Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

Abstract

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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 .…”

Quantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus X253

“…L. rhamnosus has been utilized as a kind of probiotic bacteria for over 30 years, and its efficacy has been demonstrated in several studies [ 5 ]. It has been shown to be able to tolerate and colonize the human gastrointestinal tract [ 6 ], inhibit Salmonella typhimurium growth [ 7 ], alleviate antibiotic-associated diarrhea [ 8 ], remove cadmium and aflatoxin B1 from aqueous solution [ 9 ], enhance the immune response [ 10 ], and attenuate allergic reactions [ 11 ].…”

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.…”

“…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.…”