bluuebunny/crossref_metadata_2025_split huggingface dataset:
Confirmation and Elimination of Xylose Metabolism Bottlenecks in Glucose Phosphoenolpyruvate-Dependent Phosphotransferase System-Deficient Clostridium acetobutylicum for Simultaneous Utilization of Glucose, Xylose, and Arabinose
Authors: Xiao Han , Gu Yang , Ning Yuanyuan , Yang Yunliu , Mitchell Wilfrid J. , Jiang Weihong , Yang Sheng 
Published: September 2011

ABSTRACT

Efficient cofermentation of
d
-glucose,
d
-xylose, and
l
-arabinose, three major sugars present in lignocellulose, is a fundamental requirement for cost-effective utilization of lignocellulosic biomass. The Gram-positive anaerobic bacterium
Clostridium acetobutylicum
, known for its excellent capability of producing ABE (acetone, butanol, and ethanol) solvent, is limited in using lignocellulose because of inefficient pentose consumption when fermenting sugar mixtures. To overcome this substrate utilization defect, a predicted
glcG
gene, encoding enzyme II of the
d
-glucose phosphoenolpyruvate-dependent phosphotransferase system (PTS), was first disrupted in the ABE-producing model strain
Clostridium acetobutylicum
ATCC 824, resulting in greatly improved
d
-xylose and
l
-arabinose consumption in the presence of
d
-glucose. Interestingly, despite the loss of GlcG, the resulting mutant strain 824glcG fermented
d
-glucose as efficiently as did the parent strain. This could be attributed to residual glucose PTS activity, although an increased activity of glucose kinase suggested that non-PTS glucose uptake might also be elevated as a result of
glcG
disruption. Furthermore, the inherent rate-limiting steps of the
d
-xylose metabolic pathway were observed prior to the pentose phosphate pathway (PPP) in strain ATCC 824 and then overcome by co-overexpression of the
d
-xylose proton-symporter (cac1345),
d
-xylose isomerase (cac2610), and xylulokinase (cac2612). As a result, an engineered strain (824glcG-TBA), obtained by integrating
glcG
disruption and genetic overexpression of the xylose pathway, was able to efficiently coferment mixtures of
d
-glucose,
d
-xylose, and
l
-arabinose, reaching a 24% higher ABE solvent titer (16.06 g/liter) and a 5% higher yield (0.28 g/g) compared to those of the wild-type strain. This strain will be a promising platform host toward commercial exploitation of lignocellulose to produce solvents and biofuels.
Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure
Authors: Bassin J. P. , Pronk M. , Muyzer G. , Kleerebezem R. , Dezotti M. , van Loosdrecht M. C. M. 
Published: September 2011

ABSTRACTThe long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA andamoAgenes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescencein situhybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance ofNitrospirasp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “CandidatusAccumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonassp.) and phosphate removal (“CandidatusAccumulibacter”).
Engineering Escherichia coli for Biodiesel Production Utilizing a Bacterial Fatty Acid Methyltransferase
Authors: Nawabi Parwez , Bauer Stefan , Kyrpides Nikos , Lykidis Athanasios 
Published: September 2011

