Comparative genomic analysis of Lactobacillus mucosae LM1 identifies potential niche-specific genes and pathways for gastrointestinal adaptation

Abstract

Lactobacillus mucosae is currently of interest as putative probiotics due to their metabolic capabilities and ability to colonize host mucosal niches. L. mucosae LM1 has been studied in its functions in cell adhesion and pathogen inhibition, etc. It demonstrated unique abilities to use energy from carbohydrate and non-carbohydrate sources. Due to these functions, we report the first complete genome sequence of an L. mucosae strain, L. mucosae LM1. Analysis of the pan-genome in comparison with closely-related Lactobacillus species identified a complete glycogen metabolism pathway, as well as folate biosynthesis, complementing previous proteomic data on the LM1 strain. It also revealed common and unique niche-adaptation genes among the various L. mucosae strains. The aim of this study was to derive genomic information that would reveal the probable mechanisms underlying the probiotic effect of L. mucosae LM1, and provide a better understanding of the nature of L. mucosae sp.

Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches

“…Therefore, the current study followed their method to identify L. mucosae with certain credibility. The ANI value of L. mucosae was between 0.955 and 0.999, which was consistent with a previous result [6]. Compared with other Lactobacilli, the ANI value span of L. mucosae was relatively large, indicating that the proportion of variable genes was large, and the diversity was rich.…”

“…ANI analysis was carried out to evaluate the relationship among the species with a threshold greater than 95% being the same species. The method of calculating ANI was based on the average of the identity of the homologous genes of each pair of sequences [6]. The protein sequences extracted from those 101 strains were aligned using Orthomcl software (maintaining 50% identity; the cut-point parameter E-value was 1e-4) [17].…”

“…In addition, EPS also has associated healthy benefits, such as anti-inflammation, reducing blood fat, and lowering cholesterol [4], which provides a basis for the related animal model. It has been reported that L. mucosae has antitoxin and antibacterial activity, which could clear up the Zen toxin [5], and inhibit a variety of Gram-positive and negative pathogens [6], such as Escherichia coli, Salmonella typhimurium [7], and Staphylococcus [8].…”

“…With the rapid development of bioinformatics, comparative genomics provides a novel way to effectively assess the genetic diversity of bacteria [14], which could explore the origin of the strain and determine the genetic distribution of a particular species [15]. In 2017, Valeriano et al [6] firstly analyzed the potential specific genes and intestinal adaptability of L. mucosae LM1 through genome comparison, such as the average nucleotide identity (ANI) analysis with other species and collinearity analysis within species; unfortunately, the number of strains involved was limited. Heretofore, the comparative genomic research on L. mucosae, particularly the genes involved in carbohydrate utilization, bacteriocin, and the CRISPR system, has not been conducted.…”

Genetic and Biochemical Characterization of an Exopolysaccharide With in vitro Antitumoral Activity Produced by Lactobacillus fermentum YL-11

“…The whole genome of strain YL-11 was annotated via Rapid Annotation Subsystem Technology (RAST). Identification of coding proteins was predicted by using databases of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Cluster of Orthologous Groups of proteins (COG) databases (Valeriano et al, 2019). The EPS genes were aligned using the NCBI database.…”