bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Hydrostatic Pressure for Inactivation of Microbial Contaminants in Cheese
Authors: O'Reilly Ciara E. , O'Connor Paula M. , Kelly Alan L. , Beresford Thomas P. , Murphy Patrick M. 
Published: July 2002

ABSTRACT

The objective of this study was to determine the effect of high pressure (HP) on the inactivation of microbial contaminants in Cheddar cheese (
Escherichia coli
K-12,
Staphylococcus aureus
ATCC 6538, and
Penicillium roqueforti
IMI 297987). Initially, cheese slurries inoculated with
E. coli
,
S. aureus
, and
P. roqueforti
were used as a convenient means to define the effects of a range of pressures and temperatures on the viability of these microorganisms. Cheese slurries were subjected to pressures of 50 to 800 MPa for 20 min at temperatures of 10, 20, and 30°C. At 400 MPa, the viability of
P. roqueforti
in cheese slurry decreased by >2-log-unit cycles at 10°C and by 6-log-unit cycles at temperatures of 20 and 30°C.
S. aureus
and
E. coli
were not detected after HP treatments in cheese slurry of >600 MPa at 20°C and >400 MPa at 30°C, respectively. In addition to cell death, the presence of sublethally injured cells in HP-treated slurries was demonstrated by differential plating using nonselective agar incorporating salt or glucose. Kinetic experiments of HP inactivation demonstrated that increasing the pressure from 300 to 400 MPa resulted in a higher degree of inactivation than increasing the pressurization time from 0 to 60 min, indicating a greater antimicrobial impact of pressure. Selected conditions were subsequently tested on Cheddar cheese by adding the isolates to cheese milk and pressure treating the resultant cheeses at 100 to 500 MPa for 20 min at 20°C. The relative sensitivities of the isolates to HP in Cheddar cheese were similar to those observed in the cheese slurry, i.e.,
P. roqueforti
was more sensitive than
E. coli
, which was more sensitive than
S. aureus
. The organisms were more sensitive to pressure in cheese than slurry, especially with
E. coli
. On comparison of the sensitivities of the microorganisms in a pH 5.3 phosphate buffer, cheese slurry, and Cheddar cheese, greatest sensitivity to HP was shown in the pH 5.3 phosphate buffer by
S. aureus
and
P. roqueforti
while greatest sensitivity to HP by
E. coli
was exhibited in Cheddar cheese. Therefore, the medium in which the microorganisms are treated is an important determinant of the level of inactivation observed.
Phylogenetic Characterization and In Situ Detection of a
Cytophaga-Flexibacter-Bacteroides
Phylogroup Bacterium in
Tuber borchii
Vittad. Ectomycorrhizal Mycelium
Authors: Barbieri Elena , Potenza Lucia , Rossi Ismaela , Sisti Davide , Giomaro Giovanna , Rossetti Simona , Beimfohr Claudia , Stocchi Vilberto 
Published: July 2002

ABSTRACT

Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus
Tuber borchii
Vittad. Universal eubacterial primers specific for the 5′ and 3′ ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of
T. borchii
Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each
T. borchii
mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to the
Cytophaga-Flexibacter-Bacteroides
(CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus
T. borchii
was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the
Cytophaga-Flexibacter
phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genus
Tuber
.
Evaluation of
p
-Naphtholbenzein-β-
d
-Galactoside as a Substrate for Bacterial β-Galactosidase
Authors: James A. L. , Chilvers K. F. , Perry J. D. , Armstrong L. , Gould F. K. 
Published: July 2002

ABSTRACT

We describe the synthesis of a new substrate for the detection of β-galactosidase and evaluate its performance in comparison with 5-bromo-4-chloro-3-indolyl-β-
d
-galactopyranoside (X-Gal) and cyclohexenoesculetinβ-
d
-galactoside (CHE-Gal). Of 206
Enterobacteriaceae
strains able to hydrolyze X-Gal, 194 (94.2%) hydrolyzed CHE-Gal and 192 (93.2%) hydrolyzed
p
-naphtholbenzein-β-
d
-galactoside (PNB-Gal). We conclude that PNB-Gal is an effective substrate for the detection of β-galactosidase.
Identification and Characterization of a Bile Acid 7α-Dehydroxylation Operon in
Clostridium
sp. Strain TO-931, a Highly Active 7α-Dehydroxylating Strain Isolated from Human Feces
Authors: Wells James E. , Hylemon Phillip B. 
Published: July 2002

