Non‐gene‐editing microbiome engineering of spontaneous food fermentation microbiota—Limitation control, design control, and integration

Abstract

Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.

Regulating microbiome metabolic stability for stable indigenous liquor fermentation

“…The convergent succession in solid-state media is heavily influenced by the initial transcription of microbial genes [26,34,62]. In addition, this transcription can vary depending on the microbial immigration and probabilistic spatial dispersal that occur at the beginning of solid-state indigenous fermentation [63]. Fast dispersal rate of species would benefit uptake speed of resources [63][64][65].…”

“…In addition, this transcription can vary depending on the microbial immigration and probabilistic spatial dispersal that occur at the beginning of solid-state indigenous fermentation [63]. Fast dispersal rate of species would benefit uptake speed of resources [63][64][65]. Thus, the convergent succession process is not only reminiscent of microbial spatial exploration theory [64] but also contains elements of consumer-resource models applied to microbial coexistence [66].…”