Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium
            <i>Lactobacillus sakei</i>

Chaillou, Stéphane; Daty, Marie; Baraige, Fabienne; Dudez, Anne Marie; Anglade, Patricia; Jones, Rhys J.; Alpert, Carl-Alfred; Champomier‐Vergès, Marie‐Christine; Zagorec, Monique

doi:10.1128/aem.01721-08

Cited by 67 publications

(76 citation statements)

References 43 publications

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“…We then compared their genome sizes and organizations. PFGE analysis showed that L. sakei FLEC01 harbored seven rrn operons distributed on the chromosome, as previously observed for L. sakei (11,20,32). The genome size of L. sakei FLEC01 was evaluated to be 1,966 Ϯ 5 kb, thus, comparable to those of L. sakei 23K (1,885 kb) (20) and LTH5590 (1,915 Ϯ 22 kb) (11).…”

Section: Resultsmentioning

confidence: 58%

“…sakei shows high degrees of phenotypic and genomic diversity (11)(12)(13) that may explain the difficult detection and misidentification of it in the past. For instance, although the human gut microbiota has been intensively investigated by different microbial and molecular methods for many years, the presence of L. sakei in the feces of healthy humans was reported only recently (16,17,26,39).…”

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confidence: 99%

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Behavior of the Meat-Borne Bacterium Lactobacillus sakei during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice

Chiaramonte

Blugeon²,

Chaillou

et al. 2009

Appl Environ Microbiol

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A Lactobacillus sakei strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne L. sakei strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three L. sakei strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10 9 CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total L. sakei population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that L. sakei is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of Escherichia coli strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade grampositive bacterium for the first time.Although initially characterized from rice wine (28), the lactic acid bacterium species Lactobacillus sakei is considered the main representative flora of meat products, representing the major population of many fermented meat products and of raw meat stored under vacuum-packaged conditions (10,12,13). L. sakei is naturally present in many fish and meat products that are traditionally processed without the use of starter cultures (33). In addition, when small-scale facilities producing traditional dry fermented sausage were searched, L. sakei was detected only in the meat matrix, suggesting that meat is contaminated by this species mainly during the early processing steps (certainly by hide or feces of the animals) and not later on or by contact with the environment or materials within the facilities (2).L. sakei shows high degrees of phenotypic and genomic diversity (11-13) that may explain the difficult detection and misidentification of it in the past. For instance, although the human gut microbiota has been intensively investigated by different microbial and molecular methods for many years, the presence of L. sakei in the feces of healthy humans was reported only recently (16,17,26,39). The presence of the meat-borne species L. sakei in human feces, similar to that of several other lactobacilli, could be correlated to human diet, including raw and fermented meat (or fish), for millennia (37). Considering its relatively high concentration in human feces (10 6 per g) that was p...

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Section: Resultsmentioning

confidence: 58%

mentioning

confidence: 99%

Behavior of the Meat-Borne Bacterium Lactobacillus sakei during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice

Chiaramonte

Blugeon²,

Chaillou

et al. 2009

Appl Environ Microbiol

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“…It has already been shown that pathways responsible for biogenic amine production are strain specific, with horizontal gene transfer being the mechanism responsible for this strain variation (8). Although extensive intraspecies genomic variability within L. sakei has been shown before (3,24), its occurrence solely in meat isolates may suggest a putative role of the AgDI pathway in meat adaptation. The two L. sakei strains with an operational AgDI pathway were able to produce the biogenic amine putrescine from agmatine through the AgDI pathway, thereby producing ammonia toward acid stress and extra ATP to improve competitiveness.…”

