Genome Investigation and Functional Annotation of Lactiplantibacillus plantarum YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens

Abstract

All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as Lactobacillus plantarum. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel disease, and immune responses along with the analysis of the secondary metabolites’ characteristics of Lp YW11. Whole genome sequencing of Lp YW11 revealed 2297 genes and 1078 functional categories of which 223 relate to carbohydrate metabolism, 21 against stress response, and the remaining 834 are involved in different cellular and metabolic pathways. Moreover, it was found that Lp YW11 consists of carbohydrate-active enzymes, which mainly contribute to 37 glycoside hydrolase and 28 glycosyltransferase enzyme coding genes. The probiotics obtained from the BACTIBASE database (streptin and Ruminococcin-A bacteriocins) were docked with virulent proteins (cdt, spvB, stxB, and ymt) of Salmonella, Shigella, Campylobacter, and Yersinia, respectively. These bacteria are the main pathogenic gut microbes that play a key role in causing various gastrointestinal diseases. The molecular docking, dynamics, and immune simulation analysis in this study predicted streptin and Ruminococcin-A as potent nutritive bacteriocins against gut symbiotic pathogens.

Keywords: LP YW11; gut microbiota; nutritive bacteriocin; ruminococcin; streptin; whole genome.

Figure 1

Subsystem coverage and distribution of Lp YW11 genome by RAST.

Figure 2

PHASTER’s prediction of phage sites (A) Complete genome prediction of Lp YW11 with phage areas in the lactoplantibacillus plantarum genome (B) Expanded view of the genome with phage sites.

Figure 3

The prediction of the glycoside hydrolase family, glycosyltransferase family, carbohydrate esterase family, auxiliary esterase family, and carbohydrate-binding module family by the CAZy database.

Figure 4

Shows the Lp YW11 genome’s EPS-producing sites. Core biosynthetic genes are represented by the colors red, pink, green, blue, and grey. Regulatory genes are represented by the color green (Other genes). (A) The autoinducer cyclic lactone (B) terpene (C) T3PKS (D) RiPP likes.

Figure 5

Prediction of Exopolysaccharides (EPS) in red by antiSMASH along with the genomic comparison of Lp YW11 with other strains of Lactiplantibacillus plantarum.

Figure 6

STRING network of 43 genes involved in EPS production that causes immune stress response and intestinal bowel disease improvement.

Figure 7

Collinearity relationship of YW-11 with (A) WLPL04, (B). TMW, (C) pc-26 and (D) HC-2, strains of Lactiplantibacillus plantarum using SEED Viewer of RAST.

Figure 8

(A) Collinearity relationship of Lp YW11 with HC-2, LLY-606, pc-26, TMW, and WLPL04 showing aligned EPS-producing genes (Pink), transporter genes (Blue), regulatory genes (Green). (B) Phylogenetic Analysis of Lp YW11 with HC-2, LLY-606, pc-26, TMW and WLPL04.

Figure 9

3-D structure prediction of the virulent genes of gut bacteria via trRossetta. (A) cdt, (B) spvB, (C) stxB, and (D) ymt.

Figure 10

3-D modeled structures of bacteriocins via trRosetta (A) Streptin (B) Ruminococcin-A.

Figure 11

Interactome prediction through STRING. (A) ctd (B) spvB (C) stxB and (D) ymt.

Figure 12

Visualized docked complexes by Pymol of streptin with (A) cdt (B) spvB (C) stxB (D) ymt and of Ruminococcin-A with (E) cdt (F) spvB (G) stxB (H) ymt.

Figure 13

Shows a simulation of molecular dynamics of the best docked complex of streptin with spvB. (A) Deformability of the complex; (B) B-Factor graph, the plot indicates a comparative PDB plot, but there are no validated structures of our molecules on PDB; (C) Elastic Network (Grey matter indicates stiffer region); (D) Covariance Map: correlated (red), uncorrelated (white), or anti-correlated (blue) motions; (E) The eigenvalue plot illustrates the minimum energy required to deform the complex; (F) Variance individual variance (purple) and cumulative variance (green).

Figure 14

Shows a simulation of molecular dynamics of the best-docked complex of Ruminococ-cin-A with ymt. (A). Deformability of the complex; (B). B-Factor graph, the plot indicates a comparative PDB plot, but there are no validated structures of our molecules on PDB; (C). Elastic Network (Grey matter indicates stiffer region); (D). Covariance Map: correlated (red), uncorrelated (white), or anti-correlated (blue) motions; (E). Variance individual variance (purple) and cumulative variance (green); (F). The eigenvalue plot illustrates the minimum energy required to deform the complex.