From Microbial Communities to Distributed Computing Systems

Abstract

A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.

A synthetic distributed genetic multi-bit counter

“…However, it critically relies on high expression levels of Cas9 which is toxic to the host cells ( Zhang and Voigt, 2018 ). Hence, adopting new principles and new synthetic architectures like distributed computation have also been widely discussed ( Xiang et al., 2018 ; Karkaria et al., 2020 ; Al- Radhawi et al., 2020 ). Similarly, our approach for designing a multi-bit counter system tries to solve scalability issues via distributed computation using cell-cell communication.…”

A synthetic distributed genetic multi-bit counter

“…However, it critically relies on high expression levels of Cas9 which is toxic to the host cells (Zhang & Voigt 2018). Hence, adopting new principles and new synthetic architectures like distributed computation have also been widely discussed (Xiang, Dalchau & Wang 2018, Karkaria, Treloar, Barnes & Fedorec 2020, Al-Radhawi et al 2020. Similarly, our approach for designing a multi-bit counter system tries to solve scalability issues via distributed computation using cell-cell communication.…”

Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

“…Understanding and designing microbial consortia with distributed functionality is of increasing interest in synthetic biology [1][2][3][4][5][6][7]. Assigning different functions to genetically distinct strains in a bacterial consortium reduces the metabolic load on each strain and thus allows for more complex functionality and greater robustness [8][9][10][11][12].…”