ABSTRACT

Clostridium
sp. strain TO-931 can rapidly convert the primary bile acid cholic acid to a potentially toxic compound, deoxycholic acid. Mixed oligonucleotide probes were used to isolate a gene fragment encoding a putative bile acid transporter from
Clostridium
sp. strain TO-931. This DNA fragment had 60% nucleotide sequence identity to a known bile acid transporter gene from
Eubacterium
sp. strain VPI 12708, another bile acid-7α-dehydroxylating intestinal bacterium. The DNA (9.15 kb) surrounding the transporter gene was cloned from
Clostridium
sp. strain TO-931 and sequenced. Within this larger DNA fragment was a 7.9-kb region, containing six successive open reading frames (ORFs), that was encoded by a single 8.1-kb transcript, as determined by Northern blot analysis. The gene arrangement and DNA sequence of the
Clostridium
sp. strain TO-931 operon are similar to those of a
Eubacterium
sp. strain VPI 12708 bile acid-inducible operon containing nine ORFs. Several genes in the
Eubacterium
sp. strain VPI 12708 operon have been shown to encode products required for bile acid 7α-dehydroxylation. In
Clostridium
sp. strain TO-931, genes potentially encoding bile acid-coenzyme A (CoA) ligase, 3α-hydroxysteroid dehydrogenase, bile acid 7α-dehydratase, bile acid-CoA hydrolase, and a bile acid transporter were similar in size and exhibited amino acid homology to similar gene products from
Eubacterium
sp. strain VPI 12708 (encoded by
baiB
,
baiA
,
baiE
,
baiF
, and
baiG
, respectively). However, no genes similar to
Eubacterium
sp. strain VPI 12708
biaH
or
baiI
were found in the
Clostridium
sp. strain TO-931
bai
operon, and the two putative
Eubacterium
sp. strain VPI 12708 genes,
baiC
and
baiD
, were arranged in one continuous ORF in
Clostridium
sp. strain TO-931. Intergene regions showed no significant DNA sequence similarity, but primer extension analysis identified a region 115 bp upstream from the first ORF that exhibited 58% identity to a
bai
operator/promoter region identified in
Eubacterium
sp. strain VPI 12708. These results indicate that the gene organization, gene product amino acid sequences, and promoters of the bile acid-inducible operons of
Clostridium
sp. strain TO-931 and
Eubacterium
sp. strain VPI 12708 are highly conserved.
Nitrite Reductase Genes (
nirK
and
nirS
) as Functional Markers To Investigate Diversity of Denitrifying Bacteria in Pacific Northwest Marine Sediment Communities
Authors: Braker Gesche , Zhou Jizhong , Wu Liyou , Devol Allan H. , Tiedje James M. 
Published: July 2002

