bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of Viable but Nonculturable Escherichia coli O157:H7 in the Phyllosphere of Lettuce: a Food Safety Risk Factor
Authors: Dinu Laura-Dorina , Bach Susan 
Published: October 2011

ABSTRACT

Escherichia coli
O157:H7 continues to be an important human pathogen and has been increasingly linked to food-borne illness associated with fresh produce, particularly leafy greens. The aim of this work was to investigate the fate of
E. coli
O157:H7 on the phyllosphere of lettuce under low temperature and to evaluate the potential hazard of viable but nonculturable (VBNC) cells induced under such stressful conditions. First, we studied the survival of six bacterial strains following prolonged storage in water at low temperature (4ï¿½C) and selected two strains with different nonculturable responses for the construction of
E. coli
O157:H7 Tn
7gfp
transformants in order to quantitatively assess the occurrence of human pathogens on the plant surface. Under a suboptimal growth temperature (16ï¿½C), both
E. coli
O157:H7 strains maintained culturability on lettuce leaves, but under more stressful conditions (8ï¿½C), the bacterial populations evolved toward the VBNC state. The strain-dependent nonculturable response was more evident in the experiments with different inoculum doses (10
9
and 10
6
E. coli
O157:H7 bacteria per g of leaf) when strain BRMSID 188 lost culturability after 15 days and strain ATCC 43895 lost culturability within 7 days, regardless of the inoculum dose. However, the number of cells entering the VBNC state in high-cell-density inoculum (approximately 55%) was lower than in low-cell-density inoculum (approximately 70%). We recorded the presence of verotoxin for 3 days in samples that contained a VBNC population of 4 to 5 log
10
cells but did not detect culturable cells. These findings indicate that
E. coli
O157:H7 VBNC cells are induced on lettuce plants, and this may have implications regarding food safety.
Hemolytic Porcine Intestinal Escherichia coli without Virulence-Associated Genes Typical of Intestinal Pathogenic E. coli
Authors: Schierack Peter , Weinreich Joerg , Ewers Christa , Tachu Babila , Nicholson Bryon , Barth Stefanie 
Published: October 2011

ABSTRACT

Testing 1,666 fecal or intestinal samples from healthy and diarrheic pigs, we obtained hemolytic
Escherichia coli
isolates from 593 samples. Focusing on hemolytic
E. coli
isolates without virulence-associated genes (VAGs) typical for enteropathogens, we found that such isolates carried a broad variety of VAGs typical for extraintestinal pathogenic
E. coli
.
Mother-to-Child Transmission of and Multiple-Strain Colonization by Bacteroides fragilis in a Cohort of Mothers and Their Children
Authors: Bjerke G. A. , Wilson R. , Storr� O. , �yen T. , Johnsen R. , Rudi K. 
Published: October 2011

ABSTRACT

Bacteroides fragilis
represents an early infant colonizer with important host interactions. Our knowledge about the diversity, transmission, and persistence of this bacterium, however, is limited. Here, we addressed these questions using a combination of multilocus sequence typing (MLST) and variable-number tandem repeat (VNTR) sequence analyses. We used both culture-dependent and -independent typing. We genotyped
B. fragilis
in fecal samples from a cohort of 93 mothers and their children, with samples taken from the mothers and from the children at the ages 1 to 10 days, 4 months, 1 year, and 2 years. By MLST we found two main
B. fragilis
groups, which we denoted clades A and B. Direct typing of stool samples using the
icd
gene revealed seven sequence types, five within clade A and two within clade B. A single clade A sequence type, however, represented 79% of all the sequences. This sequence type was further subtyped using VNTR. VNTR subtyping revealed 16 different VNTR types. Based on the distribution patterns of these, we show mother-to-child transmission and multiple-strain colonization. We argue that negative host selection promotes the coexistence of multiple strains. The significance of our findings is that we have started unraveling the transmission and persistence patterns of one of the most important human gut colonizers.
DNA Detection and Genotypic Identification of Potentially Human-Pathogenic Microsporidia from Asymptomatic Pet Parrots in South Korea as a Risk Factor for Zoonotic Emergence
Authors: Lee So-Young , Lee Sung-Seok , Lyoo Young S. , Park Hee-Myung 
Published: October 2011