ABSTRACT

The production of low-cost biofuels in engineered microorganisms is of great interest due to the continual increase in the world's energy demands. Biodiesel is a renewable fuel that can potentially be produced in microbes cost-effectively. Fatty acid methyl esters (FAMEs) are a common component of biodiesel and can be synthesized from either triacylglycerol or free fatty acids (FFAs). Here we report the identification of a novel bacterial fatty acid methyltransferase (FAMT) that catalyzes the formation of FAMEs and 3-hydroxyl fatty acid methyl esters (3-OH-FAMEs) from the respective free acids and
S
-adenosylmethionine (AdoMet). FAMT exhibits a higher specificity toward 3-hydroxy free fatty acids (3-OH-FFAs) than FFAs, synthesizing 3-hydroxy fatty acid methyl esters (3-OH-FAMEs)
in vivo
. We have also identified bacterial members of the fatty acyl-acyl carrier protein (ACP) thioesterase (FAT) enzyme family with distinct acyl chain specificities. These bacterial FATs exhibit increased specificity toward 3-hydroxyacyl-ACP, generating 3-OH-FFAs, which can subsequently be utilized by FAMTs to produce 3-OH-FAMEs. PhaG (3-hydroxyacyl ACP:coenzyme A [CoA] transacylase) constitutes an alternative route to 3-OH-FFA synthesis; the coexpression of PhaG with FAMT led to the highest level of accumulation of 3-OH-FAMEs and FAMEs. The availability of AdoMet, the second substrate for FAMT, is an important factor regulating the amount of methyl esters produced by bacterial cells. Our results indicate that the deletion of the global methionine regulator
metJ
and the overexpression of methionine adenosyltransferase result in increased methyl ester synthesis.
Persistence of Bacillus thuringiensis subsp. kurstaki in Urban Environments following Spraying
Authors: Van Cuyk Sheila , Deshpande Alina , Hollander Attelia , Duval Nathan , Ticknor Lawrence , Layshock Julie , Gallegos-Graves LaVerne , Omberg Kristin M. 
Published: September 2011

ABSTRACT

Bacillus thuringiensis
subsp.
kurstaki
is applied extensively in North America to control the gypsy moth,
Lymantria dispar
. Since
B. thuringiensis
subsp.
kurstaki
shares many physical and biological properties with
Bacillus anthracis
, it is a reasonable surrogate for biodefense studies. A key question in biodefense is how long a biothreat agent will persist in the environment. There is some information in the literature on the persistence of
Bacillus anthracis
in laboratories and historical testing areas and for
Bacillus thuringiensis
in agricultural settings, but there is no information on the persistence of
Bacillus
spp. in the type of environment that would be encountered in a city or on a military installation. Since it is not feasible to release
B. anthracis
in a developed area, the controlled release of
B. thuringiensis
subsp.
kurstaki
for pest control was used to gain insight into the potential persistence of
Bacillus
spp. in outdoor urban environments. Persistence was evaluated in two locations: Fairfax County, VA, and Seattle, WA. Environmental samples were collected from multiple matrices and evaluated for the presence of viable
B. thuringiensis
subsp.
kurstaki
at times ranging from less than 1 day to 4 years after spraying. Real-time PCR and culture were used for analysis.
B. thuringiensis
subsp.
kurstaki
was found to persist in urban environments for at least 4 years. It was most frequently detected in soils and less frequently detected in wipes, grass, foliage, and water. The collective results indicate that certain species of
Bacillus
may persist for years following their dispersal in urban environments.
Expression of Virulence Factors by Staphylococcus aureus Grown in Serum
Authors: Oogai Yuichi , Matsuo Miki , Hashimoto Masahito , Kato Fuminori , Sugai Motoyuki , Komatsuzawa Hitoshi 
Published: September 2011

ABSTRACT

Staphylococcus aureus
produces many virulence factors, including toxins, immune-modulatory factors, and exoenzymes. Previous studies involving the analysis of virulence expression were mainly performed by
in vitro
experiments using bacterial medium. However, when
S. aureus
infects a host, the bacterial growth conditions are quite different from those in a medium, which may be related to the different expression of virulence factors in the host. In this study, we investigated the expression of virulence factors in
S. aureus
grown in calf serum. The expression of many virulence factors, including hemolysins, enterotoxins, proteases, and iron acquisition factors, was significantly increased compared with that in bacterial medium. In addition, the expression of RNA III, a global regulon for virulence expression, was significantly increased. This effect was partially restored by the addition of 300 μM FeCl
3
into serum, suggesting that iron depletion is associated with the increased expression of virulence factors in serum. In chemically defined medium without iron, a similar effect was observed. In a mutant with
agr
inactivated grown in serum, the expression of RNA III,
psm
, and
sec4
was not increased, while other factors were still induced in the mutant, suggesting that another regulatory factor(s) is involved. In addition, we found that serum albumin is a major factor for the capture of free iron to prevent the supply of iron to bacteria grown in serum. These results indicate that
S. aureus
expresses virulence factors in adaptation to the host environment.
Staphylococcus epidermidis Bacteriophages from the Anterior Nares of Humans
Authors: Aswani Vijay , Tremblay Denise M. , Moineau Sylvain , Shukla Sanjay K. 
Published: September 2011

