bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lectin Microarray Reveals Binding Profiles of Lactobacillus casei Strains in a Comprehensive Analysis of Bacterial Cell Wall Polysaccharides
Authors: Yasuda Emi , Tateno Hiroaki , Hirabarashi Jun , Iino Tohru , Sako Tomoyuki 
Published: May 2011

ABSTRACT

We previously showed a pivotal role of the polysaccharide (PS) moiety in the cell wall of the
Lactobacillus casei
strain Shirota (YIT 9029) as a possible immune modulator (E. Yasuda M. Serata, and T. Sako, Appl. Environ. Microbiol. 74:4746-4755, 2008). To distinguish PS structures on the bacterial cell surface of individual strains in relation to their activities, it would be useful to have a rapid and high-throughput methodology. Recently, a new technique called lectin microarray was developed for rapid profiling of glycosylation in eukaryotic polymers and cell surfaces. Here, we report on the development of a simple and sensitive method based on this technology for direct analysis of intact bacterial cell surface glycomes. The method involves labeling bacterial cells with SYTOX Orange before incubation with the lectin microarray. After washing, bound cells are directly detected using an evanescent-field fluorescence scanner in a liquid phase. Using this method, we compared the cell surface glycomes from 16 different strains of
L. casei
. The patterns of lectin-binding affinity of most strains were found to be unique. There appears to be two types of lectin-binding profiles: the first is characterized by a few lectins, and the other is characterized by multiple lectins with different specificities. We also showed a dramatic change in the lectin-binding profile of a YIT 9029 derivative with a mutation in the
cps1C
gene, encoding a putative glycosyltransferase. In conclusion, the developed technique provided a novel strategy for rapid profiling and, more importantly, differentiating numerous bacterial strains with relevance to the biological functions of PS.
Phylogenetic and Functional Analysis of Aspergillus fumigatus MGTC, a Fungal Protein Homologous to a Bacterial Virulence Factor
Authors: Gastebois Amandine , Blanc Potard Anne-Beatrice , Gribaldo Simonetta , Beau Rémi , Latgé Jean Paul , Mouyna Isabelle 
Published: May 2011

ABSTRACT

MgtC is important for the survival of several bacterial pathogens in macrophages and for growth under magnesium limitation. Among eukaryotes, a gene homologous to
mgtC
was found only in the pathogenic fungus
Aspergillus fumigatus
. Our data show that the
A. fumigatus
MgtC (AfuMgtC) protein does not have the same function as the bacterial MgtC proteins.
Responses of Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus to Simulated Food Processing Treatments, Determined Using Fluorescence-Activated Cell Sorting and Plate Counting
Authors: Kennedy Deirdre , Cronin Ultan P. , Wilkinson Martin G. 
Published: May 2011

ABSTRACT

Three common food pathogenic microorganisms were exposed to treatments simulating those used in food processing. Treated cell suspensions were then analyzed for reduction in growth by plate counting. Flow cytometry (FCM) and fluorescence-activated cell sorting (FACS) were carried out on treated cells stained for membrane integrity (Syto 9/propidium iodide) or the presence of membrane potential [DiOC
2
(3)]. For each microbial species, representative cells from various subpopulations detected by FCM were sorted onto selective and nonselective agar and evaluated for growth and recovery rates. In general, treatments giving rise to the highest reductions in counts also had the greatest effects on cell membrane integrity and membrane potential. Overall, treatments that impacted cell membrane permeability did not necessarily have a comparable effect on membrane potential. In addition, some bacterial species with extensively damaged membranes, as detected by FCM, appeared to be able to replicate and grow after sorting. Growth of sorted cells from various subpopulations was not always reflected in plate counts, and in some cases the staining protocol may have rendered cells unculturable. Optimized FCM protocols generated a greater insight into the extent of the heterogeneous bacterial population responses to food control measures than did plate counts. This study underlined the requirement to use FACS to relate various cytometric profiles generated by various staining protocols with the ability of cells to grow on microbial agar plates. Such information is a prerequisite for more-widespread adoption of FCM as a routine microbiological analytical technique.
Combined Application of PCR-Based Functional Assays for the Detection of Aromatic-Compound-Degrading Anaerobes
Authors: Kuntze Kevin , Vogt Carsten , Richnow Hans-Hermann , Boll Matthias 
Published: May 2011