ABSTRACT

Genetic heterogeneity of denitrifying bacteria in sediment samples from Puget Sound and two sites on the Washington continental margin was studied by PCR approaches amplifying
nirK
and
nirS
genes. These structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for denitrifying bacteria.
nirS
sequences could be amplified from samples of both sampling sites, whereas
nirK
sequences were detected only in samples from the Washington margin. To assess the underlying
nir
gene structure, PCR products of both genes were cloned and screened by restriction fragment length polymorphism (RFLP). Rarefraction analysis revealed a high level of diversity especially for
nirS
clones from Puget Sound and a slightly lower level of diversity for
nirK
and
nirS
clones from the Washington margin. One group dominated within
nirK
clones, but no dominance and only a few redundant clones were seen between sediment samples for
nirS
clones in both habitats. Hybridization and sequencing confirmed that all but one of the 228 putative
nirS
clones were
nirS
with levels of nucleotide identities as low as 45.3%. Phylogenetic analysis grouped
nirS
clones into three distinct subclusters within the
nirS
gene tree which corresponded to the two habitats from which they were obtained. These sequences had little relationship to any strain with known
nirS
sequences or to isolates (mostly close relatives of
Pseudomonas stutzeri
) from the Washington margin sediment samples.
nirK
clones were more closely related to each other than were the
nirS
clones, with 78.6% and higher nucleotide identities; clones showing only weak hybridization signals were not related to known
nirK
sequences. All
nirK
clones were also grouped into a distinct cluster which could not be placed with any strain with known
nirK
sequences. These findings show a very high diversity of
nir
sequences within small samples and that these novel
nir
clusters, some very divergent from known sequences, are not known in cultivated denitrifiers.
Production of Exopolysaccharide by
Lactobacillus rhamnosus
R and Analysis of Its Enzymatic Degradation during Prolonged Fermentation
Authors: Pham P. L. , Dupont I. , Roy D. , Lapointe G. , Cerning J. 
Published: July 2002

ABSTRACT

The potential of
Lactobacillus rhamnosus
R for producing exopolysaccharide (EPS) when grown on basal minimum medium supplemented with glucose or lactose was investigated. EPS production by
L. rhamnosus
R is partially growth associated and about 500 mg of EPS per liter was synthesized with both sugars. The product yield coefficient (
Y
EPS/S
) was 3.15 (0.0315 g of EPS [g of lactose]
−1
) and 2.88 (0.0288 g of EPS [g of glucose]
−1
). It was clearly shown that the amount of EPS produced declined upon prolonged fermentation. Degradation of EPS in fermentation processes was also assessed by measuring its molecular weights and viscosities. As these reductions might have a negative effect on the yield and viscosifying properties of EPS, it was essential to examine possible causes related to this breakdown. The decrease in viscosities and molecular weights of EPS withdrawn at different cultivation times permitted us to suspect the presence of a depolymerizing enzyme in the fermentation medium. Our study on enzymatic production profiles showed a large spectrum of glycohydrolases (α-
d
-glucosidase, β-
d
-glucosidase, α-
d
-galactosidase, β-
d
-galactosidase, β-
d
-glucuronidase, and some traces of α-
l
-rhamnosidase). These enzymes were localized, two of them (α-
d
-glucosidase and β-
d
-glucuronidase) were partially purified and characterized. When incubated with EPS, these enzymes were capable of lowering the viscosity of the polymer as well as liberating some reducing sugars. Upon prolonged incubation (27 h), the loss of viscosity was increased up to 33%.
A Novel Protein-Deamidating Enzyme from
Chryseobacterium proteolyticum
sp. nov., a Newly Isolated Bacterium from Soil
Authors: Yamaguchi Shotaro , Yokoe Masaaki 
Published: July 2002

ABSTRACT

A novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of
Chryseobacterium proteolyticum
strain 9670
T
isolated from rice field soil in Tsukuba, Japan. The deamidating activities on carboxybenzoxy (Cbz)-Gln-Gly and caseins and protease activity were produced synchronously by the isolate. Both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-Sepharose chromatography of the culture supernatant. The enzyme catalyzed the deamidation of native caseins with no protease and transglutaminase activities. Phenotypic characterization and DNA analyses of the isolate were performed to determine its taxonomy. Physiological and biochemical characteristics, 16S rRNA gene sequence analysis, and DNA-DNA relatedness data indicated that the isolate should be placed as a new species belonging to the genus
Chryseobacterium
. The isolate showed no growth on MacConkey agar and produced acid from sucrose. The levels of DNA-DNA relatedness between the isolate and other related strains were less than 17%. The name
Chryseobacterium proteolyticum
is proposed for the new species; strain 9670 is the type strain (=FERM P-17664).
Comparative Characterization of Complete and Truncated Forms of
Lactobacillus amylovorus
α-Amylase and Role of the C-Terminal Direct Repeats in Raw-Starch Binding
Authors: Rodriguez Sanoja R. , Morlon-Guyot J. , Jore J. , Pintado J. , Juge N. , Guyot J. P. 
Published: July 2002

