Shigella is a major foodborne pathogen that infects humans and non-human primates and is the majo... more Shigella is a major foodborne pathogen that infects humans and non-human primates and is the major cause of dysentery and reactive arthritis worldwide. This is the initial public release of 16 Shigella genome sequences from four species sequenced as part of the 100K Pathogen Genome Project.
Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This public... more Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public release of 15 Campylobacter jejuni genome sequences from isolates linked to abortion in livestock. These isolates are part of the 100K Pathogen Genome Project and are from clinical cases at the University of California (UC) Davis.
Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including Amer... more Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings and are likely zoonotic vectors of Campylobacter. Their proximity to humans and livestock increases the potential spreading of Campylobacter via crows between the environment, livestock, and humans. However , no studies have definitively demonstrated that crows are a vector for pathogenic Campylobacter. We used genomics to evaluate the zoonotic and pathogenic potential of Campylobacter from crows to other animals with 184 isolates obtained from crows, chickens, cows, sheep, goats, humans, and nonhuman primates. Whole-genome analysis uncovered two distinct clades of Campylobacter jejuni genotypes; the first contained genotypes found only in crows, while a second genotype contained " generalist " genomes that were isolated from multiple host species, including isolates implicated in human disease, primate gastroenteritis, and livestock abortion. Two major-lactamase genes were observed frequently in these genomes (oxa-184, 55%, and oxa-61, 29%), where oxa-184 was associated only with crows and oxa-61 was associated with generalists. Mutations in gyrA, indicative of fluoroquinolone resistance, were observed in 14% of the isolates. Tetracycline resistance (tetO) was present in 22% of the isolates, yet it occurred in 91% of the abortion isolates. Virulence genes were distributed throughout the genomes; however, cdtC alleles recapitulated the crow-only and generalist clades. A specific cdtC allele was associated with abortion in livestock and was concomitant with tetO. These findings indicate that crows harboring a generalist C. jejuni genotype may act as a vector for the zoonotic transmission of Campylobacter. IMPORTANCE This study examined the link between public health and the genomic variation of Campylobacter in relation to disease in humans, primates, and livestock. Use of large-scale whole-genome sequencing enabled population-level assessment to find new genes that are linked to livestock disease. With 184 Campylobacter genomes, we assessed virulence traits, antibiotic resistance susceptibility, and the potential for zoonotic transfer to observe that there is a " generalist " genotype that may move between host species.
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 2002
This review summarizes a collection of lactic acid bacteria that are now undergoing genomic seque... more This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis.
Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We... more Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We report complete genome sequences for two V. parahaemolyticus strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin, respectively. These two sequences might assist in the investigation of differential virulence of this organism.
Applied and Environmental Microbiology, Sep 1, 1998
Methanethiol has been strongly associated with desirable Cheddar cheese flavor and can be formed ... more Methanethiol has been strongly associated with desirable Cheddar cheese flavor and can be formed from the degradation of methionine (Met) via a number of microbial enzymes. Methionine ␥-lyase is thought to play a major role in the catabolism of Met and generation of methanethiol in several species of bacteria. Other enzymes that have been reported to be capable of producing methanethiol from Met in lactic acid bacteria include cystathionine -lyase and cystathionine ␥-lyase. The objective of this study was to determine the production, stability, and activities of the enzymes involved in methanethiol generation in bacteria associated with cheese making. Lactococci and lactobacilli were observed to contain high levels of enzymes that acted primarily on cystathionine. Enzyme activity was dependent on the concentration of sulfur amino acids in the growth medium. Met aminotransferase activity was detected in all of the lactic acid bacteria tested and ␣ketoglutarate was used as the amino group acceptor. In Lactococcus lactis subsp. cremoris S2, Met aminotransferase was repressed with increasing concentrations of Met in the growth medium. While no Met aminotransferase activity was detected in Brevibacterium linens BL2, it possessed high levels of L-methionine ␥-lyase that was induced by addition of Met to the growth medium. Met demethiolation activity at pH 5.2 with 4% NaCl was not detected in cell extracts but was detected in whole cells. These data suggest that Met degradation in Cheddar cheese will depend on the organism used in production, the amount of enzyme released during aging, and the amount of Met in the matrix.
