Revealing the genomic differences between two subgroups in &lt;i&gt;Lactobacillus gasseri&lt;/i&gt;

Tada, Isao; Tanizawa, Yasuhiro; Endo, Akihito; Tohno, Masanori; Arita, Masanori

doi:10.12938/bmfh.17-006

Cited by 8 publications

(4 citation statements)

References 21 publications

(24 reference statements)

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“…The three L. gasseri groups we identified correspond to two previously defined groups with distinct gene content [51]. Notably, recent studies [52, 53] suggest our L.…”

Section: Discussionsupporting

confidence: 67%

“…iners strains identified appeared to be unique and average nucleotide diversity among L. iners strains was greater than that seen among L. crispatus strains ( Table 1 ). The three L. gasseri groups we identified correspond to two previously defined groups with distinct gene content [ 51 ]. Notably, recent studies [ 52, 53 ] suggest our L. gasseri group 3 represents the closely related L. paragasseri .…”

Section: Discussionmentioning

confidence: 99%

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The structure and diversity of strain-level variation in vaginal bacteria

2021

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The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria: Gardnerella vaginalis , Lactobacillus crispatus , Lactobacillus iners , Lactobacillus jensenii , Lactobacillus gasseri and Atopobium vaginae . Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain-level variation provides both the motivation and means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.

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“…The three L. gasseri groups we identified correspond to two previously defined groups with distinct gene content [51]. Notably, recent studies [52, 53] suggest our L.…”

Section: Discussionsupporting

confidence: 67%

Section: Discussionmentioning

confidence: 99%

The structure and diversity of strain-level variation in vaginal bacteria

2021

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“…Indeed, most L. iners strains identified appeared to be unique and average nucleotide diversity among L. iners strains was greater than that seen among L. crispatus strains (Table 1). The three L. gasseri groups we identified correspond to two previously defined groups with distinct gene content (52). Notably, recent studies (53,54) suggest our L. gasseri Group 3 represents the closely related L. paragasseri.…”

Section: Strain Level Variationsupporting

confidence: 67%

The structure and diversity of strain level variation in vaginal bacteria

Tortelli

Lewis

Fay

2020

Preprint

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The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core-genomes for six species of vaginal bacteria: G. vaginalis, L. crispatus, L. iners, L. jensenii, L. gasseri, and A. vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain level variation provides both the motivation and means of testing whether strain level differences contribute to the function and health consequences of the vaginal microbiome.Data SummaryAll vaginal metagenomic sequence data generated for this project can be found on the Sequence Read Archive under BioProject PRJNA639592.

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“…The ANI values were higher than 62% within a genus, while more than 95% of ANI values was recommended as the delimitation criterion for same species [14]. Seventyfive L. gasseri strains with publically available genomes were divided into two intraspecific groups by ANI at the threshold of 94% [15], subsequently some strains were reclassified as a new group, L. paragasseri, based on wholegenome analysis [16].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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Revealing the genomic differences between two subgroups in <i>Lactobacillus gasseri</i>

Cited by 8 publications

References 21 publications

The structure and diversity of strain-level variation in vaginal bacteria

The structure and diversity of strain-level variation in vaginal bacteria

The structure and diversity of strain level variation in vaginal bacteria

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

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