Rapidly engineering an osmotic-pressure-tolerant gut bacterium for efficient non-sterile production of bulk chemicals

Abstract

The concept of next-generation industrial biotechnology (NGIB) has been presented as a green biomanufacturing approach based on the use of low-cost substrates in an open and continuous non-sterilization fermentation process. However, the realization of NGIB, partially through the utilization of extremophiles, has been impeded by the challenges in engineering these extremophiles. A previously unexplored solution for advancing NGIB is to obtain readily engineerable microorganisms with osmotic-pressure tolerance. Here, Jejubacter sp. L23 strain, a Gram-negative, rod-shaped, osmotic-pressure-tolerant bacterium, was isolated from the gut of superworm Zophobas atratus and identified as a new member of the family Enterobacteriaceae, with high 16S rDNA similarity to Escherichia coli (95.2 %). The growth of L23 strain was observed at 10 to 45 °C and pH 4.0 to 10.0 in the presence of 0 to 12 % (w/v) NaCl. We systematically investigated the genetic parts, molecular tools, and manipulation approaches applicable to the L23 strain, and successfully conducted chromosomal genetic engineering, e.g. base-editing and deletion, by using high-efficiency CRISPR systems under low-salt conditions. Furthermore, the metabolic network of L23 strain was rewired to obtain the engineered L23R7 strain, which could display stable expression of exogenous genes and produce bulk chemicals at high yields using inulin, abundant non-food biomass, and salt water without sterilization. For example, 41 g/L isobutanol was produced by utilizing inulin in a 3-L bioreactor through a non-sterile fermentation process. This potent industrial strain holds the promise of promoting the development of NGIB as a sustainable biomanufacturing solution.