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

Adult Asian People Bacterial Proteins / genetics Bacteriocins / genetics CRISPR-Cas Systems / genetics DNA, Bacterial / genetics Feces / microbiology Genome, Bacterial / genetics Genomics / methods Humans Infant Lactobacillus gasseri / genetics Phylogeny Probiotics / metabolism RNA, Ribosomal, 16S / genetics
ANI Genotype Lactobacillus gasseri Lactobacillus paragasseri Pan/core-genome

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
03 Feb 2020
Historique:
received: 12 02 2019
accepted: 22 01 2020
entrez: 5 2 2020
pubmed: 6 2 2020
medline: 2 10 2020
Statut: epublish

Résumé

Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. 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. 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.

Sections du résumé

BACKGROUND BACKGROUND
Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis.
RESULTS 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 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.

Identifiants

DOI: 10.1186/s12864-020-6527-y PMID: 32013858 PMC: PMC6998098
pubmed: 32013858
doi: 10.1186/s12864-020-6527-y
pii: 10.1186/s12864-020-6527-y
pmc: PMC6998098
doi:

Substances chimiques

Bacterial Proteins 0
Bacteriocins 0
DNA, Bacterial 0
RNA, Ribosomal, 16S 0

Types de publication

Comparative Study Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

119

Subventions

Organisme : National Natural Science Foundation of China
ID : Nos. 31530056, 31820103010, 31801521
Organisme : Fundamental Research Funds for the Central Universities
ID : JUSRP11733
Organisme : National Firs-Class Discipline Program of Food Science and Technology
ID : JUFSTR20180102

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Auteurs

Xingya Zhou (X)

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.
School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.

Bo Yang (B)

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China. bo.yang@jiangnan.edu.cn.
School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. bo.yang@jiangnan.edu.cn.
International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China. bo.yang@jiangnan.edu.cn.
ORCID: 0000-0002-1347-3718

Catherine Stanton (C)

International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.
Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
APC Microbiome Ireland, University College Cork, Cork, Ireland.

R Paul Ross (RP)

International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.
Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
APC Microbiome Ireland, University College Cork, Cork, Ireland.

Jianxin Zhao (J)

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.
School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China.

Hao Zhang (H)

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China. zhanghao61@jiangnan.edu.cn.
School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. zhanghao61@jiangnan.edu.cn.
National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China. zhanghao61@jiangnan.edu.cn.
Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China. zhanghao61@jiangnan.edu.cn.

Wei Chen (W)

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.
School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
Beijing Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China.

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Classifications MeSH

questionsmedicales.fr › Personnes › Tranches d'âge › Adulte › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Personnes › Asiatiques › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines membranaires › Perforines › Bactériocines › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › ADN bactérien › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Liquides et sécrétions biologiques › Fèces › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Comparative analysis of Lactobacillus gasseri...
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questionsmedicales.fr › Personnes › Tranches d'âge › Nourrisson › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Lactobacillales › Lactobacillaceae › Lactobacillus › Lactobacillus gasseri › Comparative analysis of Lactobacillus gasseri...
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questionsmedicales.fr › Aliments et boissons › Aliments › Compléments alimentaires › Probiotiques › Comparative analysis of Lactobacillus gasseri...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN ribosomique › ARN ribosomique 16S › Comparative analysis of Lactobacillus gasseri...