Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods

Rahkila, Riitta; Johansson, Per; Säde, Elina; Paulín, Lars; Auvinen, Petri; Björkroth, Johanna

doi:10.1128/aem.04013-14

Cited by 13 publications

(15 citation statements)

References 34 publications

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“…These factors, and the interactions among them, have the potential to generate a wide diversity of bacterial strains through selective pressures. Furthermore, many food-borne bacteria that are involved in spoilage also display broad genomic diversity at the intraspecies level [ 11 – 15 ]. Within a given species, certain strains may carry key gene clusters involved in the fitness or adaptation to specific conditions or in the production of compounds important for food fermentation or spoilage while other strains do not.…”

Section: Introductionmentioning

confidence: 99%

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Poirier¹,

Rué²,

Peguilhan³

et al. 2018

PLoS ONE

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Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.

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Section: Introductionmentioning

confidence: 99%

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Poirier¹,

Rué²,

Peguilhan³

et al. 2018

PLoS ONE

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“…) and Leuconostoc gelidum (Rahkila et al . ) have been recognized as the dominant species in vegetable and animal foods that are stored at cold temperature for long time. The hypermutable state of Oenococcus oeni , that separated it from the branch of the neighbouring taxon Leuconostoc , has been revealed to be the consequence of the lack of the mutation mismatch repair genes (Marcobal et al .…”

Section: Introductionmentioning

confidence: 99%

“…Since the current available starter cultures do not perform this biologic transformation in wine at temperatures lower than 15°C, the winemakers of the Aosta Valley are mostly reluctant to induce MLF by using selected strains, which have not previously given positive results. Actually, within the genus Leuconostoc, to which Oenococcus belonged until a former past (Dicks et al 1995), the psychrotrophic character have been documented and in particular Leuconostoc mesenteroides (Yamaner et al 2010) and Leuconostoc gelidum (Rahkila et al 2015) have been recognized as the dominant species in vegetable and animal foods that are stored at cold temperature for long time. The hypermutable state of Oenococcus oeni, that separated it from the branch of the neighbouring taxon Leuconostoc, has been revealed to be the consequence of the lack of the mutation mismatch repair genes (Marcobal et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Characterization of malolactic bacteria isolated from Aosta Valley wines and evidence of psychrotrophy in some strains

et al. 2016

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The natural emergence of strains able to perform the MLF at 10°C in wine is a new finding, interesting because it confirms the ecological ability of O. oeni species to adapt itself to environmental conditions by strain phenotype variations. It can be also a starting point for more sustainable oenological practices, since it would be alternative to the conditioning systems of the tanks or of the wineries where they are costly in terms of investment and energy consumption.

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“…toxicus . Therefore, a more analytical approach for identifying informative genome regions for MLST may be necessary to finely resolve population structure in some pathogenic bacteria [ 46 ]. This result also supports the value of pan-genomic analysis for the identification of gene targets of value to ecological investigations that require the identification of pathogenic bacteria at sub-specific levels of discrimination (e.g., race, pathovar, biovar) [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium

Arif

Busot

Mann³

et al. 2016

PLoS ONE

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Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of isolation was determined for isolates collected over a forty-year period. Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. Population RT-I, detected in 2013 and 2014 from the Yorke Peninsula in South Australia, is a newly emerged population of R. toxicus not previously reported. Commonly used housekeeping genes failed to discriminate among the R. toxicus isolates. However, strategically selected and genome-dispersed MLST genes representing an array of cellular functions from chromosome replication, antibiotic resistance and biosynthetic pathways to bacterial acquired immunity were discriminative. Genetic variation among isolates within the RT-I population was less than the within-population variation for the previously reported RT-II and RT-III populations. The lower relative genetic variation within the RT-I population and its absence from sampling over the past 40 years suggest its recent emergence. RT-I was the dominant population on the Yorke Peninsula during the 2013–2014 sampling period perhaps indicating a competitive advantage over the previously detected RT-II population. The potential for introduction of this bacterial plant pathogen into new geographic areas provide a rationale for understanding the ecological and evolutionary trajectories of R. toxicus.

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Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods

Cited by 13 publications

References 34 publications

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

Characterization of malolactic bacteria isolated from Aosta Valley wines and evidence of psychrotrophy in some strains

Emergence of a New Population of Rathayibacter toxicus: An Ecologically Complex, Geographically Isolated Bacterium

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