ABSTRACTTo explore the reliability of assays that detect aromatic-compound-degrading anaerobes, a combination of three functional-gene-targeting assays was applied to microcosms from benzene-contaminated aquifers. Results of the assays were consistent and suggest that species related to the generaAzoarcusandGeobacterdominated benzene degradation at the individual sites.
FadD19 of Rhodococcus rhodochrous DSM43269, a Steroid-Coenzyme A Ligase Essential for Degradation of C-24 Branched Sterol Side Chains
Authors: Wilbrink M. H. , Petrusma M. , Dijkhuizen L. , van der Geize R. 
Published: May 2011

ABSTRACT

The actinobacterial cholesterol catabolic gene cluster contains a subset of genes that encode β-oxidation enzymes with a putative role in sterol side chain degradation. We investigated the physiological roles of several genes, i.e.,
fadD17
,
fadD19
,
fadE26
,
fadE27
, and

ro04690
DSM43269

, by gene inactivation studies in mutant strain RG32 of
Rhodococcus rhodochrous
DSM43269. Mutant strain RG32 is devoid of 3-ketosteroid 9α-hydroxylase (KSH) activity and was constructed following the identification, cloning, and sequential inactivation of five
kshA
gene homologs in strain DSM43269. We show that mutant strain RG32 is fully blocked in steroid ring degradation but capable of selective sterol side chain degradation. Except for RG32Δ
fadD19
, none of the mutants constructed in RG32 revealed an aberrant phenotype on sterol side chain degradation compared to parent strain RG32. Deletion of
fadD19
in strain RG32 completely blocked side chain degradation of C-24 branched sterols but interestingly not that of cholesterol. The additional inactivation of
fadD17
in mutant RG32Δ
fadD19
also did not affect cholesterol side chain degradation. Heterologously expressed FadD19
DSM43269
nevertheless was active toward steroid-C
26
-oic acid substrates. Our data identified FadD19 as a steroid-coenzyme A (CoA) ligase with an essential
in vivo
role in the degradation of the side chains of C-24 branched-chain sterols. This paper reports the identification and characterization of a CoA ligase with an
in vivo
role in sterol side chain degradation. The high similarity (67%) between the FadD19
DSM43269
and FadD19
H37Rv
enzymes further suggests that FadD19
H37Rv
has an
in vivo
role in sterol metabolism of
Mycobacterium tuberculosis
H37Rv.
Goose-Type Lysozyme Inhibitor (PliG) Enhances Survival of Escherichia coli in Goose Egg Albumen
Authors: Vanderkelen Lise , Van Herreweghe Joris M. , Callewaert Lien , Michiels Chris W. 
Published: May 2011

ABSTRACT

The goose-type lysozyme inhibitor PliG enhances the survival of
Escherichia coli
in goose but not in chicken egg white, which contains goose- and chicken-type lysozymes, respectively. These results indicate that both the type of host lysozyme and the type of bacterial lysozyme inhibitor may affect bacterium-host interactions.
Thalassospira sp. Isolated from the Oligotrophic Eastern Mediterranean Sea Exhibits Chemotaxis toward Inorganic Phosphate during Starvation
Authors: Hütz Annemarie , Schubert Karin , Overmann Jörg 
Published: May 2011

ABSTRACT

The eastern Mediterranean Sea represents an ultraoligotrophic environment where soluble phosphate limits the growth of bacterioplankton. Correspondingly, genes coding for high-affinity phosphate uptake systems and for organophosphonate utilization are highly prevalent in the plankton metagenome. Chemotaxis toward inorganic phosphate constitutes an alternative strategy to cope with phosphate limitation, but so far has only been demonstrated for two bacterial pathogens and an archaeon, and not in any free-living planktonic bacterium. In the present study, bacteria affiliated with the genus
Thalassospira
were found to constitute a regular, low-abundance member of the bacterioplankton that can be detected throughout the water column of the eastern Mediterranean Sea. A representative (strain EM) was isolated in pure culture and exhibited a strong positive chemotaxis toward inorganic phosphate that was induced exclusively in phosphate-starved cultures. Phosphate-depleted cells were 2-fold larger than in exponentially growing cultures, and 43% of the cells retained their motility even during prolonged starvation over 10 days. In addition,
Thalassospira
sp. strain EM was chemotactically attracted by complex substrates (yeast extract and peptone), amino acids, and 2-aminoethylphosphonate but not by sugar monomers. Similarly to the isolate from the eastern Mediterranean, chemotaxis toward phosphate was observed in starved cultures of the other two available isolates of the genus,
T. lucentensis
DSM 14000
T
and
T. profundimaris
WP0211
T
. Although
Thalassospira
sp. represents only up to 1.2% of the total bacterioplankton community in the water column of the eastern Mediterranean Sea, its chemotactic behavior potentially leads to an acceleration of nutrient cycling and may also explain the persistence of marine copiotrophs in this extremely nutrient-limited environment.
Dehydrogenase GRD1 Represents a Novel Component of the Cellulase Regulon in Trichoderma reesei (Hypocrea jecorina)
Authors: Schuster André , Kubicek Christian P. , Schmoll Monika 
Published: May 2011

