Fabienne Baraige

Proteomic Analysis of Global Changes in Protein Expression during Bile Salt Exposure of Bifidobacterium longum NCIMB 8809

Adaptation to and tolerance of bile stress are among the main limiting factors to ensure survival of bifidobacteria in the intestinal environment of humans. The effect of bile salts on protein expression patterns of Bifidobacterium longum was examined. Protein pattern comparison of strains grown with or without bile extract allowed us to identify 34 different proteins whose expression was regulated. The majority of these proteins were induced after both a minor (0.6 g liter(-1)) and a major (1.2 g liter(-1)) exposure to bile. These include general stress response chaperones, proteins involved in transcription and translation and in the metabolism of amino acids and nucleotides, and several enzymes of glycolysis and pyruvate catabolism. Remarkably, xylulose 5-phosphate/fructose 6-phosphate phosphoketolase, the key enzyme of the so-called bifidobacterial shunt, was found to be upregulated, and the activity on fructose 6-phosphate was significantly higher for protein extracts of cells grown in the presence of bile. Changes in the levels of metabolic end products (acetate and lactate) were also detected. These results suggest that bile salts, to which bifidobacteria are naturally exposed, induce a complex physiological response rather than a single event in which proteins from many different functional categories take part. This study has extended our understanding of the molecular mechanism underlying the capacity of intestinal bifidobacteria to tolerate bile.

Low-pH Adaptation and the Acid Tolerance Response of Bifidobacterium longum Biotype longum

ABSTRACT Bifidobacteria are one of the main microbial inhabitants of the human colon. Usually administered in fermented dairy products as beneficial microorganisms, they have to overcome the acidic pH found in the stomach during the gastrointestinal transit to be able to colonize the lower parts of the intestine. The mechanisms underlying acid response and adaptation in Bifidobacterium longum biotype longum NCIMB 8809 and its acid-pH-resistant mutant B. longum biotype longum 8809dpH were studied. Comparison of protein maps, and protein identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis, allowed us to identify nine different proteins whose production largely changed in the mutant strain. Furthermore, the production of 47 proteins was modulated by pH in one or both strains. These included general stress response chaperones and proteins involved in transcription and translation as well as in carbohydrate and nitrogen metabolism, among others. Significant differences in the levels of metabolic end products and in the redox status of the cells were also detected between the wild-type strain and its acid-pH-resistant mutant in response to, or as a result of, adaptation to acid. Remarkably, the results of this work indicated that adaptation and response to low pH in B. longum biotype longum involve changes in the glycolytic flux and in the ability to regulate the internal pH. These changes were accompanied by a higher content of ammonium in the cytoplasm, likely coming from amino acid deamination, and a decrease of the bile salt hydrolase activity.

Adaptation and Response of Bifidobacterium animalis subsp. lactis to Bile: a Proteomic and Physiological Approach

ABSTRACT Bile salts are natural detergents that facilitate the digestion and absorption of the hydrophobic components of the diet. However, their amphiphilic nature makes them very inhibitory for bacteria and strongly influences bacterial survival in the gastrointestinal tract. Adaptation to and tolerance of bile stress is therefore crucial for the persistence of bacteria in the human colonic niche. Bifidobacterium animalis subsp. lactis, a probiotic bacterium with documented health benefits, is applied largely in fermented dairy products. In this study, the effect of bile salts on proteomes of B. animalis subsp. lactis IPLA 4549 and its bile-resistant derivative B. animalis subsp. lactis 4549dOx was analyzed, leading to the identification of proteins which may represent the targets of bile salt response and adaptation in B. animalis subsp. lactis. The comparison of the wild-type and the bile-resistant strain responses allowed us to hypothesize about the resistance mechanisms acquired by the derivative resistant strain and about the bile salt response in B. animalis subsp. lactis. In addition, significant differences in the levels of metabolic end products of the bifid shunt and in the redox status of the cells were also detected, which correlate with some differences observed between the proteomes. These results indicate that adaptation and response to bile in B. animalis subsp. lactis involve several physiological mechanisms that are jointly dedicated to reduce the deleterious impact of bile on the cells physiology.

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

ABSTRACT Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.

A Preliminary Analysis of Bifidobacterium longum Exported Proteins by Two-Dimensional Electrophoresis

Extracellular proteins of Bifidobacterium longum may mediate important interactions with the host. Here, we report on a comprehensive analysis of such proteins by using protein-free culture conditions and two-dimensional gel electrophoresis followed by mass spectrometry for protein identification. Seventeen proteins were detected in the culture supernatant, and 14 of them could be identified. Among these were 3 hypothetical solute-binding proteins of ABC transporters, an invasion-associated protein homolog, putative enzymes catalyzing cell wall turnover, several polypeptides with similarity to bacterial conjugation proteins, and 3 proteins of unknown function. Surprisingly, aldolase, usually considered as a cytoplasmic protein, was found in the culture supernatant. All proteins, excluding aldolase, were predicted to contain a signal peptide and a signal peptide cleavage site in their immature form. Some of the excreted proteins are interesting targets for further genetic and physiological studies.

