3D printing tiny bacterial communities

Some papers take you on a journey into areas and ideas completely new. Our recent paper ‘Droplet printing reveals micron-sized structure is important for bacterial ecology’ has been one of those for me. 

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After finishing the projects that had sprung from my PhD, I was convinced that the most interesting thing I could do next was to engineer synthetic cells that can interact with bacterial communities – so I joined Hagan’s and Kevin’s research groups. However, I then found out that Gökçe Su Pulcu, Linna Zhou, and Wook Kim, across the two labs had, some time ago, tried printing bacteria using the Bayley group’s 3D printing technology1. After some lively discussions in the pub, I realised that this had great potential as a new technology and so I decided to take things up where they had left off. The reason I found this so exciting is that the arrangement of bacterial strains in their tiny communities is thought to be critical for how they function2. When strains are apart, they will interact less, so goes the logic, and so they generally should affect each other less. This can be a good thing for them if they are competing via toxins, but a bad thing if one is trying to feed off the secretions of the other. Either way, the spatial organisation of their communities is hypothesised to affect all manner of things from community productivity to stability and diversity. However, what was unknown was whether patterning at the tiny scales that are normally seen in nature was sufficient to have these effects. To test this one needs – you guessed it – a 3D printer that can pattern on the micron-scale. 

The technology development I was comfortable with, but these ideas from ecology and evolution were largely new to me. But the Foster lab knows their ecology and evolution and I soon found myself immersed in a fascinating literature I barely knew existed. Theoretical ecology is by now a vast subject that goes back at least a hundred years, with some of the earliest experiments from the 1930s using microbes (albeit with the protist Paramecium, rather than bacteria)3.

Back to it: we had the potential technology, but which bacteria should we print? The obvious choice for a first project was E. coli. Not only is it a model organism but  strains naturally compete with each other using protein toxins called colicins. Also, thankfully, two postdoctoral researchers at the time, Despoina Mavridou and Diego Gonzalez, were working on a colicin tool box for the lab4. Studying toxin interactions also made sense because the phenotypes should be strong and clear: if cells are killed, they should simply disappear from view.

Based on this, the 3D printing method was optimised to handle bacteria and increase the pattern-fidelity. As is often the case, this took much longer than we thought. The challenge was getting a method that was reliable enough to print the intended patterns every time5.

And then it was the big test, which was genuinely a bit of a gamble. It is important to remember how small the printed arrays are. Even when two strains are put side by side (so they are as separate as possible), the whole experiment is less than a millimetre across. By contrast, colicins can diffuse and kill across centimetre scales on agar plates. What we found amazing then is that these tiny, side-by-side prints were often sufficient to stop one strain killing the other. How could this happen? Well, it turns out dying cells mop up large numbers of colicin molecules as they go down, and this means that they protect cells behind them from the toxin. So the gamble paid off, and you can read more about micron-sized spatial structure and bacterial ecology here: https://doi.org/10.1038/s41467-021-20996-w

Crossing two normally disparate disciplines – ecology and 3D printing – was at times a challenge to say the least, but as I say, also a great journey. And I hope we have managed to offer something new for both fields, as well as in combination. Where to now? Well, we now want to print a whole range of strains and species so that we can build truly complex ecosystems on these tiny scales, and this is going well. Well, some bacteria, it turns out, die when you put them through the original printer, but with a bit of tweaking here and there, you are rewarded by happy cells popping out of the nozzle. As for myself, I still have not succeeded in getting back to what I initially intended to do. I find the miniature ecologies of bacteria fascinating, so I’m here to stay!

References 

  1. Villar, G., Graham, A. D. & Bayley, H. A tissue-like printed material. Science 340, 48–52 (2013).
  2. Nadell, C. D., Drescher, K. & Foster, K. R. Spatial structure, cooperation and competition in biofilms. Nat. Rev. Microbiol. 14, 589–600 (2016).
  3. Leslie, P. H. AN ANALYSIS OF THE DATA FOR SOME EXPERIMENTS CARRIED OUT BY GAUSE WITH POPULATIONS OF THE PROTOZOA, PARAMECIUM AURELIA AND PARAMECIUM CAUDATUM. Biometrika 44, 314–327 (1957)
  4. Mavridou, D. A. I., Gonzalez, D., Kim, W., West, S. A. & Foster, K. R. Bacteria use collective behavior to generate diverse combat strategies. Curr. Biol. 28, 345–355 (2018).
  5. Alcinesio, A. et al. Controlled packing and single-droplet resolution of 3D-printed functional synthetic tissues. Nat. Commun. 11, 2105 (2020).

Ravinash Krishna Kumar

Postdoctoral Research Associate , University of Oxford