ABSTRACT

Trichoderma reesei
(
Hypocrea jecorina
) is nowadays the most important industrial producer of cellulase and hemicellulase enzymes, which are used for pretreatment of cellulosic biomass for biofuel production. In this study, we introduce a novel component, GRD1 (glucose-ribitol dehydrogenase 1), which shows enzymatic activity on cellobiose and positively influences cellulase gene transcription, expression, and extracellular endo-1,4-β-
d
-glucanase activity.
grd1
is differentially transcribed upon growth on cellulose and the induction of cellulase gene expression by sophorose. The transcription of
grd1
is coregulated with that of
cel7a
(
cbh1
) under inducing conditions. GRD1 is further involved in carbon source utilization on several carbon sources, such as those involved in lactose and
d
-galactose catabolism, in several cases in a light-dependent manner. We conclude that GRD1 represents a novel enhancer of cellulase gene expression, which by coregulation with the major cellulase may act via optimization of inducing mechanisms.
Shedding Light on Selenium Biomineralization: Proteins Associated with Bionanominerals
Authors: Lenz Markus , Kolvenbach Boris , Gygax Benjamin , Moes Suzette , Corvini Philippe F. X. 
Published: May 2011

ABSTRACT

Selenium-reducing microorganisms produce elemental selenium nanoparticles with particular physicochemical properties due to an associated organic fraction. This study identified high-affinity proteins associated with such bionanominerals and with nonbiogenic elemental selenium. Proteins with an anticipated functional role in selenium reduction, such as a metalloid reductase, were found to be associated with nanoparticles formed by one selenium respirer,
Sulfurospirillum barnesii
.
Preferential Feeding by the Ciliates Chilodonella and Tetrahymena spp. and Effects of These Protozoa on Bacterial Biofilm Structure and Composition
Authors: Dopheide Andrew , Lear Gavin , Stott Rebecca , Lewis Gillian 
Published: May 2011

ABSTRACT

Protozoa are important components of microbial food webs, but protozoan feeding preferences and their effects in the context of bacterial biofilms are not well understood. The feeding interactions of two contrasting ciliates, the free-swimming filter feeder
Tetrahymena
sp. and the surface-associated predator
Chilodonella
sp., were investigated using biofilm-forming bacteria genetically modified to express fluorescent proteins. According to microscopy, both ciliates readily consumed cells from both
Pseudomonas
costantinii
and
Serratia
plymuthica
biofilms. When offered a choice between spatially separated biofilms, each ciliate showed a preference for
P. costantinii
biofilms. Experiments with bacterial cell extracts indicated that both ciliates used dissolved chemical cues to locate biofilms.
Chilodonella
sp. evidently used bacterial chemical cues as a basis for preferential feeding decisions, but it was unclear whether
Tetrahymena
sp. did also. Confocal microscopy of live biofilms revealed that
Tetrahymena
sp. had a major impact on biofilm morphology, forming holes and channels throughout
S. plymuthica
biofilms and reducing
P. costantinii
biofilms to isolated, grazing-resistant microcolonies. Grazing by
Chilodonella
sp. resulted in the development of less-defined trails through
S. plymuthica
biofilms and caused
P. costantinii
biofilms to become homogeneous scatterings of cells. It was not clear whether the observed feeding preferences for spatially separated
P. costantinii
biofilms over
S. plymuthica
biofilms resulted in selective targeting of
P. costantinii
cells in mixed biofilms. Grazing of mixed biofilms resulted in the depletion of both types of bacteria, with
Tetrahymena
sp. having a larger impact than
Chilodonella
sp., and effects similar to those seen in grazed single-species biofilms.
Functional Characterization of a Mucus-Specific LPXTG Surface Adhesin from Probiotic Lactobacillus rhamnosus GG
Authors: von Ossowski Ingemar , Satokari Reetta , Reunanen Justus , Lebeer Sarah , De Keersmaecker Sigrid C. J. , Vanderleyden Jos , de Vos Willem M. , Palva Airi 
Published: May 2011

