Structure-Activity Relationship Studies of Novel Gut-derived Lantibiotics Against Human Gut Commensals

Abstract

Recent advances in sequencing techniques unveiled the vast potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) encoded in microbiomes. Class I lantibiotics such as nisin A, widely used as a food preservative, have been investigated for their efficacy in killing pathogens. However, the impact of nisin and nisin-like class I lantibiotics on commensal bacteria residing in the human gut remains unclear. Here, we report six gut-derived class I lantibiotics that are close homologs of nisin, four of which are novel. We applied an improved lantibiotic expression platform to produce and purify these lantibiotics for antimicrobial assays. We determined their minimal inhibitory concentration (MIC) against both Gram-positive human pathogens and gut commensals, and profiled the lantibiotic resistance genes in these pathogens and commensals. SAR studies with variants revealed key regions and residues that impact their antimicrobial properties. Our characterization and SAR studies of nisin-like lantibiotics against both pathogens and human gut commensals could shed light on the future development of lantibiotic-based therapeutics and food preservatives.

Exposure and resistance to lantibiotics impact microbiota composition and function

“…Our studies demonstrate significant impact on gut microbiome by dietary lantibiotic, and further investigation on structural-activity relationship of lantibiotics should help design novel lantibiotics that have improved selectivity towards pathogens but spares normal gut residents 19 . While worldwide healthcare system is encountering increasing burden of AMR, we have revealed prevalence, abundance and physiological significance of previously underappreciated AMR genes in human gut microbiome, which will help development of novel therapeutics and strategy to cope with AMR [60][61][62] .…”

“…In mice, administration of defined bacterial consortia can reduce susceptibility to enteric infections by bacterial pathogens [16][17][18] . For example, a four-bacterial strain consortium prevents and clears Vancomycin Resistant Enterococcus (VRE) by in vivo production of the lantibiotic Blauticin [18][19][20] .…”

“…We selected pairs of bacterial isolates of the same species that are discordant in the presence of LRS in their genomes for comparison. These isolates were cultured in 96-well plates with a concentration gradient of Nisin, a diet-derived lantibiotic, and Blauticin, a gut commensal-derived lantibiotic 19,20 , both heterologously expressed and purified 19,41 , and determined their minimal inhibitory concentrations (MIC). We found that isolates with LRS in their genomes have consistent higher resistance against both lantibiotics compared to their LRS-negative counterparts (Figure 4a,b,c, Extended Data Figure 4a,b,c).…”

“…While it is generally regarded as safe, Nisin is an antimicrobial peptide, and how it might impact gut microbiome remains understudied. We showed previously that Nisin-like lantibiotics impacted differentially to various gut microbes 19,20 , and we set out to characterize how dietary Nisin might impact the composition and function of gut microbiome in vivo . We supplemented the drinking water of Specific-Pathogen Free (SPF) mice with 10 mg/L Nisin, a concentration commonly found in processed food and drinks 27 , while the other group of SPF mice were maintained with plain water as control.…”