ABSTRACT

We detected and identified genotypes of human-pathogenic microsporidia in fecal samples from 51 asymptomatic captive-bred pet parrots in South Korea. Microsporidia were identified in 8 samples (15.7%); 7 parrots tested positive for
Encephalitozoon hellem
, and 1 parrot tested positive for both
E. hellem
and
Encephalitozoon cuniculi
. In genotypic identifications,
E. hellem
was present in genotypes 1A and 2B and
E. cuniculi
was present in genotype II. Pet parrots might be a source of human microsporidian infection.
National Validation Study of a Cellulose Sponge Wipe-Processing Method for Use after Sampling Bacillus anthracis Spores from Surfaces
Authors: Rose Laura J. , Hodges Lisa , O'Connell Heather , Noble-Wang Judith 
Published: October 2011

ABSTRACT

This work was initiated to address the gaps identified by Congress regarding validated biothreat environmental sampling and processing methods. Nine Laboratory Response Network-affiliated laboratories participated in a validation study of a cellulose sponge wipe-processing protocol for the recovery, detection, and quantification of viable
Bacillus anthracis
Sterne spores from steel surfaces. Steel coupons (645.16 cm
2
) were inoculated with 1 to 4 log
10
spores and then sampled with cellulose sponges (Sponge-Stick; 3M, St. Paul, MN). Surrogate dust and background organisms were added to the sponges to mimic environmental conditions. Labs processed the sponges according to the provided protocol. Sensitivity, specificity, and mean percent recovery (%R), between-lab variability, within-lab variability, and total percent coefficient of variation were calculated. The mean %R (standard error) of spores from the surface was 32.4 (4.4), 24.4 (2.8), and 30.1 (2.3) for the 1-, 2-, and 4-log
10
inoculum levels, respectively. Sensitivities for colony counts were 84.1%, 100%, and 100% for the 1-, 2-, and 4-log
10
inocula, respectively. These data help to characterize the variability of the processing method and thereby enhance confidence in the interpretation of the results of environmental sampling conducted during a
B. anthracis
contamination investigation.
Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentation, Oxygen Limitation, and Fumarate Respiration Conditions
Authors: Pinchuk Grigoriy E. , Geydebrekht Oleg V. , Hill Eric A. , Reed Jennifer L. , Konopka Allan E. , Beliaev Alexander S. , Fredrickson Jim K. 
Published: October 2011

ABSTRACT

Shewanella oneidensis
MR-1 is a facultative anaerobe that derives energy by coupling organic matter oxidation to the reduction of a wide range of electron acceptors. Here, we quantitatively assessed the lactate and pyruvate metabolism of MR-1 under three distinct conditions: electron acceptor-limited growth on lactate with O
2
, lactate with fumarate, and pyruvate fermentation. The latter does not support growth but provides energy for cell survival. Using physiological and genetic approaches combined with flux balance analysis, we showed that the proportion of ATP produced by substrate-level phosphorylation varied from 33% to 72.5% of that needed for growth depending on the electron acceptor nature and availability. While being indispensable for growth, the respiration of fumarate does not contribute significantly to ATP generation and likely serves to remove formate, a product of pyruvate formate-lyase-catalyzed pyruvate disproportionation. Under both tested respiratory conditions,
S. oneidensis
MR-1 carried out incomplete substrate oxidation, whereby the tricarboxylic acid (TCA) cycle did not contribute significantly. Pyruvate dehydrogenase was not involved in lactate metabolism under conditions of O
2
limitation but was required for anaerobic growth, likely by supplying reducing equivalents for biosynthesis. The results suggest that pyruvate fermentation by
S. oneidensis
MR-1 cells represents a combination of substrate-level phosphorylation and respiration, where pyruvate serves as an electron donor and an electron acceptor. Pyruvate reduction to lactate at the expense of formate oxidation is catalyzed by a recently described new type of oxidative NAD(P)H-independent
d
-lactate dehydrogenase (Dld-II). The results further indicate that pyruvate reduction coupled to formate oxidation may be accompanied by the generation of proton motive force.
Endo-β-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family
Authors: Sakamoto Yuichi , Nakade Keiko , Konno Naotake 
Published: October 2011