ABSTRACT

In spite of the wealth of clinical evidence supporting the health benefits of
Lactobacillus rhamnosus
GG in humans, there is still a lack of understanding of the molecular mechanisms behind its probiosis. Current knowledge suggests that the health-promoting effects of this probiotic strain might be partly dependent on its persistence in the intestine and adhesion to mucosal surfaces. Moreover,
L. rhamnosus
GG contains mucus-binding pili that might also explain the occupation of its ecological niche as a comparatively less stringent allochthonous intestine-dwelling bacterium. To uncover additional surface proteins involved in mucosal adhesion, we investigated the adherence properties of the only predicted protein (LGG_02337) in
L. rhamnosus
GG that exhibits homology with a known mucus-binding domain. We cloned a recombinant form of the gene for this putative mucus adhesin and established that the purified protein readily adheres to human intestinal mucus. We also showed that this mucus adhesin is visibly distributed throughout the cell surface and participates in the adhesive interaction between
L. rhamnosus
GG and mucus, although less prominently than the mucus-binding pili in this strain. Based on primary structural comparisons, we concluded that the current annotation of the LGG_02337 protein likely does not accurately reflect its predicted properties, and we propose that this mucus-specific adhesin be called the mucus-binding factor (MBF). Finally, we interpret our results to mean that
L. rhamnosus
GG MBF, as an active mucus-specific surface adhesin with a presumed ancillary involvement in pilus-mediated mucosal adhesion, plays a part in the adherent mechanisms during intestinal colonization by this probiotic.
Development of a Streptomyces venezuelae-Based Combinatorial Biosynthetic System for the Production of Glycosylated Derivatives of Doxorubicin and Its Biosynthetic Intermediates
Authors: Han Ah Reum , Park Je Won , Lee Mi Kyeong , Ban Yeon Hee , Yoo Young Ji , Kim Eun Ji , Kim Eunji , Kim Byung-Gee , Sohng Jae Kyung , Yoon Yeo Joon 
Published: May 2011

ABSTRACTDoxorubicin, one of the most widely used anticancer drugs, is composed of a tetracyclic polyketide aglycone andl-daunosamine as a deoxysugar moiety, which acts as an important determinant of its biological activity. This is exemplified by the fewer side effects of semisynthetic epirubicin (4′-epi-doxorubicin). An efficient combinatorial biosynthetic system that can convert the exogenous aglycone ε-rhodomycinone into diverse glycosylated derivatives of doxorubicin or its biosynthetic intermediates, rhodomycin D and daunorubicin, was developed through the use ofStreptomyces venezuelaemutants carrying plasmids that direct the biosynthesis of different nucleotide deoxysugars and their transfer onto aglycone, as well as the postglycosylation modifications. This system improved epirubicin production from ε-rhodomycinone by selecting a substrate flexible glycosyltransferase, AknS, which was able to transfer the unnatural sugar donors and a TDP-4-ketohexose reductase, AvrE, which efficiently supported the biosynthesis of TDP-4-epi-l-daunosamine. Furthermore, a range of doxorubicin analogs containing diverse deoxysugar moieties, seven of which are novel rhodomycin D derivatives, were generated. This provides new insights into the functions of deoxysugar biosynthetic enzymes and demonstrates the potential of theS. venezuelae-based combinatorial biosynthetic system as a simple biological tool for modifying structurally complex sugar moieties attached to anthracyclines as an alternative to chemical syntheses for improving anticancer agents.
Spatiotemporal Changes in the Structure and Composition of a Less-Abundant Bacterial Phylum (Planctomycetes) in Two Perialpine Lakes
Authors: Pollet Thomas , Tadonléké Rémy D. , Humbert Jean François 
Published: May 2011

