Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches

Abstract

The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.

Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

“…Of the 1,001 Lactobacillus strains deposited in the NCBI GenBank database, 391 were released as part of our previous studies ( 22 , 81 – 84 ), and the remaining 610 genomes were deposited under project accession no. PRJNA658852 .…”

Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus

“…Through the prediction of mathematical models, even if hundreds of genomes of each species were sequenced, there would be newly discovered genes in subsequent studies [ 43 ]. However, compared with the pan-genome of other lactobacilli, such as Limosilactobacillus mucosae (8100 genes) [ 16 ], Ligilactobacillus ruminis (10,000 genes) [ 17 ], Lacticaseibacillus rhamnosus (8200 genes) [ 44 ] and L. gasseri (6500 genes) [ 45 ], the pan-genome of L. acidophilus was smaller (5200 genes) and open. From the perspective of habitat, with Limosilactobacillus mucosae as an example, in addition to human feces and fermented dairy products, they had different habitat sources such as piglets, dogs and cattles.…”

“…All the 46 strains with ANI value above 97% were classified into two clusters, with five strains showing an ANI value over 99%, and the other group consisted of 41 strains including L. acidophilus NCFM with an ANI range 97–98% compared with another group. The ANI value of L. acidophilus was relatively narrow, compared with Limosilactobacillus mucosae (95.5%) [ 16 ] and Ligilactobacillus ruminis (96%) [ 17 ], representing that the proportion of variable genes was less, and the diversity was not rich. Combining the results of pan-genome analysis, it was speculated that L. acidophilus may not need many genes to adapt to different niches.…”

“…In this study, only six strains carried out intact prophages sequences, and the number was very few compared to other lactobacilli [ 16 , 17 , 44 , 46 ]. Moreover, as the result of COG analysis, the number of prophages and transposons genes of those six strains clustered in clade A were more than twice as much as clade C. The reason could be due to the niche of L. acidophilus , which is the small intestine, a place where the living environment is much worse than the colon and cecum.…”

“…With the development of high-throughput sequencing technology and comparative genomics approaches, numerous reports focused on genomes of lactobacilli, such as Lacticaseibacillus rhamnosus [ 10 ], Lacticaseibacillus paracasei [ 11 ], Limosilactobacillus reuteri [ 12 , 13 ], Ligilactobacillus salivarius [ 14 ], Limosilactobacillus fermentum [ 15 ], Limosilactobacillus mucosae [ 16 ], and Ligilactobacillus ruminis [ 17 ]. These studies used comparative genomics methods to reveal general genome characteristics, phylogenetic relationships and functional genes related to niche adaptation and probiotic activity of different strains, which let researchers have a new understanding of the metabolic capabilities and function roles of lactobacilli at the genetic level.…”