Genomics of lactic acid bacteria

Schroeter, Joel; Klaenhammer, Todd R.

doi:10.1111/j.1574-6968.2008.01442.x

Cited by 47 publications

(43 citation statements)

References 35 publications

(47 reference statements)

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“…Because of their industrial relevance, numerous LAB genome sequencing initiatives have been conducted (13,17,32). Comparative genomics of LAB has revealed the existence of a large inter-and intraspecies genomic diversity (4,5,9,18,26,27,35,39).…”

mentioning

confidence: 99%

Molecular Description and Industrial Potential of Tn 6098 Conjugative Transfer Conferring Alpha-Galactoside Metabolism in Lactococcus lactis

Machielsen

Siezen

Hijum

et al. 2011

Appl Environ Microbiol

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A novel 51-kb conjugative transposon of Lactococcus lactis, designated Tn6098, encoding the capacity to utilize ␣-galactosides such as raffinose and stachyose, was identified and characterized. Alpha-galactosides are a dominant carbon source in many plant-derived foods. Most dairy lactococcus strains are unable to use ␣-galactosides as a growth substrate, yet many of these strains are known to have beneficial industrial traits. Conjugal transfer of Tn6098 was demonstrated from the plant-derived donor strain L. lactis KF147 to the recipient L. lactis NZ4501, a derivative of the dairy model strain L. lactis MG1363. The integration of Tn6098 into the genome of the recipient strain was confirmed by Illumina sequencing of the transconjugant L. lactis NIZO3921. The molecular structure of the integration site was confirmed by a PCR product spanning the insertion site. A 15-bp direct repeat sequence (TTATACCATAATTAC) is present on either side of Tn6098 in the chromosome of L. lactis KF147. One copy of this sequence is also present in the L. lactis MG1363 chromosome and represents the sole integration site. Phenotypic characterization of all strains showed that the transconjugant has not only acquired the ability to grow well in soy milk, a substrate rich in ␣-galactosides, but also has retained the flavor-forming capabilities of the recipient strain L. lactis MG1363. This study demonstrates how (induced) conjugation can be used to exploit the beneficial industrial traits of industrial dairy lactic acid bacteria in fermentation of plant-derived substrates.Lactic acid bacteria (LAB) are widely applied in food fermentations, where they contribute to the organoleptic, preservation, and health properties of the fermented food stuffs. Because of their industrial relevance, numerous LAB genome sequencing initiatives have been conducted (13,17,32). Comparative genomics of LAB has revealed the existence of a large inter-and intraspecies genomic diversity (4,5,9,18,26,27,35,39). Horizontal gene transfer (HGT) appears to be a primary driver in LAB evolution and the creation of diversity. HGT is facilitated by the widespread occurrence of plasmids, phages, and mobile genetic elements such as insertion sequence (IS) elements and conjugative transposons, which serve as effective vectors for the spread of genes and traits within and over the species barrier (20,40).Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, especially cheese and butter. Because of its tremendous industrial importance, it has long been the primary model organism for LAB research revealing molecular insight into many traits relevant for industrial applications, including the production of flavor compounds, vitamins and other nutraceuticals, and exopolysaccharides relevant for texture development (3, 8, 39).L. lactis occupies two distinct niches. The occurrence of the species in dairy substrates has long been described, and L. lactis strains are readily isolated from artisanal and spontaneo...

