similar to those found in ‘kombucha mother’ – a mixture used to brew the fermented tea drink kombucha. It is also known as symbiotic culture of bacteria and yeast (SCOBY).

ELMs have previously been created using non-food microbes like E. coli and filamentous fungi, but scalability – the potential for the technology to be produced on a larger scale – has always been a challenge, meaning ELMs aren’t yet widely used. Current ELM technologies also require trained personnel and stringent conditions to grow microbes, hindering their accessibility to the general public.

This new type of ELM solves these problems by taking inspiration from the natural symbiotic approach of the kombucha SCOBY and combining genetically engineered yeast cells with cellulose-producing bacteria, making a ‘Syn-SCOBY’.

The researchers found that the Syn-SCOBY-produced cellulose acts as a scaffold which can hold the multi-functional enzymes produced by the yeast. This combination led to programmable and tough materials that were easy to produce at a larger scale from cheap sugar mixtures.

First author Charlie Gilbert of Imperial’s Department of Bioengineering, said: “Although we are still far from a future in which people can cheaply grow their own biological sensors, our new system moves us forward by creating materials that are scalable and therefore more likely to be useful in the real world.”

The findings are published in Nature Materials.

Tea trial

The researchers created a microbe population similar to a kombucha mother, which usually contains one or two strains of bacteria and at least two yeast strains that produce cellulose and acetic acid, which gives kombucha tea its distinctive flavour.

Many yeast strains used for fermentation are difficult to genetically modify, so the MIT researchers replaced them with Baker’s yeast – the yeast used worldwide in laboratories and in bread, beer and wine production. They combined this yeast with a bacteria called Komagataeibacter rhaeticus, which the Imperial researchers had previously isolated from a kombucha mother and which can produce large quantities of cellulose.

Because the researchers used a well-known yeast that is widely engineered in biotechnology, they were able to easily modify these cells with DNA-encoded programmes to make enzymes that glow in the dark, or release proteins on demand. The yeast could even be programmed to detect and break down pollutants in the environment.

We used this division-of-labour strategy so we could first focus on engineering the yeast cells and explore the possibilities of various living functional materials. Professor Tom Ellis Department of Bioengineering

Meanwhile, the bacteria in the culture produce large quantities of tough cellulose to serve as a scaffold. The researchers designed their system so that they control whether the yeast themselves, or just the enzymes that they produce, are incorporated into the cellulose structure. It takes only a few days to grow the material, and if left long enough, it can expand to occupy a space as large as a bathtub.

Senior author Professor Tom Ellis, also of Imperial’s Department of Bioengineering, said: “The genetic toolbox for engineering these bacteria is underdeveloped compared to the number of tools available for manipulating yeast DNA. That is why we used this division-of-labour strategy so we could first focus on engineering the yeast cells and explore the possibilities of various living functional materials.”

Plug and play

Because almost any version of yeast modified in the lab can be immediately used to produce kombucha-inspired materials, hundreds of different cell engineering options can be easily incorporated into their system in a ‘plug and play’ manner.

To demonstrate the potential of their Syn-SCOBY, the researchers tested the ‘plug and play’ function. They created a material incorporating yeast that senses estradiol, a hormone which is sometimes found as an environmental pollutant. In another version, they used a strain of yeast that produces a glowing protein called luciferase when exposed to blue light. These yeasts could be swapped out for other strains that detect other pollutants, metals, or pathogens.

The culture can be grown in normal yeast culture media, which the researchers used for most of their studies, but they have also shown that it can grow in tea with sugar. The researchers envision that the cultures could be customised in future for people to use outside of labs for growing water filters or other useful materials.

The researchers say that in future they could even be used to supplement health. For example, patients with metabolic deficiencies might benefit from consuming tea fermented by Syn-SCOBY engineered to produce essential nutrients and release therapeutic proteins.

They are now working on teaching the cellulose-producing bacteria to also do the jobs the yeast cells did in this research.

The research was funded in part by the UK Engineering and Physical Sciences Research Council (EPSRC), U.S. Army Research Office, the MIT Institute for Soldier Nanotechnologies, and the MIT-MISTI MIT-Imperial College London Seed Fund.

“Living materials with programmable functionalities grown from engineered microbial co-cultures” by Tom Ellis et al., published 11 January in Nature Materials.

Main image: Imperial College London/MIT

Image 2: Imperial College London/MIT

Image 3: Imperial College London/MIT

Image 4: Imperial College London/MIT

Image 5: Chenfu Hsing

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