Section: Discussionmentioning

confidence: 99%

Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH

Rimaux

Rivière

Illeghems

et al. 2012

Appl Environ Microbiol

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ABSTRACTThe adaptation ofLactobacillus sakeito a meat environment is reflected in its metabolic potential. For instance, the ability to utilize arginine through the arginine deiminase (ADI) pathway, resulting in additional ATP, represents a competitive benefit. InL. sakeiCTC 494, thearcoperon (arcABCTDR) shows the same gene order and organization as that inL. sakei23K, the genome sequence of which is known. However, differences in relative gene expression were found, and these seemed to be optimal in different growth phases, namely, the highest relative gene expression level was in the end exponential growth phase in the case ofL. sakeiCTC 494 and in the mid-exponential growth phase ofL. sakei23K. Also, the environmental pH influenced the relative expression level of thearcoperon, as shown forL. sakeiCTC 494, with the highest relative expression level occurring at the optimal pH for growth (pH 6.0). Deviations from this optimal pH (pH 5.0 and pH 7.0) resulted in an overall decline of the relative expression level of all genes of thearcoperon. Furthermore, a differential relative expression of the individual genes of thearcoperon was found, with the highest relative gene expression occurring for the first two genes of thearcoperon (arcAandarcB). Finally, it was shown that someL. sakeistrains were able to convert agmatine into putrescine, suggesting an operational agmatine deiminase pathway in these strains, a metabolic trait that is undesirable in meat fermentations. This study shows that this metabolic trait is most probably encoded by a previously erroneously annotated second putativearcoperon.

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“…25) Previous study of the C. albicans isolate ATCC10231 identified 42 variable genes, including 5 amplified, and 37 absent/divergent genes, as compared with SC5314.…”

Section: Discussionmentioning

confidence: 99%

High-Frequency Genetic Contents Variations in Clinical Candida albicans Isolates

Yang

Yan

Rustchenko

et al. 2011

Biological & Pharmaceutical Bulletin

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Candida albicans is the most common fungal pathogen, causing skin and mucosal infections in generally healthy individuals, life-threatening infections in immunocompromised patients, and leading to death in up to 50% of patients with bloodstream infections. 1,2)C. albicans is known for its unstable genome. The instability of the chromosome copy number of entire chromosomes, as well as the large portions of chromosomes was extensively studied with laboratory and freshly isolated strains using pulse-field gene electrophoresis (PFGE) as reviewed by Rustchenko,3) Rustchenko and Sherman,4) and Selmecki et al. 5) Combined with Southern blot analysis, PFGE allowed limited analysis of gene copy number, and also could be extended to the analysis of chromosome deletions and other rearrangements. [6][7][8][9][10][11][12][13][14][15] Recently, array technology opened a new dimension in the study of genome instability. Array comparative genomic hybridization (array CGH) allows the detection of genomic variations across a whole genome. When the CGH intensity data are plotted as a function of position on the genetic map, aneuploidy of chromosomes or chromosomal segments are readily identified. The availability of the C. albicans strain SC5314 genome sequence has allowed the construction of microarrays for the analysis of gene copy number. Berman's laboratory largely used array CGH to demonstrate aneuploidies in C. albicans derivatives of the sequencing strain SC5314, several laboratory strains, as well as clinical isolates, as reviewed by Selmecki et al. 5)Also, Thewes et al. 16) used array CGH to elucidate the genomic diversity among C. albicans less virulent strain ATCC10231 and the reference sequencing strain SC5314 in the hope to uncover genetic basis of pathogenicity. Although some variable genes were identified, this study was limited to a single strain.Despite the extensive effort of various laboratories, a comprehensive study, which would include various strains and which would focus on the DNA sequence and gene copy number variability is still lacking, although this approach was applied to other organisms, including Saccharomyces cerevisiae. 17,18) In order to fill this need, we examined the genomic contents of eight clinical isolates, as compared to the SC5314 reference strain, using array CGH. The Cluster Along Chromosomes (CLAC) algorithm was employed to identify variable genes. Medical School; Rochester, N.Y., 14642, U.S.A.: and c Department of Pharmacology, School of Pharmacy, Second Military Medical University; Shanghai 200433, China. Received October 25, 2010; accepted January 24, 2011; published online February 16, 2011 Genome plasticity is a hallmark of Candida albicans and is believed to be an adaptation strategy. But the extent of such genomic variability is not well investigated. In this study, genetic contents of clinical C. albicans isolates were investigated at whole-genome level with array-based comparative genomic hybridization (array CGH) technology. It was revealed that C. albicans possess...

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Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei

Cited by 67 publications

References 43 publications

Behavior of the Meat-Borne Bacterium Lactobacillus sakei during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice

Behavior of the Meat-Borne Bacterium Lactobacillus sakei during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice

Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH

High-Frequency Genetic Contents Variations in Clinical Candida albicans Isolates

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