ABSTRACT

Two constructs derived from the α-amylase gene (
amyA
) of
Lactobacillus amylovorus
were expressed in
Lactobacillus plantarum
, and their expression products were purified, characterized, and compared. These products correspond to the complete (AmyA) and truncated (AmyAΔ) forms of α-amylase; AmyAΔ lacks the 66-kDa carboxyl-terminal direct-repeating-unit region. AmyA and AmyAΔ exhibit similar amylase activities towards a range of soluble substrates (amylose, amylopectin and α-cyclodextrin, and soluble starch). The specific activities of the enzymes towards soluble starch are similar, but the

K
M

and
V
max
values of AmyAΔ were slightly higher than those of AmyA, whereas the thermal stability of AmyAΔ was lower than that of AmyA. In contrast to AmyA, AmyAΔ is unable to bind to β-cyclodextrin and is only weakly active towards glycogen. More striking is the fact that AmyAΔ cannot bind or hydrolyze raw starch, demonstrating that the carboxyl-terminal repeating-unit domain of AmyA is required for raw-starch binding activity.
Growth of the Bacteriocin-Producing
Lactobacillus sakei
Strain CTC 494 in MRS Broth Is Strongly Reduced Due to Nutrient Exhaustion: a Nutrient Depletion Model for the Growth of Lactic Acid Bacteria
Authors: Leroy Frédéric , De Vuyst Luc 
Published: July 2002

ABSTRACT

Although commercial MRS broth has been designed to allow excellent growth of lactobacilli, most of these bacteria are still subjected to a self-inhibiting process. The most likely explanation is the accumulation of lactic acid or other toxic end products and the depletion of nutrients. In this study, the self-inhibition of
Lactobacillus sakei
CTC 494 was analyzed in a kinetic way, and a nutrient depletion model was set up to describe the growth inhibition process. This simple model has considerable advantages compared to commonly used descriptive models such as the logistic growth equation. It offers a better fit and a more realistic description of the growth data by taking into account both growth inhibition due to lactic acid production and changes in growth rates due to nutrient depletion. Depending on the fermentation conditions, in MRS broth there appears to be a strong decrease of the specific growth rate over time. Some undefined compounds present in the complex nitrogen source of MRS broth appear to be of crucial importance because of their limited availability. Moreover, nutrient availability affects bacteriocin production through its effect on cell growth as well as on the bacteriocin production per cell. A plateau value for the bacteriocin production by
L. sakei
CTC 494 was observed.
New Additive for Culture Media for Rapid Identification of Aflatoxin-Producing
Aspergillus
Strains
Authors: Fente C. A. , Ordaz J. Jaimez , Vázquez B. I. , Franco C. M. , Cepeda A. 
Published: July 2002

ABSTRACT

A new reliable, fast, and simple method for the detection of aflatoxigenic
Aspergillus
strains, consisting of the addition of a cyclodextrin (a methylated β-cyclodextrin derivative) to common media used for testing mycotoxin production ability, was developed. We propose the use of this compound as an additive for fungal culture media to enhance the natural fluorescence of aflatoxins. The production of aflatoxins coincided with the presence of a bright blue or blue-green fluorescent area surrounding colonies when observed under long-wavelength (365-nm) UV light after 3 days of incubation at 28°C. The presence of aflatoxins was confirmed by extracting the medium with chloroform and examining the extracts by high-pressure liquid chromatography with fluorescence detection.
Improved Method for Detection of
Vibrio parahaemolyticus
in Seafood
Authors: Hara-Kudo Yukiko , Nishina Tokuhiro , Nakagawa Hiroshi , Konuma Hirotaka , Hasegawa Junko , Kumagai Susumu 
Published: July 2002

