Insights into constructing a stable and efficient microbial consortium system

Abstract

The concept of labor division and multi-module cooperation of microbial consortia offers it promising potentials in various areas, such as the utilization of complex substrates, synthesis of natural compounds with long metabolic pathways and remediation of environmental pollutants within a hostile environment. Consequently, synthetic microbial consortia represent a new frontier for synthetic biology because they can solve more complex problems than monocultures. However, current research on microbial consortia often involves the simple mixing of multiphase systems, where strains are co-cultured sequentially or individually cultured and then mixed-cultured. The instability and low efficiency of microbial consortia systems hindered their practical application. To construct a stable and efficient microbial consortium, it is essential to consider the different growth and metabolic characteristics of strains, the competition for various nutrients as well as the complex carbon, energy and signaling dynamics within the system. In this review, we provide a progressive strategy for constructing a stable and efficient microbial consortium system across three stages: compromised stage (work together), microenvironment-oriented stage (work better), and metabolite delivery-enhanced stage (work best). The detailed methods and points for attention of each stage are summarized, with a highlight on the technical bottleneck and application limitations. Through the integration of interdisciplinary strategies, such as materials science and mathematical models, the goal of building a stable and efficient microbial consortium is constantly advanced.

1. Introduction

Artificially synthesized microbial consortia have shattered the limitations imposed by monoculture, as they can reduce metabolic burden, streamline metabolic module optimization, and concurrently execute multiple tasks [1]. Accordingly, numerous research efforts have been dedicated to harnessing microbial consortia for diverse applications, such as the utilization of stubborn substrate, synthesis of complex natural chemicals, and remediation of hostile cultivation environments within the realm of synthetic biology [2]. However, recent studies have predominantly pursued purpose-oriented approaches, often relying on simplistic combinations of two microbial species, and occasionally employing sequential cultivation methods [3]. Regrettably, achieving a genuinely stable, controllable, high-yield, and robust microbial consortium remains an elusive goal in the present scientific landscape.

Maintaining stability and continuity in microbial consortia presents a substantial challenge compared to single-cell cultures, primarily due to the diverse cultivation conditions required, dynamic characteristics, and intricate communication among different microbial species [4,5]. Within microbial communities, fast-growing populations often outcompete slower-growing ones for nutrients, leading to the eventual disappearance of the latter from the consortia [6]. Moreover, various strains exhibit distinct temperature, pH and substrate cultivation preferences, making simple mixed cultures inadequate for providing the optimal growth environment. Furthermore, limitations in molecular transport across cell membranes and the dilution of intermediates in the extracellular space can reduce the effective concentration of substrates, thereby diminishing the efficiency of metabolic reactions [7]. Addressing these complexities necessitates innovative strategies and meticulous optimization to achieve the desired stability and performance in microbial consortia.