Abstract
BackgroundLactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis.ResultsIn 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.ConclusionsThis 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.
Highlights
Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis
Strains and sequencing Based on 16S rDNA sequencing, 92 L. gasseri strains were isolated from fecal samples obtained from adults and children from different regions in China, with 66 strains being obtained from adults and 26 from children (47 strains were isolated from females, 45 were isolated from males) (Table 1)
The draft genomes of all strains were sequenced using Generation Sequencing (NGS) technology and strains were sequenced to a coverage depth no less than the genome 100 ×, and using the genome of L. gasseri ATCC33323 and L. paragasseri K7 as reference sequences
Summary
Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. The core genome consists of genes presented in all strains and is generally associated with biological functions and major phenotypic characteristics, reflecting the stability of the species. Variable genome consists of genes that exist only in a single strain or a portion of strains, and is generally related to adaptation to particular environments or to unique biological characteristics, reflecting the characteristics of the species [17]. It is necessary to study CRISPR-Cas system to understand the adaptive immune system that protect Lactobacillus from phages and other invasive mobile genetic elements in engineering food microbes, and explore powerful genome engineering tool. A variety of strategies identify bacteriocin culture-based and in silico-based approaches, and to date, bacteriocin screening by in silico-based approaches have been reported in many research investigations [25]
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