ABSTRACT

The cell wall of the fruiting body of the mushroom
Lentinula edodes
is degraded after harvesting by enzymes such as β-1,3-glucanase. In this study, a novel endo-type β-1,3-glucanase, GLU1, was purified from
L. edodes
fruiting bodies after harvesting. The gene encoding it,
glu1
, was isolated by rapid amplification of cDNA ends (RACE)-PCR using primers designed from the N-terminal amino acid sequence of GLU1. The putative amino acid sequence of the mature protein contained 247 amino acid residues with a molecular mass of 26 kDa and a pI of 3.87, and recombinant GLU1 expressed in
Pichia pastoris
exhibited β-1,3-glucanase activity. GLU1 catalyzed depolymerization of glucans composed of β-1,3-linked main chains, and reaction product analysis by thin-layer chromatography (TLC) clearly indicated that the enzyme had an endolytic mode. However, the amino acid sequence of GLU1 showed no significant similarity to known glycoside hydrolases. GLU1 has similarity to several hypothetical proteins in fungi, and GLU1 and highly similar proteins should be classified as a novel glycoside hydrolase family (GH128).
Subtilase Cytotoxin-Coding Genes in Verotoxin-Producing Escherichia coli Strains from Sheep and Goats Differ from Those from Cattle
Authors: Orden Josï¿½ A. , Horcajo Pilar , de la Fuente Ricardo , Ruiz-Santa-Quiteria Josï¿½ A. , Domï¿½nguez-Bernal Gustavo , Carriï¿½n Javier 
Published: October 2011

ABSTRACT

Subtilase cytotoxin (SubAB) from verotoxin (VT)-producing
Escherichia coli
(VTEC) strains was first described in the 98NK2 strain and has been associated with human disease. However, SubAB has recently been found in two VT-negative
E. coli
strains (ED 591 and ED 32). SubAB is encoded by two closely linked, cotranscribed genes (
subA
and
subB
). In this study, we investigated the presence of
subAB
genes in 52 VTEC strains isolated from cattle and 209 strains from small ruminants, using PCR. Most (91.9%) VTEC strains from sheep and goats and 25% of the strains from healthy cattle possessed
subAB
genes. The presence of
subAB
in a high percentage of the VTEC strains from small ruminants might increase the pathogenicity of these strains for human beings. Some differences in the results of PCRs and in the association with some virulence genes suggested the existence of different variants of
subAB
. We therefore sequenced the
subA
gene in 12 strains and showed that the
subA
gene in most of the
subAB
-positive VTEC strains from cattle was almost identical (about 99%) to that in the 98NK2 strain, while the
subA
gene in most of the
subAB
-positive VTEC strains from small ruminants was almost identical to that in the ED 591 strain. We propose the terms
subAB1
to describe the SubAB-coding genes resembling that in the 98NK2 strain and
subAB2
to describe those resembling that in the ED 591 strain.
Development and Characterization of a Xylose-Inducible Gene Expression System for Clostridium perfringens
Authors: Nariya Hirofumi , Miyata Shigeru , Kuwahara Tomomi , Okabe Akinobu 
Published: October 2011

ABSTRACT

A xylose-inducible gene expression vector for
Clostridium perfringens
was developed. Plasmid pXCH contains a chromosomal region from
Clostridium difficile
(
xylR
-P

xy

lB

):
xylR
, encoding the xylose repressor,
xylO
, the
xyl
operator sequence, and P

xylB

, the divergent promoter upstream of
xylBA
encoding xylulo kinase and xylose isomerase. pXCH allows tightly regulated expression of the chloramphenicol acetyltransferase reporter and the α-toxin genes in response to the inducer concentration. Thus, pXCH could constitute a new valuable genetic tool for study of
C. perfringens
.
Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites
Authors: Lazzaro Anna , Gauer Andreas , Zeyer Josef 
Published: October 2011