ABSTRACT

We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of
Planctomycetes
in two perialpine lakes with contrasting environmental conditions.
Planctomycetes
, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems,
Planctomycetes
communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of “abundant or core” and “rare” bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of
Planctomycetes
were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the
Planctomycetes
community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as
Planctomycetes
, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column.
Selection Pressure Required for Long-Term Persistence of
bla
CMY-2
-Positive IncA/C Plasmids
Authors: Subbiah Murugan , Top Eva M. , Shah Devendra H. , Call Douglas R. 
Published: May 2011

ABSTRACT

Multidrug resistance
bla
CMY-2
plasmids that confer resistance to expanded-spectrum cephalosporins have been found in multiple bacterial species collected from different hosts worldwide. The widespread distribution of
bla
CMY-2
plasmids may be driven by antibiotic use that selects for the dissemination and persistence of these plasmids. Alternatively, these plasmids may persist and spread in bacterial populations in the absence of selection pressure if a balance exists among conjugative transfer, segregation loss during cell division, and fitness cost to the host. We conducted a series of experiments (both
in vivo
and
in vitro
) to study these mechanisms for three
bla
CMY-2
plasmids, peH4H, pAR060302, and pAM04528. Results of filter mating experiments showed that the conjugation efficiency of
bla
CMY-2
plasmids is variable, from <10
−7
for pAM04528 and peH4H to ∼10
−3
for pAR060302. Neither peH4H nor pAM04528 was transferred from
Escherichia coli
strain DH10B, but peH4H was apparently mobilized by the coresident trimethoprim resistance-encoding plasmid pTmpR. Competition studies showed that carriage of
bla
CMY-2
plasmids imposed a measurable fitness cost on the host bacteria both
in vitro
(0.095 to 0.25) and
in vivo
(dairy calf model). Long-term passage experiments in the absence of antibiotics demonstrated that plasmids with limited antibiotic resistance phenotypes arose, but eventually drug-sensitive, plasmid-free clones dominated the populations. Given that plasmid decay or loss is inevitable, we infer that some level of selection is required for the long-term persistence of
bla
CMY-2
plasmids in bacterial populations.
Impact of Medicated Feed on the Development of Antimicrobial Resistance in Bacteria at Integrated Pig-Fish Farms in Vietnam
Authors: Dang Son Thi Thanh , Petersen Andreas , Van Truong Dung , Chu Huong Thi Thanh , Dalsgaard Anders 
Published: May 2011

ABSTRACT

Integrated livestock-fish aquaculture utilizes animal excreta, urine, and feed leftovers as pond fertilizers to enhance the growth of plankton and other microorganisms eaten by the fish. However, antimicrobial-resistant bacteria may be transferred and develop in the pond due to selective pressure from antimicrobials present in animal feed, urine, and feces. In an experimental pig-fish farm located in periurban Hanoi, Vietnam, nine piglets were provided feed containing 5 μg of tetracycline (TET)/kg pig weight/day and 0.45 μg of enrofloxacin (ENR)/kg pig weight/day during the second and fourth (last) months of the experiment. The aim of this study was to determine the association between the provision of pig feed with antimicrobials and the development of antimicrobial resistance, as measured in a total of 520
Escherichia coli
and 634
Enterococcus
strains isolated from pig manure and water-sediment pond samples. MIC values for nalidixic acid (NAL) and ENR showed that
E. coli
and
Enterococcus
spp. overall exhibited significant higher frequencies of resistance toward NAL and ENR during the 2 months when pigs were administered feed with antimicrobials, with frequencies reaching 60 to 80% in both water-sediment and manure samples. TET resistance for both indicators was high (>80%) throughout the study period, which indicates that TET-resistant
E. coli
and
Enterococcus
spp. were present in the piglets before the initiation of the experiment. PCR-based identification showed similar relative occurrences of
Enterococcus faecium
,
Enterococcus faecalis
, and other
Enterococcus
spp. in the water-sediment and manure samples, suggesting that
Enterococcus
spp. isolated in the ponds originated mainly from the pig manure. The development of antimicrobial resistance in integrated animal husbandry-fish farms and possible transfers and the impact of such resistance on food safety and human health should be further assessed.