The o-phthaldialdehyde test and amino acid analysis were used to characterize proteolysis of milk... more The o-phthaldialdehyde test and amino acid analysis were used to characterize proteolysis of milk proteins during growth of Lactobacillus delbrueckii ssp. bulgaricus. Thirty-four strains were incubated in sterile 10% NDM for 12 h. Extent of proteolysis as estimated by the 0-phthaldialdehyde test revealed a large variance in total proteolysis. For seven strains, trichloroacetic acid filtrates of inoculated 10% NDM were analyzed by classical ion-exchange amino acid analysis. Each strain had a distinct pattern of individual amino acid concentrations. Amino acid profiles provided information about the proteolytic activity of these strains that was not available from the ophthaldiddehyde test. Cluster analysis, based on amino acid profiles of each strain, differentiated the seven strains beyond what was possible by visual comparison of the amino acid analysis results. (Key words: thermolactic cultures, proteolysis, amino acid analysis, Lactobacillus delbrueckii ssp. bulgaricus) Abbreviation key: OPA = o-phthaldialdehyde test, TNBS = triniaobenzene sulfonic acid assay. REFERENCES 1 Accolas, I. P., and J. Auclair. 1983. Thermophilic lactic startm. Ir. J. Food Sci. Technol. 727. LAttan, D., P. Laloi, and R. Portalicr. 1989. Isolation a d charactfaizatim of aminopepti-deficient &IC-roboc111~ bJgoricus mutants. Appl. Enviroa Miaobiol. 55:1717.
Newborns are colonized with an intestinal microbiota shortly after birth but the factors governin... more Newborns are colonized with an intestinal microbiota shortly after birth but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-Nneotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when bi-associated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucusadapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion.
We developed a method for concentrating pathogens from samples without enrichment. Immobilized ga... more We developed a method for concentrating pathogens from samples without enrichment. Immobilized gangliosides concentrated bacteria for detection with real-time PCR. A sensitivity of ϳ4 CFU/ml (3 h) in samples without competing microflora was achieved. Samples with competing microflora had a sensitivity of 40,000 CFU/ml. The variance was less than one cycle.
ABSTRACT Lactic acid bacteria are exposed to a series of stresses during environmental transit an... more ABSTRACT Lactic acid bacteria are exposed to a series of stresses during environmental transit and food fermentation processes. Stresses unique to fermented foods are high acid, low temperature, and limited to no free sugar. In fermented foods, lactobacilli and lactococci recently have been recognized to become nonculturable (NC) under these conditions. It has been shown that lactococci become NC under carbohydrate starvation, which leads to additional metabolic changes during 180 days of incubation. Important end products include branched-chain fatty acids from the catabolism of branched-chain amino acids. In addition, sulfur metabolism changes. It has yet to be demonstrated that NC lactococci can be resuscitated with known compounds or peptides. The NC state of lactococci leads to new metabolic end products not produced during log-phase growth.
Volatile sulfur compounds such as methanethiol, dimethyl disulfide, dimethyl trisulfide, and hydr... more Volatile sulfur compounds such as methanethiol, dimethyl disulfide, dimethyl trisulfide, and hydrogen sulfide constitute an important fraction of Cheddar cheese flavor. These compounds are products of the catabolism of methionine and cysteine by bacteria in the cheese matrix. The objectives of this study were to examine the levels and types of volatile sulfur compounds produced from methionine by lactic acid bacteria frequently used in cheese making and to investigate cystathionine degrading activity, which may be responsible for the liberation of these compounds. Gas chromatography with headspace sampling was used to determine volatile sulfur compounds (VSC) produced by whole cells of 24 strains of lactobacilli and 13 strains of lactococci incubated with methionine. Total VSC production varied widely in the species and subspecies tested. Nearly all strains produced VSC from methionine, but the enzyme responsible for this activity remains unclear. Cystathionine-degrading ability and...
Lactic acid bacteria have been reported to be useful as a health adjunct and are commonly added t... more Lactic acid bacteria have been reported to be useful as a health adjunct and are commonly added to food as the delivery mechanism. The literature contains many conflicting observations for their proposed benefits, and the mechanism of action is undefined. One source of variation is the large number of strains used without proper controls supplemented. Additionally, many of the organisms are not characterized for their acid shock response or the acid-tolerance response, which are known to vary among bacterial species. Our objective was to isolate acid-resistant and bile-resistant variants of Lactobacillus acidophilus and to determine the phenotypic changes. The acid- and bile-tolerant isolates were obtained using natural selection techniques after sequential exposure to hydrochloric acid (pH 3.5 to 7.0) and mixed bile salts. The acid- and bile-tolerant isolates retained their ability to grow at pH 3.5 with 0.3% bile after the selective pressure was removed and reapplied. Isolates var...