Adaptive response of Lactobacillus sakei 23K during growth in the presence of meat extracts: A proteomic approach

Lactobacillus sakei is a lactic acid bacterium mainly found in meat and meat products. In order to understand the factors favoring its adaptation to meat matrix, growth parameters and survival of the strain L. sakei 23K in the presence of sarcoplasmic or myofibrillar extracts were assessed. Cytosolic proteins putatively involved in the response of this strain to meat proteins were determined using 2D electrophoresis and the significantly regulated proteins were identified by Maldi Tof-MS analyses. From the 31 differentially expressed spots, 16 occurred in the presence of myofibrillar extract while 6 proteins were modulated by the sarcoplasmic extract. Two dipeptidases were overexpressed in the presence of sarcoplasmic proteins, in correlation to the protein degradation patterns obtained by SDS-PAGE. In the presence of the myofibrillar extract, L. sakei 23K overexpressed proteins related to energy and pyrimidine metabolism as well as ala- and tyr-tRNA synthetases, involved in translation, while others corresponding to general stress response, pyrimidine, vitamin and cofactor biosynthesis were down-regulated. The supplementary nutrients furnished by meat extracts modulated the overexpression of proteins related to translation, peptide/amino acid metabolism and energy production while the stress proteins were under regulated. The results obtained here suggest that meat proteins would not represent a stress environment per se for L. sakei 23K in contrast to the harsh conditions during meat processing. This study has extended the understanding of the molecular responses and growth mechanisms of L. sakei 23K in the presence of meat proteins. The transference of genomic information into useful biological insight is an important step for the selection of well-adapted strains for the achievement of high-quality fermented products.

Proteomic comparison of the cytosolic proteins of three Bifidobacterium longum human isolates and B. longum NCC2705

BackgroundBifidobacteria are natural inhabitants of the human gastrointestinal tract. In full-term newborns, these bacteria are acquired from the mother during delivery and rapidly become the predominant organisms in the intestinal microbiota. Bifidobacteria contribute to the establishment of healthy intestinal ecology and can confer health benefits to their host. Consequently, there is growing interest in bifidobacteria, and various strains are currently used as probiotic components in functional food products. However, the probiotic effects have been reported to be strain-specific. There is thus a need to better understand the determinants of the observed benefits provided by these probiotics. Our objective was to compare three human B. longum isolates with the sequenced model strain B. longum NCC2705 at the chromosome and proteome levels.ResultsPulsed field electrophoresis genotyping revealed genetic heterogeneity with low intraspecies strain relatedness among the four strains tested. Using two-dimensional gel electrophoresis, we analyzed qualitative differences in the cytosolic protein patterns. There were 45 spots that were present in some strains and absent in others. Spots were excised from the gels and subjected to peptide mass fingerprint analysis for identification. The 45 spots represented 37 proteins, most of which were involved in carbohydrate metabolism and cell wall or cell membrane synthesis. Notably, the protein patterns were correlated with differences in cell membrane properties like surface hydrophobicity and cell agglutination.ConclusionThese results showed that proteomic analysis can be valuable for investigating differences in bifidobacterial species and may provide a better understanding of the diversity of bifidobacteria and their potential use as probiotics.

Response of a Lactobacillus plantarum human isolate to tannic acid challenge assessed by proteomic analyses.

SCOPE To gain insight on the mechanisms used by intestinal bacteria to adapt and resist the antimicrobial action of dietary tannins and identify targets for tannic acid in Lactobacillus plantarum. METHODS AND RESULTS A proteomic analysis of an L. plantarum human isolate exposed to the tannic acid challenge was undertaken. Tannic acid targeted proteins involved in outstanding processes for bacterial stress resistance including cyclopropanation of membrane lipids, stress response at population scale and maintenance of cell shape. To respond to this aggression, tannic acid-misfit cells of L. plantarum challenged with tannic acid reorganized their metabolic capacity to economize energy and express proteins involved in oxidative stress defense and cell wall biogenesis, indicating that the injury incurred by tannic acid was based on oxidative damage and disruption of the cell envelope. The induction of 3-octaprenyl-4-hydroxybenzoate carboxy-lyase, which is sensitive to changes in redox conditions and involved in ubiquinone biosynthesis in other bacteria, suggests for a tannic acid-induced redox imbalance. CONCLUSION The results reveal the adaptation of a gastrointestinal isolate of L. plantarum to tannic acid and identify antibacterial targets for this dietary compound. This provides the basis for the selection of tannin-resistant microorganisms and their use to obtain health benefits from tannin-containing diets.

Analysis of Lactobacillus sakei Mutants Selected after Adaptation to the Gastrointestinal Tracts of Axenic Mice

ABSTRACT We recently showed that Lactobacillus sakei, a natural meat-borne lactic acid bacterium, can colonize the gastrointestinal tracts (GIT) of axenic mice but that this colonization in the intestinal environment selects L. sakei mutants showing modified colony morphology (small and rough) and cell shape, most probably resulting from the accumulation of various mutations that confer a selective advantage for persistence in the GIT. In the present study, we analyzed such clones, issued from three different L. sakei strains, in order to determine which functions were modified in the mutants. In the elongated filamentous cells of the rough clones, transmission electron microscopy (TEM) analysis showed a septation defect and dotted and slanted black bands, suggesting the presence of a helical structure around the cells. Comparison of the cytoplasmic and cell wall/membrane proteomes of the meat isolate L. sakei 23K and of one of its rough derivatives revealed a modified expression for 38 spots. The expression of six oxidoreductases, several stress proteins, and four ABC transporters was strongly reduced in the GIT-adapted strain, while the actin-like MreB protein responsible for cell shaping was upregulated. In addition, the expression of several enzymes involved in carbohydrate metabolism was modified, which may correlate with the observation of modified growth of mutants on various carbon sources. These results suggest that the modifications leading to a better adaptation to the GIT are pleiotropic and are characterized in a rough mutant by a different stress status, a cell wall modification, and modified use of energy sources, leading to an improved fitness for the colonization of the GIT.