bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annual Variations in the Diversity, Viability, and Origin of Airborne Bacteria
Authors: Fahlgren Camilla , Hagström Åke , Nilsson Douglas , Zweifel Ulla Li 
Published: March 2010

ABSTRACT

The presence of bacteria in aerosols has been known for centuries, but information on their identity and role in dispersing microbial traits is still limited. This study monitored the airborne bacterial community during an annual survey using samples collected from a 25-m tower near the Baltic Sea coast. The number of CFU was estimated using agar plates while the most probable number (MPN) of viable bacteria was estimated using dilution-to-extinction culturing assays (DCAs). The MPN and CFU values produced quantitatively similar results, displaying a pronounced seasonal pattern, with the highest numbers in winter. The most dominant bacteria growing in the DCAs all formed colonies on agar plates, were mostly pigmented (80%), and closely resembled (>97%) previously cultured bacteria based on their 16S rRNA gene sequences. 16S rRNA gene clone libraries were constructed on eight occasions during the survey; these revealed a highly diverse community with a few abundant operational taxonomic units (OTUs) and a long tail of rare OTUs. A majority of the cloned sequences (60%) were also most closely related to previously “cultured” bacteria. Thus, both culture-dependent and culture-independent techniques indicated that bacteria able to form colonies on agar plates predominate in the atmosphere. Both the DCAs and clone libraries indicated the dominance of bacteria belonging to the genera
Sphingomonas
sp. and
Pseudomonas
sp. on several sampling occasions. Potentially pathogenic strains as well as sequences closely resembling bacteria known to act as ice nuclei were found using both approaches. The origin of the sampled air mass was estimated using backward trajectories, indicating a predominant marine source.
Diversity of Anaerobic Microbes in Spacecraft Assembly Clean Rooms
Authors: Probst Alexander , Vaishampayan Parag , Osman Shariff , Moissl-Eichinger Christine , Andersen Gary L. , Venkateswaran Kasthuri 
Published: March 2010

ABSTRACT
Although the cultivable and noncultivable microbial diversity of spacecraft assembly clean rooms has been previously documented using conventional and state-of-the-art molecular techniques, the occurrence of obligate anaerobes within these clean rooms is still uncertain. Therefore, anaerobic bacterial communities of three clean-room facilities were analyzed during assembly of the Mars Science Laboratory rover. Anaerobic bacteria were cultured on several media, and DNA was extracted from suitable anaerobic enrichments and examined with conventional 16S rRNA gene clone library, as well as high-density phylogenetic 16S rRNA gene microarray (PhyloChip) technologies. The culture-dependent analyses predominantly showed the presence of clostridial and propionibacterial strains. The 16S rRNA gene sequences retrieved from clone libraries revealed distinct microbial populations associated with each clean-room facility, clustered exclusively within gram-positive organisms. PhyloChip analysis detected a greater microbial diversity, spanning many phyla of bacteria, and provided a deeper insight into the microbial community structure of the clean-room facilities. This study presents an integrated approach for assessing the anaerobic microbial population within clean-room facilities, using both molecular and cultivation-based analyses. The results reveal that highly diverse anaerobic bacterial populations persist in the clean rooms even after the imposition of rigorous maintenance programs and will pose a challenge to planetary protection implementation activities.
Listeria seeligeri
Isolates from Food Processing Environments Form Two Phylogenetic Lineages
Authors: Müller Andrea A. , Schmid Michael W. , Meyer Ortwin , Meussdoerffer Franz G. 
Published: March 2010

ABSTRACT

Seven different
actA
subtypes forming two phylogenetic lineages could be distinguished by sequencing the
actA
gene of
Listeria seeligeri
isolates from different habitats. Isolates of the two lineages differ in hemolytic as well as phospholipase activities and in the arrangement of the virulence gene cluster. The presence of a serine protease gene resembling
orf2110
of
L. monocytogenes
in some isolates further supports the hypothesis that
L. seeligeri
is subject to ongoing adaptation to changing environments.
Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva
Authors: Takeshita Toru , Suzuki Nao , Nakano Yoshio , Shimazaki Yoshihiro , Yoneda Masahiro , Hirofuji Takao , Yamashita Yoshihisa 
Published: March 2010

