Enhancing the antibacterial function of probiotic Escherichia coli Nissle: when less is more

• Published in: Applied and environmental microbiology Vol. 89; no. 11; p. e0097523
• Main Authors: Bartram, Emma, Asai, Masanori, Gabant, Philippe, Wigneshweraraj, Sivaramesh
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 29.11.2023
• Subjects: Anti-Bacterial Agents - pharmacology; Bacteria; Bacteriocins; Bacteriocins - genetics; Bacteriocins - pharmacology; Biotechnology; Colonization; E coli; Effectiveness; Enterohemorrhagic Escherichia coli; Escherichia coli; Escherichia coli Proteins - genetics; Peptides; Probiotics; Promoters; Retrofitting; Transcriptomics; microcin C; Escherichia coli Nissle; promoters; probiotics
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/aem.00975-23

Probiotic bacteria confer multiple health benefits, including preventing the growth, colonization, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria, and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probiotic strain Nissle (EcN) the ability to produce microcin C (McC) from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon while ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in a infection model of enterohemorrhagic , we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little-to-none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic, or diagnostic applications. Bacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial "probiotic" bacteria to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side effects on the performance of such bacteria, thereby compromising their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic, or diagnostic applications.