ABSTRACT

The role of virulent bacteriophages in staphylococcal colonization of the human anterior nares is not known. This report of lytic bacteriophages against
Staphylococcus epidermidis
in the anterior nares of 5.5% of human subjects (
n
= 202) suggests their potential role in modulating staphylococcal colonization in this ecological niche.
Fimbrial Adhesins Produced by Atypical Enteropathogenic Escherichia coli Strains
Authors: Hernandes Rodrigo T. , Velsko Irina , Sampaio Suely C. F. , Elias Waldir P. , Robins-Browne Roy M. , Gomes Tï¿½nia A. T. , Girï¿½n Jorge A. 
Published: September 2011

ABSTRACT

Atypical enteropathogenic
Escherichia coli
(aEPEC) has emerged as a significant cause of pediatric diarrhea worldwide; however, information regarding its adherence mechanisms to the human gut mucosa is lacking. In this study, we investigated the prevalence of several (
fimA
,
ecpA
,
csgA
,
elfA
, and
hcpA
) fimbrial genes in 71 aEPEC strains isolated from children with diarrhea (54 strains) and healthy individuals (17 strains) in Brazil and Australia by PCR. These genes are associated with adhesion and/or biofilm formation of pathogenic and commensal
E. coli
. Here, the most prevalent fimbrial genes found, in descending order, were
hcpA
(98.6%),
ecpA
(86%),
fimA
(76%),
elfA
(72%), and
csgA
(19.7%). Phenotypic expression of pili in aEPEC strains was assessed by several approaches. We were not able to detect the hemorrhagic coli pilus (HCP) or the
E. coli
laminin-binding fimbriae (ELF) in these strains by using immunofluorescence. Type 1 pili and curli were detected in 59% (by yeast agglutination) and 2.8% (by Congo red binding and immunofluorescence) of the strains, respectively. The
E. coli
common pilus (ECP) was evidenced in 36.6% of the strains on bacteria adhering to HeLa cells by immunofluorescence, suggesting that ECP could play an important role in cell adherence for some aEPEC strains. This study highlights the complex nature of the adherence mechanisms of aEPEC strains involving the coordinated function of fimbrial (e.g., ECP) and nonfimbrial (e.g., intimin) adhesins and indicates that these strains bear several pilus operons that could potentially be expressed in different niches favoring colonization and survival in and outside the host.
Correlation between Protection against Sepsis by Probiotic Therapy and Stimulation of a Novel Bacterial Phylotype
Authors: Gerritsen Jacoline , Timmerman Harro M. , Fuentes Susana , van Minnen L. Paul , Panneman Henk , Konstantinov Sergey R. , Rombouts Frans M. , Gooszen Hein G. , Akkermans Louis M. A. , Smidt Hauke , Rijkers Ger T. 
Published: September 2011