ABSTRACT

Oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. In this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (T-RFLP) profiles using hierarchical cluster analysis, and the patterns of the microbial community composition of those exhibiting higher and lower malodor were explored. Four types of bacterial community compositions were detected (clusters I, II, III, and IV). Two parameters for measuring oral malodor intensity (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) were noticeably lower in cluster I than in the other clusters. Using multivariate analysis, the differences in the levels of oral malodor were significant after adjustment for potential confounding factors such as total bacterial count, mean periodontal pocket depth, and tongue coating score (
P
< 0.001). Among the four clusters with different proportions of indigenous members, the T-RFLP profiles of cluster I were implicated as the bacterial populations with higher proportions of
Streptococcus
,
Granulicatella
,
Rothia
, and
Treponema
species than those of the other clusters. These results clearly correlate the global composition of indigenous bacterial populations with the severity of oral malodor.
Isolation and Characterization of Potentially Pathogenic Antimicrobial-Resistant
Escherichia coli
Strains from Chicken and Pig Farms in Spain
Authors: Cortés Pilar , Blanc Vanessa , Mora Azucena , Dahbi Ghizlane , Blanco Jesús E. , Blanco Miguel , López Cecilia , Andreu Antonia , Navarro Ferran , Alonso María Pilar , Bou Germán , Blanco Jorge , Llagostera Montserrat 
Published: March 2010

ABSTRACT

To ascertain whether on animal farms there reside extended-spectrum β-lactamase (ESBL) and plasmidic class C β-lactamase-producing
Escherichia coli
isolates potentially pathogenic for humans, phylogenetic analyses, pulsed-field gel electrophoresis (PFGE) typing, serotyping, and virulence genotyping were performed for 86 isolates from poultry (57 isolates) and pig (29 isolates) farms.
E. coli
isolates from poultry farms carried genes encoding enzymes of the CTX-M-9 group as well as CMY-2, whereas those from pig farms mainly carried genes encoding CTX-M-1 enzymes. Poultry and pig isolates differed significantly in their phylogenetic group assignments, with phylogroup A predominating in pig isolates and phylogroup D predominating in avian isolates. Among the 86 farm isolates, 23 (26.7%) carried two or more virulence genes typical of extraintestinal pathogenic
E. coli
(ExPEC). Of these, 20 were isolated from poultry farms and only 3 from pig farms. Ten of the 23 isolates belonged to the classic human ExPEC serotypes O2:H6, O2:HNM, O2:H7, O15:H1, and O25:H4. Despite the high diversity of serotypes and pulsotypes detected among the 86 farm isolates, 13 PFGE clusters were identified. Four of these clusters contained isolates with two or more virulence genes, and two clusters exhibited the classic human ExPEC serotypes O2:HNM (ST10) and O2:H6 (ST115). Although O2:HNM and O2:H6 isolates of human and animal origins differed with respect to their virulence genes and PFGE pulsotypes, the O2:HNM isolates from pigs showed the same sequence type (ST10) as those from humans. The single avian O15:H1 isolate was compared with human clinical isolates of this serotype. Although all were found to belong to phylogroup D and shared the same virulence gene profile, they differed in their sequence types (ST362-avian and ST393-human) and PFGE pulsotypes. Noteworthy was the detection, for the first time, in poultry farms of the clonal groups O25b:H4-ST131-B2, producing CTX-M-9, and O25a-ST648-D, producing CTX-M-32. The virulence genes and PFGE profiles of these two groups were very similar to those of clinical human isolates. While further studies are required to determine the true zoonotic potential of these clonal groups, our results emphasize the zoonotic risk posed especially by poultry farms, but also by pig farms, as reservoirs of ESBL- and CMY-2-encoding
E. coli
.
Correlation of the Capsular Phenotype in
Propionibacterium freudenreichii
with the Level of Expression of
gtf
, a Unique Polysaccharide Synthase-Encoding Gene
Authors: Deutsch Stéphanie-Marie , Bivic Pierre Le , Hervé Christophe , Madec Marie-Noëlle , LaPointe Gisèle , Jan Gwenaël , Loir Yves Le , Falentin Hélène 
Published: March 2010