ABSTRACT

Studies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO
3
−
showed a seasonal pattern, increasing from 1 to 3 μg NO
3
−
(g soil dry weight)
−1
after the melting of snow but decreasing to <1 μg NO
3
−
(g soil dry weight)
−1
in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field.
Mutations Suppressing the Loss of DegQ Function in Bacillus subtilis (natto) Poly-γ-Glutamate Synthesis
Authors: Do Thi-Huyen , Suzuki Yuki , Abe Naoki , Kaneko Jun , Itoh Yoshifumi , Kimura Keitarou 
Published: October 2011

ABSTRACT

The
degQ
gene of
Bacillus subtilis
(natto), encoding a small peptide of 46 amino acids, is essential for the synthesis of extracellular poly-gamma-glutamate (γPGA). To elucidate the role of DegQ in γPGA synthesis, we knocked out the
degQ
gene in
Bacillus subtilis
(natto) and screened for suppressor mutations that restored γPGA synthesis in the absence of DegQ. Suppressor mutations were found in
degS
, the receptor kinase gene of the DegS-DegU two-component system. Recombinant DegS-His
6
mutant proteins were expressed in
Escherichia coli
cells and subjected to an
in vitro
phosphorylation assay. Compared with the wild type, mutant DegS-His
6
proteins showed higher levels of autophosphorylation (R208Q, M195I, L248F, and D250N), reduced autodephosphorylation (D250N), reduced phosphatase activity toward DegU, or a reduced ability to stimulate the autodephosphorylation activity of DegU (R208Q, D249G, M195I, L248F, and D250N) and stabilized DegU in the phosphorylated form. These mutant DegS proteins mimic the effect of DegQ on wild-type DegSU
in vitro
. Interestingly, DegQ stabilizes phosphorylated DegS only in the presence of DegU, indicating a complex interaction of these three proteins.
Use of a DNA Microarray for Detection and Identification of Bacterial Pathogens Associated with Fishery Products
Authors: Cao Boyang , Li Rongrong , Xiong Songjin , Yao Fangfang , Liu Xiangqian , Wang Min , Feng Lu , Wang Lei 
Published: October 2011

ABSTRACT

We established a microarray for the simultaneous detection and identification of diverse putative pathogens often associated with fishery products by targeting specific genes of
Listeria monocytogenes
,
Salmonella
,
Shigella
,
Staphylococcus aureus
,
Streptococcus pyogenes
,
Vibrio cholerae
,
Vibrio parahaemolyticus
,
Vibrio vulnificus
, and
Yersinia enterocolitica
and the 16S-23S rRNA gene internal transcribed spacer (ITS) region of
Proteus mirabilis
and
Proteus vulgaris
. The microarray contained 26 specific probes and was tested against a total of 123 target bacterial strains that included 55 representative strains, 68 clinical isolates, and 45 strains of other bacterial species that belonged to 8 genera and 34 species, and it was shown to be specific and reproducible. A detection sensitivity of 10 ng DNA or 10 CFU/ml for pure cultures of each target organism demonstrated that the assay was highly sensitive and reproducible. Mock and real fishery product samples were tested by the microarray, and the accuracy was 100%. The DNA microarray method described in this communication is specific, sensitive, and reliable and has several advantages over traditional methods of bacterial culture and antiserum agglutination assays.
Competitive Selection of Lactic Acid Bacteria That Persist in the Human Oral Cavity
Authors: Snel Johannes , Marco Maria L. , Kingma Fedde , Noordman Wouter M. , Rademaker Jan , Kleerebezem Michiel 
Published: October 2011

ABSTRACT

Lactic acid bacteria (LAB) might offer opportunities as oral probiotics provided candidate strains persist in the mouth. After intake of a mixture of 69 LAB, strains of
Lactobacillus fermentum
and
Lactobacillus salivarius
were especially recovered. Coaggregation with other microbes is likely not a prerequisite for persistence since
L. salivarius
strongly coaggregated with typical oral cavity isolates, whereas
L. fermentum
failed to display this phenotype.
Significance of Microbial Communities and Interactions in Safeguarding Reactive Mine Tailings by Ecological Engineering
Authors: N̆ancucheo Ivan , Johnson D. Barrie 
Published: October 2011