ABSTRACT

Prophylactic probiotic therapy has shown beneficial effects in an experimental rat model for acute pancreatitis on the health status of the animals. Mechanisms by which probiotic therapy interferes with severity of acute pancreatitis and associated sepsis, however, are poorly understood. The aims of this study were to identify the probiotic-induced changes in the gut microbiota and to correlate these changes to disease outcome. Duodenum and ileum samples were obtained from healthy and diseased rats subjected to pancreatitis for 7 days and prophylactically treated with either a multispecies probiotic mixture or a placebo. Intestinal microbiota was characterized by terminal-restriction fragment length polymorphism (T-RFLP) analyses of PCR-amplified 16S rRNA gene fragments. These analyses showed that during acute pancreatitis the host-specific ileal microbiota was replaced by an “acute pancreatitis-associated microbiota.” This replacement was not reversed by administration of the probiotic mixture. An increase, however, was observed in the relative abundance of a novel bacterial phylotype most closely related to
Clostridium lituseburense
and referred to as commensal rat ileum bacterium (CRIB). Specific primers targeting the CRIB 16S rRNA gene sequence were developed to detect this phylotype by quantitative PCR. An ileal abundance of CRIB 16S rRNA genes of more than 7.5% of the total bacterial 16S rRNA gene pool was correlated with reduced duodenal bacterial overgrowth, reduced bacterial translocation to remote organs, improved pancreas pathology, and reduced proinflammatory cytokine levels in plasma. Our current findings and future studies involving this uncharacterized bacterial phylotype will contribute to unraveling one of the potential mechanisms of probiotic therapy.
Species Diversity, Community Dynamics, and Metabolite Kinetics of the Microbiota Associated with Traditional Ecuadorian Spontaneous Cocoa Bean Fermentations
Authors: Papalexandratou Zoi , Falony Gwen , Romanens Edwina , Jimenez Juan Carlos , Amores Freddy , Daniel Heide-Marie , De Vuyst Luc 
Published: September 2011

ABSTRACTTraditional fermentations of the local Ecuadorian cocoa type Nacional, with its fine flavor, are carried out in boxes and on platforms for a short time. A multiphasic approach, encompassing culture-dependent and -independent microbiological analyses of fermenting cocoa pulp-bean samples, metabolite target analyses of both cocoa pulp and beans, and sensory analysis of chocolates produced from the respective fermented dry beans, was applied for the investigation of the influence of these fermentation practices on the yeast and bacterial species diversity and community dynamics during cocoa bean fermentation. A wide microbial species diversity was found during the first 3 days of all fermentations carried out. The prevailing ethanol-producing yeast species werePichia kudriavzeviiandPichia manshurica, followed bySaccharomyces cerevisiae. Leuconostoc pseudomesenteroides(glucose and fructose fermenting),Fructobacillus tropaeoli-like (fructose fermenting), andLactobacillus fermentum(citrate converting, mannitol producing) represented the main lactic acid bacterial species in the fermentations studied, resulting in intensive heterolactate metabolism of the pulp substrates.Tatumella saanichensisandTatumella punctatawere among the members of the familyEnterobacteriaceaepresent during the initial phase of the cocoa bean fermentations and could be responsible for the production of gluconic acid in some cases. Also, a potential new yeast species was isolated, namely,Candida sorbosivorans-like. Acetic acid bacteria, whose main representative wasAcetobacter pasteurianus, generally appeared later during fermentation and oxidized ethanol to acetic acid. However, acetic acid bacteria were not always present during the main course of the platform fermentations. All of the data taken together indicated that short box and platform fermentation methods caused incomplete fermentation, which had a serious impact on the quality of the fermented dry cocoa beans.
Development of
phoH
as a Novel Signature Gene for Assessing Marine Phage Diversity
Authors: Goldsmith Dawn B. , Crosti Giuseppe , Dwivedi Bhakti , McDaniel Lauren D. , Varsani Arvind , Suttle Curtis A. , Weinbauer Markus G. , Sandaa Ruth-Anne , Breitbart Mya 
Published: September 2011

ABSTRACT

Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified,
phoH
was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage
phoH
sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the
phoH
gene were used to determine the diversity of phage
phoH
sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide.
phoH
was present at all sites examined, and a high diversity of
phoH
sequences was recovered. Most
phoH
sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct
phoH
composition, although most
phoH
clusters were recovered from multiple sites. Overall,
phoH
is an effective signature gene for examining phage diversity in the marine environment.
rnr
Gene from the Antarctic Bacterium Pseudomonas syringae Lz4W, Encoding a Psychrophilic RNase R
Authors: Sulthana Shaheen , Rajyaguru Purusharth I. , Mittal Pragya , Ray Malay K. 
Published: September 2011