ABSTRACT

Many food-grade bacteria produce exopolysaccharides (EPS) that affect the texture of fermented food products and that may be involved in probiotic properties.
Propionibacterium freudenreichii
is a Gram-positive food-grade bacterium with reported probiotic capabilities that is widely used as starter in Swiss-type cheese. In this study, 68 strains of
P. freudenreichii
were screened for the β-glucan capsular phenotype by immunoagglutination with a specific antibody and for the presence of the
gtf
gene coding for polysaccharide synthase. All strains were positive for PCR amplification with
gtf
gene-specific primers, but the presence of β-glucan capsular EPS was detected for only 35% of the strains studied. Disruption of
gtf
in
P. freudenreichii
revealed that
gtf
is a unique gene involved in β-glucan capsular EPS production in
P. freudenreichii
. The
gtf
gene was transferred into and expressed in
Lactococcus lactis
, in which it conferred an agglutination-positive phenotype. Expression of the
gtf
gene was measured by performing quantitative reverse transcription-PCR assays with RNA from four capsular and three noncapsular strains. A positive correlation was found between the β-glucan capsular phenotype and
gtf
gene expression. Sequencing of the region upstream of the
gtf
open reading frame revealed the presence of an insertion element (IS element) in this upstream region in the four strains with the β-glucan capsular phenotype. The role of the IS element in the expression of neighboring genes and its impact on interstrain variability of the
P. freudenreichii
capsule phenotype remain to be elucidated.
Functional Prokaryotic RubisCO from an Oceanic Metagenomic Library
Authors: Witte Brian , John David , Wawrik Boris , Paul John H. , Dayan David , Tabita F. Robert 
Published: March 2010

ABSTRACT

Culture-independent studies have indicated that there is significant diversity in the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) enzymes used by marine, freshwater, and terrestrial autotrophic bacteria. Surprisingly, little is known about the catalytic properties of many environmentally significant RubisCO enzymes. Because one of the goals of RubisCO research is to somehow modify or select for RubisCO molecules with improved kinetic properties, a facile means to isolate functional and novel RubisCO molecules directly from the environment was developed. In this report, we describe the first example of functional RubisCO proteins obtained from genes cloned and characterized from metagenomic libraries derived from DNA isolated from environmental samples. Two form IA marine RubisCO genes were cloned, and each gene supported both photoheterotrophic and photoautotrophic growth of a RubisCO deletion strain of
Rhodobacter capsulatus
, strain SBI/II
−
, indicating that catalytically active recombinant RubisCO was synthesized. The catalytic properties of the metagenomic RubisCO molecules were further characterized. These experiments demonstrated the feasibility of studying the functional diversity and enzymatic properties of RubisCO enzymes without first cultivating the host organisms. Further, this “proof of concept” experiment opens the way for development of a simple functional screen to examine the properties of diverse RubisCO genes isolated from any environment, and subsequent further bioselection may be possible if the growth conditions of complemented
R. capsulatus
strain SBI/II
−
are varied.
Accuracy and Sensitivity of Commercial PCR-Based Methods for Detection of
Salmonella enterica
in Feed
Authors: Koyuncu Sevinc , Andersson M. Gunnar , Häggblom Per 
Published: March 2010