Shigella is a major foodborne pathogen that infects humans and non-human primates and is the majo... more Shigella is a major foodborne pathogen that infects humans and non-human primates and is the major cause of dysentery and reactive arthritis worldwide. This is the initial public release of 16 Shigella genome sequences from four species sequenced as part of the 100K Pathogen Genome Project.
Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This public... more Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public release of 15 Campylobacter jejuni genome sequences from isolates linked to abortion in livestock. These isolates are part of the 100K Pathogen Genome Project and are from clinical cases at the University of California (UC) Davis.
Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including Amer... more Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings and are likely zoonotic vectors of Campylobacter. Their proximity to humans and livestock increases the potential spreading of Campylobacter via crows between the environment, livestock, and humans. However , no studies have definitively demonstrated that crows are a vector for pathogenic Campylobacter. We used genomics to evaluate the zoonotic and pathogenic potential of Campylobacter from crows to other animals with 184 isolates obtained from crows, chickens, cows, sheep, goats, humans, and nonhuman primates. Whole-genome analysis uncovered two distinct clades of Campylobacter jejuni genotypes; the first contained genotypes found only in crows, while a second genotype contained " generalist " genomes that were isolated from multiple host species, including isolates implicated in human disease, primate gastroenteritis, and livestock abortion. Two major-lactamase genes were observed frequently in these genomes (oxa-184, 55%, and oxa-61, 29%), where oxa-184 was associated only with crows and oxa-61 was associated with generalists. Mutations in gyrA, indicative of fluoroquinolone resistance, were observed in 14% of the isolates. Tetracycline resistance (tetO) was present in 22% of the isolates, yet it occurred in 91% of the abortion isolates. Virulence genes were distributed throughout the genomes; however, cdtC alleles recapitulated the crow-only and generalist clades. A specific cdtC allele was associated with abortion in livestock and was concomitant with tetO. These findings indicate that crows harboring a generalist C. jejuni genotype may act as a vector for the zoonotic transmission of Campylobacter. IMPORTANCE This study examined the link between public health and the genomic variation of Campylobacter in relation to disease in humans, primates, and livestock. Use of large-scale whole-genome sequencing enabled population-level assessment to find new genes that are linked to livestock disease. With 184 Campylobacter genomes, we assessed virulence traits, antibiotic resistance susceptibility, and the potential for zoonotic transfer to observe that there is a " generalist " genotype that may move between host species.
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, 2002
This review summarizes a collection of lactic acid bacteria that are now undergoing genomic seque... more This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis.
Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We... more Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We report complete genome sequences for two V. parahaemolyticus strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin, respectively. These two sequences might assist in the investigation of differential virulence of this organism.
Applied and Environmental Microbiology, Sep 1, 1998
Methanethiol has been strongly associated with desirable Cheddar cheese flavor and can be formed ... more Methanethiol has been strongly associated with desirable Cheddar cheese flavor and can be formed from the degradation of methionine (Met) via a number of microbial enzymes. Methionine ␥-lyase is thought to play a major role in the catabolism of Met and generation of methanethiol in several species of bacteria. Other enzymes that have been reported to be capable of producing methanethiol from Met in lactic acid bacteria include cystathionine -lyase and cystathionine ␥-lyase. The objective of this study was to determine the production, stability, and activities of the enzymes involved in methanethiol generation in bacteria associated with cheese making. Lactococci and lactobacilli were observed to contain high levels of enzymes that acted primarily on cystathionine. Enzyme activity was dependent on the concentration of sulfur amino acids in the growth medium. Met aminotransferase activity was detected in all of the lactic acid bacteria tested and ␣ketoglutarate was used as the amino group acceptor. In Lactococcus lactis subsp. cremoris S2, Met aminotransferase was repressed with increasing concentrations of Met in the growth medium. While no Met aminotransferase activity was detected in Brevibacterium linens BL2, it possessed high levels of L-methionine ␥-lyase that was induced by addition of Met to the growth medium. Met demethiolation activity at pH 5.2 with 4% NaCl was not detected in cell extracts but was detected in whole cells. These data suggest that Met degradation in Cheddar cheese will depend on the organism used in production, the amount of enzyme released during aging, and the amount of Met in the matrix.