ABSTRACT
Pyritic mine tailings (mineral waste generated by metal mining) pose significant risk to the environment as point sources of acidic, metal-rich effluents (acid mine drainage [AMD]). While the accelerated oxidative dissolution of pyrite and other sulfide minerals in tailings by acidophilic chemolithotrophic prokaryotes has been widely reported, other acidophiles (heterotrophic bacteria that catalyze the dissimilatory reduction of iron and sulfur) can reverse the reactions involved in AMD genesis, and these have been implicated in the “natural attenuation” of mine waters. We have investigated whether by manipulating microbial communities in tailings (inoculating with iron- and sulfur-reducing acidophilic bacteria and phototrophic acidophilic microalgae) it is possible to mitigate the impact of the acid-generating and metal-mobilizing chemolithotrophic prokaryotes that are indigenous to tailing deposits. Sixty tailings mesocosms were set up, using five different microbial inoculation variants, and analyzed at regular intervals for changes in physicochemical and microbiological parameters for up to 1 year. Differences between treatment protocols were most apparent between tailings that had been inoculated with acidophilic algae in addition to aerobic and anaerobic heterotrophic bacteria and those that had been inoculated with only pyrite-oxidizing chemolithotrophs; these differences included higher pH values, lower redox potentials, and smaller concentrations of soluble copper and zinc. The results suggest that empirical ecological engineering of tailing lagoons to promote the growth and activities of iron- and sulfate-reducing bacteria could minimize their risk of AMD production and that the heterotrophic populations could be sustained by facilitating the growth of microalgae to provide continuous inputs of organic carbon.
Differential Degradation of Bicyclics with Aromatic and Alicyclic Rings by Rhodococcus sp. Strain DK17
Authors: Kim Dockyu , Yoo Miyoun , Choi Ki Young , Kang Beom Sik , Kim Tai Kyoung , Hong Soon Gyu , Zylstra Gerben J. , Kim Eungbin 
Published: October 2011

ABSTRACT

The metabolically versatile
Rhodococcus
sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the
meta
-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in
Escherichia coli
, the DK17
o
-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin
cis
-dihydrodiol, indan-1,2-diol, and
cis
-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17
o
-xylene dioxygenase to perform distinct regioselective hydroxylations.
Impact of the N-Terminal Secretor Domain on YopD Translocator Function in Yersinia pseudotuberculosis Type III Secretion
Authors: Amer Ayad A. A. , Åhlund Monika K. , Bröms Jeanette E. , Forsberg Åke , Francis Matthew S. 
Published: October 2011

ABSTRACT

Type III secretion systems (T3SSs) secrete needle components, pore-forming translocators, and the translocated effectors. In part, effector recognition by a T3SS involves their N-terminal amino acids and their 5′ mRNA. To investigate whether similar molecular constraints influence translocator secretion, we scrutinized this region within YopD from
Yersinia pseudotuberculosis
. Mutations in the 5′ end of
yopD
that resulted in specific disruption of the mRNA sequence did not affect YopD secretion. On the other hand, a few mutations affecting the protein sequence reduced secretion. Translational reporter fusions identified the first five codons as a minimal N-terminal secretion signal and also indicated that the YopD N terminus might be important for
yopD
translation control. Hybrid proteins in which the N terminus of YopD was exchanged with the equivalent region of the YopE effector or the YopB translocator were also constructed. While the
in vitro
secretion profile was unaltered, these modified bacteria were all compromised with respect to T3SS activity in the presence of immune cells. Thus, the YopD N terminus does harbor a secretion signal that may also incorporate mechanisms of
yopD
translation control. This signal tolerates a high degree of variation while still maintaining secretion competence suggestive of inherent structural peculiarities that make it distinct from secretion signals of other T3SS substrates.