ABSTRACT

The present study compared the performance of commercial PCR-based
Salmonella enterica
detection methods (BAX System Q7, the iQ-Check
Salmonella
II kit, and the TaqMan
Salmonella enterica
detection kit) with culture-based methods (modified semisolid Rappaport-Vassiliadis [MSRV] and NMKL71) in spiked and naturally contaminated samples of feed mill scrapings (FMS), palm kernel meal (PKM), pelleted feed (PF), rape seed meal (RSM), soybean meal (SM), and wheat grain (WG). When results from the various feeds were compared, the number of
Salmonella enterica
CFU/25 g required to produce a positive were as follows: PKM > FMS = WG > RSM = SM = PF. These data are similar to those developed in earlier studies with culture-based
Salmonella
detection methods. PCR-based methods were performed similarly to culture-based methods, with respect to sensitivity and specificity. However, many PCR positives could not be confirmed by
Salmonella
isolation and for that reason the evaluated methods were found to be suitable only when rapid results were paramount. Nevertheless, PCR-based methods cannot presently replace culture-based methods when typing information is required for tracing studies or epidemiological investigations. The observed difference in detection levels is a potential problem when prevalence data are compared as well as when feed ingredients are tested for conformance with microbiological criteria. This paper also presents a statistical model that describes the detection probability when different levels (CFU) of
Salmonella
contamination are present in feed materials.
Evaluation of
Mycoplasma
Inactivation during Production of Biologics: Egg-Based Viral Vaccines as a Model
Authors: David Selwyn A. Wilson , Volokhov Dmitriy V. , Ye Zhiping , Chizhikov Vladimir 
Published: March 2010

ABSTRACT

Although mycoplasmas are generally considered to be harmless commensals, some mycoplasma species are able to cause infections in pediatric, geriatric, or immunocompromised patients. Thus, accidental contamination of biologics with mycoplasmas represents a potential risk for the health of individuals who receive cell-derived biological and pharmaceutical products. To assess the efficiency of inactivation of mycoplasmas by the agents used in the manufacture of egg-derived influenza vaccines, we carried out a series of experiments aimed at monitoring the viability of mycoplasmas spiked into both chicken allantoic fluid and protein-rich microbiological media and then treated with beta-propiolactone, formalin, cetyltrimethylammonium bromide, Triton X-100, and sodium deoxycholate, which are agents that are commonly used for virus inactivation and disruption of viral particles during influenza vaccine production. Twenty-two mycoplasma species (with one to four strains of each species) were exposed to these inactivating agents at different concentrations. The most efficient inactivation of the mycoplasmas evaluated was observed with either 0.5% Triton X-100 or 0.5% sodium deoxycholate. Cetyltrimethylammonium bromide at concentrations of ≥0.08% was also able to rapidly inactivate (in less than 30 min) all mycoplasmas tested. In contrast, negligible reductions in mycoplasma titers were observed with 0.0125 to 0.025% formaldehyde. However, increasing the concentration of formaldehyde to 0.1 to 0.2% improved the mycoplasmacidal effect. Incubation of mycoplasmas with 0.1% beta-propiolactone for 1 to 24 h had a marked mycoplasmacidal effect. A comparison of the mycoplasma inactivation profiles showed that strains of selected species (
M
ycoplasma synoviae
,
M
ycoplasma gallisepticum
,
M
ycoplasma orale
,
M
ycoplasma pneumoniae
, and
A
choleplasma laidlawii
) represent a set of strains that can be utilized to validate the effectiveness of mycoplasma clearance obtained by inactivation and viral purification processes used for the manufacture of an inactivated egg-based vaccine.
Distinct Patterns of Picocyanobacterial Communities in Winter and Summer in the Chesapeake Bay
Authors: Cai Haiyuan , Wang Kui , Huang Sijun , Jiao Nianzhi , Chen Feng 
Published: March 2010