The o-phthaldialdehyde test and amino acid analysis were used to characterize proteolysis of milk... more The o-phthaldialdehyde test and amino acid analysis were used to characterize proteolysis of milk proteins during growth of Lactobacillus delbrueckii ssp. bulgaricus. Thirty-four strains were incubated in sterile 10% NDM for 12 h. Extent of proteolysis as estimated by the 0-phthaldialdehyde test revealed a large variance in total proteolysis. For seven strains, trichloroacetic acid filtrates of inoculated 10% NDM were analyzed by classical ion-exchange amino acid analysis. Each strain had a distinct pattern of individual amino acid concentrations. Amino acid profiles provided information about the proteolytic activity of these strains that was not available from the ophthaldiddehyde test. Cluster analysis, based on amino acid profiles of each strain, differentiated the seven strains beyond what was possible by visual comparison of the amino acid analysis results. (Key words: thermolactic cultures, proteolysis, amino acid analysis, Lactobacillus delbrueckii ssp. bulgaricus) Abbreviation key: OPA = o-phthaldialdehyde test, TNBS = triniaobenzene sulfonic acid assay. REFERENCES 1 Accolas, I. P., and J. Auclair. 1983. Thermophilic lactic startm. Ir. J. Food Sci. Technol. 727. LAttan, D., P. Laloi, and R. Portalicr. 1989. Isolation a d charactfaizatim of aminopepti-deficient &IC-roboc111~ bJgoricus mutants. Appl. Enviroa Miaobiol. 55:1717.
Newborns are colonized with an intestinal microbiota shortly after birth but the factors governin... more Newborns are colonized with an intestinal microbiota shortly after birth but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-Nneotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when bi-associated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucusadapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion.
We developed a method for concentrating pathogens from samples without enrichment. Immobilized ga... more We developed a method for concentrating pathogens from samples without enrichment. Immobilized gangliosides concentrated bacteria for detection with real-time PCR. A sensitivity of ϳ4 CFU/ml (3 h) in samples without competing microflora was achieved. Samples with competing microflora had a sensitivity of 40,000 CFU/ml. The variance was less than one cycle.
ABSTRACT Lactic acid bacteria are exposed to a series of stresses during environmental transit an... more ABSTRACT Lactic acid bacteria are exposed to a series of stresses during environmental transit and food fermentation processes. Stresses unique to fermented foods are high acid, low temperature, and limited to no free sugar. In fermented foods, lactobacilli and lactococci recently have been recognized to become nonculturable (NC) under these conditions. It has been shown that lactococci become NC under carbohydrate starvation, which leads to additional metabolic changes during 180 days of incubation. Important end products include branched-chain fatty acids from the catabolism of branched-chain amino acids. In addition, sulfur metabolism changes. It has yet to be demonstrated that NC lactococci can be resuscitated with known compounds or peptides. The NC state of lactococci leads to new metabolic end products not produced during log-phase growth.
Volatile sulfur compounds such as methanethiol, dimethyl disulfide, dimethyl trisulfide, and hydr... more Volatile sulfur compounds such as methanethiol, dimethyl disulfide, dimethyl trisulfide, and hydrogen sulfide constitute an important fraction of Cheddar cheese flavor. These compounds are products of the catabolism of methionine and cysteine by bacteria in the cheese matrix. The objectives of this study were to examine the levels and types of volatile sulfur compounds produced from methionine by lactic acid bacteria frequently used in cheese making and to investigate cystathionine degrading activity, which may be responsible for the liberation of these compounds. Gas chromatography with headspace sampling was used to determine volatile sulfur compounds (VSC) produced by whole cells of 24 strains of lactobacilli and 13 strains of lactococci incubated with methionine. Total VSC production varied widely in the species and subspecies tested. Nearly all strains produced VSC from methionine, but the enzyme responsible for this activity remains unclear. Cystathionine-degrading ability and...
Lactic acid bacteria have been reported to be useful as a health adjunct and are commonly added t... more Lactic acid bacteria have been reported to be useful as a health adjunct and are commonly added to food as the delivery mechanism. The literature contains many conflicting observations for their proposed benefits, and the mechanism of action is undefined. One source of variation is the large number of strains used without proper controls supplemented. Additionally, many of the organisms are not characterized for their acid shock response or the acid-tolerance response, which are known to vary among bacterial species. Our objective was to isolate acid-resistant and bile-resistant variants of Lactobacillus acidophilus and to determine the phenotypic changes. The acid- and bile-tolerant isolates were obtained using natural selection techniques after sequential exposure to hydrochloric acid (pH 3.5 to 7.0) and mixed bile salts. The acid- and bile-tolerant isolates retained their ability to grow at pH 3.5 with 0.3% bile after the selective pressure was removed and reapplied. Isolates var...
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