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confidence: 99%

Molecular Description and Industrial Potential of Tn 6098 Conjugative Transfer Conferring Alpha-Galactoside Metabolism in Lactococcus lactis

Machielsen

Siezen

Hijum

et al. 2011

Appl Environ Microbiol

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“…Although genome reduction in bacteria has been shown to be commonly associated with a transition of a saprotrophic to a pathogenic or obligate symbiotic lifestyle (7,28), it has also been shown to occur in the adaptation to nutrient-rich food environments in Lactobacillus species (43). This suggests that genome reduction is generally associated with niche specialization and may indicate that strains of pathogenic and nonpathogenic Listeria with a small genome are more specialized to a specific niche than strains with a larger genome.…”

Section: Discussionmentioning

confidence: 88%

FSL J1-208, a Virulent Uncommon Phylogenetic Lineage IV Listeria monocytogenes Strain with a Small Chromosome Size and a Putative Virulence Plasmid Carrying Internalin-Like Genes

Bakker

Bowen

Rodriguez‐Rivera

et al. 2012

Appl Environ Microbiol

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The bacterial genus Listeria contains both saprotrophic and facultative pathogenic species. A small genome size has been suggested to be associated with the loss of pathogenic potential of L. welshimeri and L. seeligeri. In this paper we present data on the genome of L. monocytogenes strain FSL J1-208, a representative of phylogenetic lineage IV. Although this strain was isolated from a clinical case in a caprine host and has no decreased invasiveness in human intestinal epithelial cells, our analyses show that this strain has one of the smallest Listeria chromosomes reported to date (2.78 Mb). The chromosome contains 2,772 protein-coding genes, including well-characterized virulence-associated genes, such as inlA, inlB, and inlC and the full prfA gene cluster. The small genome size is mainly caused by the absence of prophages in the genome of L. monocytogenes FSL J1-208, and further analyses showed that the total size of prophage-related regions is highly correlated to chromosome size in the genus Listeria. L. monocytogenes FSL J1-208 carries a unique type of plasmid of approximately 80 kbp that does not carry genes annotated as being involved in resistance to antibiotics or heavy metals. The accessory genes in this plasmid belong to the internalin family, a family of virulence-associated proteins, and therefore this is the first report of a potential virulence plasmid in the genus Listeria.

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“…vary in size (0.87 kb to more than 250 kb), copy number (1 or more per cell) and gene content [43][44][45][46].…”

Section: Fluorescent Reporters and Their Applications For In Vivo Imamentioning

confidence: 99%

The Microbiome of Spodoptera littoralis: Development, Control and Adaptation to the Insect Host

Mazumdar¹,

Teh²,

Boland³

2018

Metagenomics for Gut Microbes

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The symbiotic microbial consortium in the gut of Spodoptera littoralis shows dramatic, but reproducible changes in line with the development of the insect from the egg via six larval instars to the pupa. Since the food is kept constant during development, factors from the insect host and certain microbial symbionts are assumed to control the composition of the microbiome. A GFP-tagged Enterococcus mundtii, one of the major players of the consortium, easily integrates into the microbiome and can be monitored in all gut segments at all developmental stages. The reporter organism can be recovered from the gut using a preparative flow cytometry allowing subsequent RNA extraction for transcriptomic analyses. The transcriptomic profile from the fluorescent Enterococcus cells provides information on the adaptation of the reporter organism to the local gut conditions. The concept of using a fluorescent reporter organism that can be recovered at any time from any area of the intestinal tract will allow a holistic analysis of adaptation strategies used by the microbes to adapt to the insect gut. In combination with the analysis of transcript patterns from the gut membranes, a first insight into the molecular interaction between the insect host and the microbiome can be expected.

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Genomics of lactic acid bacteria

Cited by 47 publications

References 35 publications

Molecular Description and Industrial Potential of Tn 6098 Conjugative Transfer Conferring Alpha-Galactoside Metabolism in Lactococcus lactis

Molecular Description and Industrial Potential of Tn 6098 Conjugative Transfer Conferring Alpha-Galactoside Metabolism in Lactococcus lactis

FSL J1-208, a Virulent Uncommon Phylogenetic Lineage IV Listeria monocytogenes Strain with a Small Chromosome Size and a Putative Virulence Plasmid Carrying Internalin-Like Genes

The Microbiome of Spodoptera littoralis: Development, Control and Adaptation to the Insect Host

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