Engineering Microbial Consortia as Living Materials: Advances and Prospectives

Abstract

The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.

Keywords: division of labor; engineered living materials; microbial consortia; synthetic biology toolkits.

Figure 1

Representative examples of engineering natural microbial consortia and living materials. (a) Schematic showing the production and consortia of cellulose produced from SCOBY. Figure adapted from ref (33). Copyright 2021 Springer Nature. (b) Genetic circuits in S. cerevisiae designed to manipulate mechanical properties, sense and respond to stimuli, and enable optogenetic patterning of BC. (c) The production and engineering of a fungal-bacterial biocomposite. (d) QS circuits in P. agglomerans embedded in a block to enable communication and signal propagation in biocomposite material. Figure adapted from ref (37). Copyright 2022 Springer Nature.

Figure 2

Designing and assembling synthetic microbial consortia as ELMs. (a–d) Assembly strategies: (a) Encapsulation in bulk, for example, spin-coat and drip-cross-linked. (b) 3D printing uses bioink consisting of a polymer, and living cells produce spatial patterns. (c) The proliferation of cellulose-producing bacteria in self-assembled synthetic consortia is followed by enrichment of specialized members. (d) The encapsulation of subpopulations of consortia confines subgroups while enabling the exchange of substances. (e–f) Approaches to designing synthetic consortia: (e) High-throughput characterization of synthetic consortia with droplet microfluidics or microplates. (f) Modeling methods can be used to study synthetic consortia, including ecological models and metabolic models.

Figure 3

Synthetic biology toolkits for microbial consortia engineering. (a–e) Cellular-level engineering toolkits. (a) An ORI library built by Gilbert et al. for nonmodel bacteria. (b) The constitutive promoter can continuously drive gene expression, whereas the inducible promoters boost gene expression only when specific stimuli are sensed. (c) CRISPR-based technologies make it possible to modify genetic sequences and their functions, including activation, repression, and base-editing. (d) The working mechanism of Tn-seq with essential pathways and genes, as well as the application of Tn-seq as a genetic engineering tool. (e) SPs facilitate the secretion of target proteins because their peptide sequences are fused to the N-terminal of the target proteins. (f–j) The biological toolkits for community-level engineering. (f) MAGIC was developed to modify mammalian microbiota in situ through community-wide horizontal gene transfer. Figure adapted from ref (111). Copyright 2019 Springer Nature. (g) MDOL distributes the metabolic pathway into several sequential metabolic tasks that function in distinct bacterial populations. (h) Genetic circuit design for stabilizing synthetic microbiota through a “rock–paper–scissors” relationship and synchronized lysis driven by QS. (i) A self-patterning technique established through an intercellular signaling circuit that automatically forms an out-of-phase striped pattern. Figure adapted from ref (127). Copyright 2020 Springer Nature. (j) Directed evolution is achieved by using various strategies to artificially and iteratively select microbial communities at the microbiome level.