ABSTRACT

We have developed a new, effective procedure for detecting
Vibrio parahaemolyticus
in seafoods using enrichment and plating onto a chromogenic agar medium. Samples were cultured in salt Trypticase soy broth, which is a nonselective medium, and then a portion of the culture was cultured with salt polymyxin broth, which is a selective medium for
V. parahaemolyticus
. This two-step enrichment was more effective than the one-step enrichment in salt polymyxin broth alone. The enrichment cultures were then plated onto a new chromogenic agar containing substrates for beta-galactosidase. The
V. parahaemolyticus
colonies developed a purple color on this growth medium that distinguished them from other related bacterial strains.
V. parahaemolyticus
was isolated more frequently from naturally contaminated seafood samples using the chromogenic agar than thiosulfate citrate bile salts sucrose agar medium, which is currently used for the isolation of
V. parahaemolyticus
. Our findings suggest that this new enrichment and isolation scheme is more sensitive and accurate for identifying
V. parahaemolyticus
in seafood samples than previously used methods.
Efficient Transformation System for
Propionibacterium freudenreichii
Based on a Novel Vector
Authors: Jore J. P. M. , van Luijk N. , Luiten R. G. M. , van der Werf M. J. , Pouwels P. H. 
Published: July 2002

ABSTRACT

A 3.6-kb endogenous plasmid was isolated from a
Propionibacterium freudenreichii
strain and sequenced completely. Based on homologies with plasmids from other bacteria, notably a plasmid from
Mycobacterium
, a region harboring putative replicative functions was defined. Outside this region two restriction enzyme recognition sites were used for insertion of an
Escherichia coli
-specific replicon and an erythromycin resistance gene for selection in
Propionibacterium
. Hybrid vectors obtained in this way replicated in both
E. coli
and
P. freudenreichii
. Whereas electroporation of
P. freudenreichii
with vector DNA isolated from an
E. coli
transformant yielded 10 to 30 colonies per μg of DNA, use of vector DNA reisolated from a
Propionibacterium
transformant dramatically increased the efficiency of transformation (≥10
8
colonies per μg of DNA). It could be shown that restriction-modification was responsible for this effect. The high efficiency of the system described here permitted successful transformation of
Propionibacterium
with DNA ligation mixtures.
Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing
Authors: Röling Wilfred F. M. , Kerler Josef , Braster Martin , Apriyantono Anton , Stam Hein , van Verseveld Henk W. 
Published: July 2002

ABSTRACT

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to
Bacillus subtilis, B. licheniformis,
, and
B. smithii
) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans.
Quorum Sensing in the Dimorphic Fungus
Candida albicans
Is Mediated by Farnesol
Authors: Hornby Jacob M. , Jensen Ellen C. , Lisec Amber D. , Tasto Joseph J. , Jahnke Brandon , Shoemaker Richard , Dussault Patrick , Nickerson Kenneth W. 
Published: July 2002

ABSTRACT

The inoculum size effect in the dimorphic fungus
Candida albicans
results from production of an extracellular quorum-sensing molecule (QSM). This molecule prevents mycelial development in both a growth morphology assay and a differentiation assay using three chemically distinct triggers for germ tube formation (GTF):
l
-proline,
N
-acetylglucosamine, and serum (either pig or fetal bovine). In all cases, the presence of QSM prevents the yeast-to-mycelium conversion, resulting in actively budding yeasts without influencing cellular growth rates. QSM exhibits general cross-reactivity within
C. albicans
in that supernatants from strain A72 are active on five other strains of
C. albicans
and vice versa. The QSM excreted by
C. albicans
is farnesol (C
15
H
26
O; molecular weight, 222.37). QSM is extracellular, and is produced continuously during growth and over a temperature range from 23 to 43°C, in amounts roughly proportional to the CFU/milliliter. Production is not dependent on the type of carbon source nor nitrogen source or on the chemical nature of the growth medium. Both commercial mixed isomer and (
E,E
)-farnesol exhibited QSM activity (the ability to prevent GTF) at a level sufficient to account for all the QSM activity present in
C. albicans
supernatants, i.e., 50% GTF at ca. 30 to 35 μM. Nerolidol was ca. two times less active than farnesol. Neither geraniol (C
10
), geranylgeraniol (C
20
), nor farnesyl pyrophosphate had any QSM activity.