Diversity of the genus Lactobacillus revealed by comparative genomics of five species

Canchaya, Carlos; Claesson, Marcus J.; Fitzgerald, Gerald F.; Sinderen, Douwe van; O’Toole, Paul W.

doi:10.1099/mic.0.29140-0

Cited by 115 publications

(90 citation statements)

References 62 publications

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“…S2 in the supplemental material). This is unsurprising, given that a distinguishing feature of the genus Lactobacillus is its extraordinary phenotypic and genomic diversity (9) and that lateral gene transfer is an important element in generating this diversity (39).…”

Section: Discussionmentioning

confidence: 99%

Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels

Fang

Bumann³

et al. 2009

J Bacteriol

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Commensal lactobacilli frequently produce bile salt hydrolase (Bsh) enzymes whose roles in intestinal survival are unclear. Twenty-six Lactobacillus salivarius strains from different sources all harbored a bsh1 allele on their respective megaplasmids. This allele was related to the plasmid-borne bsh1 gene of the probiotic strain UCC118. A second locus (bsh2) was found in the chromosomes of two strains that had higher bile resistance levels. Four Bsh1-encoding allele groups were identified, defined by truncations or deletions involving a conserved residue. In vitro analyses showed that this allelic variation was correlated with widely varying bile deconjugation phenotypes. Despite very low activity of the UCC118 Bsh1 enzyme, a mutant lacking this protein had significantly lower bile resistance, both in vitro and during intestinal transit in mice. However, the overall bile resistance phenotype of this and other strains was independent of the bsh1 allele type. Analysis of the L. salivarius transcriptome upon exposure to bile and cholate identified a multiplicity of stress response proteins and putative efflux proteins that appear to broadly compensate for, or mask, the effects of allelic variation of bsh genes. Bsh enzymes with different bile-degrading kinetics, though apparently not the primary determinants of bile resistance in L. salivarius, may have additional biological importance because of varying effects upon bile as a signaling molecule in the host.

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Section: Discussionmentioning

confidence: 99%

Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels

Fang

Bumann³

et al. 2009

J Bacteriol

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“…Another interesting approach to determine whole-genome distances has been described, which is based on DNA compression algorithms (4,26,31). At the protein level, an approach based on Promer, the amino acid version of Mummer, has also been investigated (2). Comparative genomic studies often require a decision tool to help select the genomes to compare and in particular which bacterial genomes are close enough to be aligned at the DNA level.…”

Section: Discussionmentioning

confidence: 99%

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Deloger¹,

Karoui²,

Petit³

2009

J Bacteriol

146

120

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The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

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“…The general trend toward metabolic simplification is reflected in changes in sugar metabolism genes, the loss of genes for the biosynthesis of cofactors and amino acids, and increased numbers of transporters and peptidases. However, direct comparison of species from different niches has been less informative due to the level of interspecies diversity at the genome level (4,8). We report here the genome sequence of Lactobacillus helveticus DPC 4571, a Swiss cheese isolate that has been thoroughly investigated as a starter and adjunct culture in cheese manufacture and that demonstrates a number of highly desirable traits, including rapid autolysis, reduced bitterness, and increased flavor notes (19,20,23).…”

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Genome Sequence of Lactobacillus helveticus , an Organism Distinguished by Selective Gene Loss and Insertion Sequence Element Expansion

et al. 2008

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Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species, considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the L. helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.Lactobacillus species are employed in the production of a wide range of fermented milk, meat, and plant products and are also routinely isolated from the vagina and gastrointestinal (GI) tract. This broad range of environmental niches is reflected in the diversity of species belonging to the genus Lactobacillus.

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Diversity of the genus Lactobacillus revealed by comparative genomics of five species

Cited by 115 publications

References 62 publications

Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels

Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Genome Sequence of Lactobacillus helveticus , an Organism Distinguished by Selective Gene Loss and Insertion Sequence Element Expansion

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