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Expanding the Synbio Toolbox: Microbial Communities Engineering by Konstantinos Vavitsas

Synthetic biology recombines biological parts to gain new functions. Does the definition of a part, however, include a whole microbial species?

Biotechnology has relied on microorganisms since the dawn of human civilization, when fermentation was discovered and first utilized. Sterilization techniques and single-species cultivation brought a dramatic boost in the field during the previous century. In fermenters and bioreactors, monocultures are used—often as clones deriving from a single colony—while ensuring that there is no contamination is a crucial part of good manufacturing practices. However, in all natural systems microbial communities prevail. In habitats as diverse as the ocean seabed, forest soil, and the human intestines, microbes compete, cooperate or simply coexist, shaping a complex ecological network by these interactions.

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Lichen: Lichens make a great example of two organisms (fungi and algae) that combine and make something totally different. Source: pd4pic.com, public domain.

It is surprising that microbial communities have not been exploited more in biotechnology. The concept of microbial consortia is elaborated in a recent review from Pamela Silver and co-workers (1). Microbial communities are more robust, they complement each other in terms of nutrient usage, and they can divide the tasks; these characteristics can be exploited for more efficient product accumulation. Some technical advances, such as microfluidics, special separation within cultures, and environmental control can coordinate the growth of different species, while synthetic biology can provide valuable tools for precise control. Nevertheless, microbial communities are complicated systems, generally difficult to manipulate and fully characterize.

There have been a few successful co-culture works so far. A 2013 engineering paper (2) describes how a fungus (Trichoderma reesei) and a bacterium (Escherichia coli) can cooperate to produce isobutanol: the former hydrolyzes cellulosic biomass and the latter ferments the available sugars and produces the desired product. Even though the biculture produces at its best half the isobutanol titers the E. coli monocultures can achieve, this work shows that using a biotechnological consortium for production purposes is possible, while elaborative mathematical modelling is valuable for designing similar future approaches.

The accumulation or secretion of metabolic intermediates in the growth medium is a common problem in metabolic engineering. These compounds are often toxic, causing decrease in cell growth or even death, while they can be turned away from the desired biosynthetic route by secretion or undesired modifications,resulting in reduced product yield. When Gregory Stephanopoulos and coworkers (3) tried to produce muconic acid in E. coli, they observed the secretion of dehydroshikimic acid. They engineered a transporter of this intermediate, and instead of trying to recapture it, they exported all of it. Dehydroshikimic acid was subsequently imported in another engineered E. coli strain that contained the muconic acid biosynthetic pathway from that point on. Each strain had different “dietary preferences”, favoring the consumption of glucose and xylose respectively. This allows the coordination of the co-culture by adjusting the sugar content of the culture medium.

Another interesting approach also comes from Stephanopoulos’s lab. In a recent Nature Biotechnology paper (4) they used a consortium of E. coli and S. cerevisiae to produce oxygenated taxanes, precursors to the antitumor compound taxol. The bacteria—already optimized for diterpenoid production—produce the precursor taxadiene, while the yeast cells carry the oxygenizing cytochrome P450s which complete the pathway (read more about the specific redox challenges P450s possess and ways to link them directly with photosynthesis in my previous blog). The co-culture is self-regulated by the following simple mechanism: E. coli secrets acetate when growing in xylose and S. cerevisiae cannot catabolize xylose, but can grow in acetate as sole carbon source. Hence, the bacterium’s waste—and potential poison—becomes the yeast’s food, and E. coli determines the growth rate of S. cerevisiae. The efficiency of using dedicated strains for parts of a metabolic pathway was also highlighted by Nakagawa et al. (5), where four dedicated E. coli strains were used in consecutive co-cultures, producing 300 times more opiates than the respective yeast host.

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Biofilm and gut: Left: X-ray microtomography of a slice of a biofilm. Right: A three-dimensional model as an approach to study how bacteria affect gut health. Courtesy of Pacific Northwest National Laboratory, Creative Commons (CC BY-NC-SA 2.0)

Those few examples show that consortium engineering is in many cases both achievable and advantageous, and I expect to see more and deeper research in this field in the future (for instance, see a recent PLOS computational biology paper on the implementation of logic gates in multicellular consortia (6)). Microbial communities, such as the well-studied biofilms and the human microbiome, so far pose interesting research questions; but maybe they can start providing real-world answers. To adapt a quote from Agapakis et al. (7), metabolic engineering has made tremendous progress in the first a second dimension—the introduction of linear pathways and optimization of metabolic fluxes respectively—however, it can expand dramatically and reach new levels by exploiting a third dimension, the use of microbial consortia.

Disclaimer: Any views and opinions belong to the author and do not necessarily reflect the PLOS Synbio community.


Konstantinos Vavitsas is a PhD student at the Copenhagen Plant Science Centre, University of Copenhagen, working on the photosynthetic production of high-value compounds, and member of the steering committee of EUSynbioS. Find him on LinkedIn or follow him on Twitter.


The banner image is public domain (link)

References

1. Hays SG, Patrick WG, Ziesack M, Oxman N, Silver PA. Better together: engineering and application of microbial symbioses. Curr Opin Biotechnol. 2015 Dec;36:40–9.

2. Minty JJ, Singer ME, Scholz SA, Bae C-H, Ahn J-H, Foster CE, et al. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc Natl Acad Sci. 2013 Sep 3;110(36):14592–7.

3. Zhang H, Pereira B, Li Z, Stephanopoulos G. Engineering Escherichia coli coculture systems for the production of biochemical products. Proc Natl Acad Sci. 2015 Jul 7;112(27):8266–71.

4. Zhou K, Qiao K, Edgar S, Stephanopoulos G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol. 2015 Apr;33(4):377–83.

5. Nakagawa A, Matsumura E, Koyanagi T, Katayama T, Kawano N, Yoshimatsu K, et al. Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli. Nat Commun. 2016 Feb 5;7:10390.

6. Macia J, Manzoni R, Conde N, Urrios A, de Nadal E, Solé R, et al. Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia. PLoS Comput Biol. 2016 Feb 1;12(2):e1004685.

7. Agapakis CM, Boyle PM, Silver PA. Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat Chem Biol. 2012 Jun;8(6):527–35.

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