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Comparative Study
. 2020 Feb 3;21(1):119.
doi: 10.1186/s12864-020-6527-y.

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

Xingya Zhou  1   2 , Bo Yang  3   4   5 , Catherine Stanton  6   7   8 , R Paul Ross  6   7   8 , Jianxin Zhao  1   2   6 , Hao Zhang  9   10   11   12 , Wei Chen  1   2   13
Affiliations
Comparative Study

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

Xingya Zhou et al. BMC Genomics. .

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.

Keywords: ANI; Genotype; Lactobacillus gasseri; Lactobacillus paragasseri; Pan/core-genome.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Average nucleotide identity (ANI) alignment of all the strains including L. gasseri ATCC33323 and L. paragasseri K7
Fig. 2
Fig. 2
The phylogenetic tree based on orthologous genes. The red area was the L. gasseri cluster and the blue area was the L. paragasseri cluster. The purple circle indicated the strains isolated from infant feces and the gray indicated strains isolated from adults. The pink indicated strains from female and the green represent strains from male subjects
Fig. 3
Fig. 3
Neighbor-joining tree based on groEL (a) and pheS (b) gene
Fig. 4
Fig. 4
Pan-genome and core-genome curve of the L. paragasseri (a) and L. gasseri (b)
Fig. 5
Fig. 5
The unique and orthologues genes of L. paragasseri genomes (a) and L. gasseri (b)
Fig. 6
Fig. 6
CRISPR-cas phylogenetic analyses for L. paragasseri and L. gasseri. a Phylogenetic tree based on the Ca1 protein, b Phylogenetic tree based on the Cas2 protein, c Phylogenetic tree based on the Cas9 protein. The CRISPR-Cas subtypes and bacterial species were written on the right and each group was colored
Fig. 7
Fig. 7
Features of DR sequences of CRISPR loci in L. paragasseri and L. gasseri. a The sequence of consensus DR sequences within L. paragasseri. b The sequence of consensus DR sequences in L. gasseri strains. The height of the letters indicates the frequency of the corresponding base at that position. c–e Predicted RNA secondary structures of CRISPR DR in L. paragasseri. f–g Predicted RNA secondary structures of the CRISPR DR in L. gasseri
Fig. 8
Fig. 8
The distribution and number of GH, CE and GT family genes. Gene copy number was indicated by color ranging from green (absent) to red. The strain number in red and in black indicated L. gasseri and L. paragasseri, respectively
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References

    1. Selle K, Klaenhammer TR. Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol Rev. 2013;37(6):915–935. doi: 10.1111/1574-6976.12021. - DOI - PubMed
    1. Ushiyama A, Tanaka K, Aiba Y, Shiba T, Takagi A, Mine T, et al. Lactobacillus gasseri OLL2716 as a probiotic in clarithromycin-resistant helicobacter pylori infection. J Gastroenterol Hepatol. 2010;18(8):986–991. doi: 10.1046/j.1440-1746.2003.03102.x. - DOI - PubMed
    1. Harata G, He F, Hiruta N, Kawase M, Kubota A, Hiramatsu M, et al. Intranasally administered Lactobacillus gasseri TMC0356 protects mice from H1N1 influenza virus infection by stimulating respiratory immune responses. World J Microbiol Technol. 2011;27(2):411–416. doi: 10.1007/s11274-010-0472-x. - DOI
    1. Strus M, Brzychczy-Włoch M, Gosiewski T, Kochan P, Heczko PB. The in vitro effect of hydrogen peroxide on vaginal microbial communities. FEMS Immunol Med Microbiol. 2013;48(1):56–63. doi: 10.1111/j.1574-695X.2006.00120.x. - DOI - PubMed
    1. Lewanika TR, Reid SJ, Abratt VR, Macfarlane GT, Macfarlane S. Lactobacillus gasseri gasser AM63(T) degrades oxalate in a multistage continuous culture simulator of the human colonic microbiota. FEMS Microbiol Ecol. 2010;61(1):110–120. doi: 10.1111/j.1574-6941.2007.00327.x. - DOI - PubMed

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