ABSTRACT

RNase R is a highly processive, hydrolytic 3′-5′ exoribonuclease belonging to the RNB/RNR superfamily which plays significant roles in RNA metabolism in bacteria. The enzyme was observed to be essential for growth of the psychrophilic Antarctic bacterium
Pseudomonas syringae
Lz4W at a low temperature. We present results here pertaining to the biochemical properties of RNase R and the RNase R-encoding gene (
rnr
) locus from this bacterium. By cloning and expressing a His
6
-tagged form of the
P. syringae
RNase R (RNase R
Ps
), we show that the enzyme is active at 0 to 4°C but exhibits optimum activity at ∼25°C. The enzyme is heat labile in nature, losing activity upon incubation at 37°C and above, a hallmark of many psychrophilic enzymes. The enzyme requires divalent cations (Mg
2+
and Mn
2+
) for activity, and the activity is higher in 50 to 150 mM KCl when it largely remains as a monomer. On synthetic substrates, RNase R
Ps
exhibited maximum activity on poly(A) and poly(U) in preference over poly(G) and poly(C). The enzyme also degraded structured
malE-malF
RNA substrates. Analysis of the cleavage products shows that the enzyme, apart from releasing 5′-nucleotide monophosphates by the processive exoribonuclease activity, produces four-nucleotide end products, as opposed to two-nucleotide products, of RNA chain by
Escherichia coli
RNase R. Interestingly, three ribonucleotides (ATP, GTP, and CTP) inhibited the activity of RNase R
Ps
in vitro
. The ability of the nonhydrolyzable ATP-γS to inhibit RNase R
Ps
activity suggests that nucleotide hydrolysis is not required for inhibition. This is the first report on the biochemical property of a psychrophilic RNase R from any bacterium.
Dynamics of Microbial Community Structure of and Enhanced Biological Phosphorus Removal by Aerobic Granules Cultivated on Propionate or Acetate
Authors: Gonzalez-Gil Graciela , Holliger Christof 
Published: September 2011

ABSTRACT

Aerobic granules are dense microbial aggregates with the potential to replace floccular sludge for the treatment of wastewaters. In bubble-column sequencing batch reactors, distinct microbial populations dominated propionate- and acetate-cultivated aerobic granules after 50 days of reactor operation when only carbon removal was detected. Propionate granules were dominated by
Zoogloea
(40%),
Acidovorax
, and
Thiothrix
, whereas acetate granules were mainly dominated by
Thiothrix
(60%). Thereafter, an exponential increase in enhanced biological phosphorus removal (EBPR) activity was observed in the propionate granules, but a linear and erratic increase was detected in the acetate ones. Besides
Accumulibacter
and
Competibacter
, other bacterial populations found in both granules were associated with
Chloroflexus
and
Acidovorax
. The EBPR activity in the propionate granules was high and stable, whereas EBPR in the acetate granules was erratic throughout the study and suffered from a deterioration period that could be readily reversed by inducing hydrolysis of polyphosphate in presumably saturated
Accumulibacter
cells. Using a new
ppk1
gene-based dual terminal-restriction fragment length polymorphism (T-RFLP) approach revealed that
Accumulibacter
diversity was highest in the floccular sludge inoculum but that when granules were formed, propionate readily favored the dominance of
Accumulibacter
type IIA. In contrast, acetate granules exhibited transient shifts between type I and type II before the granules were dominated by
Accumulibacter
type IIA. However,
ppk1
gene sequences from acetate granules clustered separately from those of propionate granules. Our data indicate that the mere presence of
Accumulibacter
is not enough to have consistently high EBPR but that the type of
Accumulibacter
determines the robustness of the phosphate removal process.