Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

Abstract

Background: Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. Results: In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. Conclusions: This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.

The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages

“…In addition to genome editing, CRISPR-Cas systems have also been proven useful in probiotic research applications. The conservation of CRISPR spacer sequences has enabled the traceability and evolutionary analysis of probiotics (Barrangou and Dudley, 2016), which has been used in Lactobacillus buchneri strains genotyping (Briner and Barrangou, 2014) and new species-level taxa identification (Zhou et al, 2020). Meanwhile, the role of prophage in antibiotic resistance genes (ARGs) transfer has been revealed (Haaber et al, 2016) and prophages carrying ARGs were also found in some Bifidobacterium strains (Mancino et al, 2019).…”

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality

“…Species that colonize diverse habitats and/or coexist with other microbes in large communities, such as many Lactobacillus species, typically have open pangenomes ( 15 ). While the majority of comparative genome studies of lactobacilli have focused on those species most relevant to the dairy industry, a recent analysis of L. paragasseri and L. gasseri considered isolates from the human gut microbiota ( 16 ). In addition to inhabiting the gut microbiota, L. paragasseri and L. gasseri are common inhabitants of the female urogenital tract, and Zhou et al ( 16 ) found that they also have an open pangenome.…”

“…While the majority of comparative genome studies of lactobacilli have focused on those species most relevant to the dairy industry, a recent analysis of L. paragasseri and L. gasseri considered isolates from the human gut microbiota ( 16 ). In addition to inhabiting the gut microbiota, L. paragasseri and L. gasseri are common inhabitants of the female urogenital tract, and Zhou et al ( 16 ) found that they also have an open pangenome. Our pangenome analysis of the L. jensenii and L. mulieris strains finds that they too have an open pangenome.…”

“…The inset shows the increase in the pangenome size as new genomes are examined. ered isolates from the human gut microbiota (16). In addition to inhabiting the gut microbiota, L. paragasseri and L. gasseri are common inhabitants of the female urogenital tract, and Zhou et al (16) found that they also have an open pangenome.…”

Can Probiotics and Diet Promote Beneficial Immune Modulation and Purine Control in Coronavirus Infection?

“…Recently, lactobacilli were isolated from human feces, and thirteen were identified as L. gasseri by 16 rDNA sequencing, showing the genetic diversity and different probiotic characteristics [ 105 ]. The resistance of L. gasseri to the human gastrointestinal tract under difficult conditions is a property that allows this microorganism to colonize the gut, improving the microbiome [ 103 , 106 ].…”