The Genomic Basis of Lactobacilli as Health-Promoting Organisms
- Authors: Elisa Salvetti1, Paul W. O’Toole2
- Editors: Robert Allen Britton3, Patrice D. Cani4
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VIEW AFFILIATIONS HIDE AFFILIATIONSAffiliations: 1: School of Microbiology and APC Microbiome Institute, University College Cork, Ireland; 2: School of Microbiology and APC Microbiome Institute, University College Cork, Ireland; 3: Baylor College of Medicine, Houston, TX; 4: Université catholique de Louvain, Brussels, Belgium
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Received 12 January 2017 Accepted 21 February 2017 Published 23 June 2017
- Correspondence: Paul W. O’Toole, [email protected]
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Abstract:
Lactobacilli occupy a unique position in human culture and scientific history. Like brewer’s and baker’s yeast, lactobacilli have been associated with food production and preservation for thousands of years. Lactobacillus species are used in mixed microbial cultures, such as the classical Lactobacillus bulgaricus/Streptococcus thermophilus inoculum for yogurt fermentation, or combinations of diverse lactobacilli/yeasts in kefir grains. The association of lactobacilli consumption with greater longevity and improved health formed the basis for developing lactobacilli as probiotics, whose market has exploded worldwide in the past 10 years. The decade that followed the determination of the first genome sequence of a food-associated species, Lactobacillus plantarum, saw the application to lactobacilli of a full range of functional genomics methods to identify the genes and gene products that govern their distinctive phenotypes and health associations. In this review, we will briefly remind the reader of the range of beneficial effects attributed to lactobacilli, and then explain the phylogenomic basis for the distribution of these traits across the genus. Recognizing the strain specificity of probiotic effects, we review studies of intraspecific genomic variation and their contributions to identifying probiotic traits. Finally we offer a perspective on classification of lactobacilli into new genera in a scheme that will make attributing probiotic properties to clades, taxa, and species more logical and more robust.
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Citation: Salvetti E, O’Toole P. 2017. The Genomic Basis of Lactobacilli as Health-Promoting Organisms. Microbiol Spectrum 5(3):BAD-0011-2016. doi:10.1128/microbiolspec.BAD-0011-2016.




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Abstract:
Lactobacilli occupy a unique position in human culture and scientific history. Like brewer’s and baker’s yeast, lactobacilli have been associated with food production and preservation for thousands of years. Lactobacillus species are used in mixed microbial cultures, such as the classical Lactobacillus bulgaricus/Streptococcus thermophilus inoculum for yogurt fermentation, or combinations of diverse lactobacilli/yeasts in kefir grains. The association of lactobacilli consumption with greater longevity and improved health formed the basis for developing lactobacilli as probiotics, whose market has exploded worldwide in the past 10 years. The decade that followed the determination of the first genome sequence of a food-associated species, Lactobacillus plantarum, saw the application to lactobacilli of a full range of functional genomics methods to identify the genes and gene products that govern their distinctive phenotypes and health associations. In this review, we will briefly remind the reader of the range of beneficial effects attributed to lactobacilli, and then explain the phylogenomic basis for the distribution of these traits across the genus. Recognizing the strain specificity of probiotic effects, we review studies of intraspecific genomic variation and their contributions to identifying probiotic traits. Finally we offer a perspective on classification of lactobacilli into new genera in a scheme that will make attributing probiotic properties to clades, taxa, and species more logical and more robust.

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FIGURE 1
Publication numbers by year using search terms (lactobacillus probiotic) in PubMed. Search performed 13 July 2016.
Tables

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TABLE 1
Selected examples of probiotic traits in lactobacilli

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