ABSTRACTIn the Chesapeake Bay, picocyanobacteria were usually 100-fold less abundant in winter than in summer. However, little is known about how picocyanobacterial populations shift between winter and summer in the bay. This is due mainly to undetectable winter picocyanobacterial populations in bacterial 16S rRNA clone libraries. In this study, the winter and summer picocyanobacterial populations in the bay were detected using picocyanobacterium-specific primers and were compared based on the analysis of rRNA internal transcribed spacer sequences. Temperature was found to be the dominant environmental factor controlling picocyanobacterial populations in the Chesapeake Bay. In the summer, marine cluster BSynechococcusdominated the upper bay, while a unique cluster, CB1 (marine cluster A [MC-A]Synechococcus), made up the vast majority in the middle and lower bay. In the winter, the picocyanobacteria shifted to completely different populations. Subclades CB6 and CB7, which belong to MC-ASynechococcusandCyanobium, respectively, made up the entire winter picocyanobacterial populations in the bay. Interestingly, the winter members in subclade CB6 clustered closely withSynechococcusCC9311, a coastal strain known to have a greater capacity to sense and respond to changing environments than oceanic strains.
Differential Regulation by Heat Stress of Novel Cytochrome P450 Genes from the Dinoflagellate Symbionts of Reef-Building Corals
Authors: Rosic Nedeljka N. , Pernice Mathieu , Dunn Simon , Dove Sophie , Hoegh-Guldberg Ove 
Published: March 2010

ABSTRACT

Exposure to heat stress has been recognized as one of the major factors leading to the breakdown of the coral-alga symbiosis and coral bleaching. Here, we describe the presence of three new cytochrome P450 (
CYP
) genes from the reef-building coral endosymbiont
Symbiodinium
(type C3) and changes in their expression during exposure to severe and moderate heat stress conditions. Sequence analysis of the
CYP
C-terminal region and two conserved domains, the “PERF” and “heme-binding” domains, confirmed the separate identities of the
CYP
genes analyzed. In order to explore the effects of different heat stress scenarios, samples of the scleractinian coral
Acropora millepora
were exposed to elevated temperatures incrementally over an 18-h period (rapid thermal stress) and over a 120-h period (gradual thermal stress). After 18 h of gradual heating and incubation at 26°C, the
Symbiodinium CYP
mRNA pool was approximately 30% larger, while a further 6°C increase to a temperature above the average sea temperature (29°C after 72 h) resulted in a 2- to 4-fold increase in
CYP
expression. Both rapid heat stress and gradual heat stress at 32°C resulted in 50% to 90% decreases in
CYP
gene transcript abundance. Consequently, the initial upregulation of expression of
CYP
genes at moderately elevated temperatures (26°C and 29°C) was followed by a decrease in expression under the greater thermal stress conditions at 32°C. These findings indicate that in the coral-alga symbiosis under heat stress conditions there is production of chemical stressors and/or transcriptional factors that regulate the expression of genes, such as the genes encoding cytochrome P450 monooxygenases, that are involved in the first line of an organism's chemical defense.
Cloning and Biochemical Characterization of a Novel Carbendazim (Methyl-1
H
-Benzimidazol-2-ylcarbamate)-Hydrolyzing Esterase from the Newly Isolated
Nocardioides
sp. Strain SG-4G and Its Potential for Use in Enzymatic Bioremediation
Authors: Pandey Gunjan , Dorrian Susan J. , Russell Robyn J. , Brearley Clint , Kotsonis Steven , Oakeshott John G. 
Published: March 2010

ABSTRACT

A highly efficient carbendazim (methyl-1
H
-benzimidazol-2-ylcarbamate, or MBC)-mineralizing bacterium was isolated from enrichment cultures originating from MBC-contaminated soil samples. This bacterium,
Nocardioides
sp. strain SG-4G, hydrolyzed MBC to 2-aminobenzimidazole, which in turn was converted to the previously unknown metabolite 2-hydroxybenzimidazole. The initial steps of this novel metabolic pathway were confirmed by growth and enzyme assays and liquid chromatography-mass spectrometry (LC-MS) studies. The enzyme responsible for carrying out the first step was purified and subjected to N-terminal and internal peptide sequencing. The cognate gene, named
mheI
(for MBC-hydrolyzing enzyme), was cloned using a reverse genetics approach. The MheI enzyme was found to be a serine hydrolase of 242 amino acid residues. Its nearest known relative is an uncharacterized hypothetical protein with only 40% amino acid identity to it. Codon optimized
mheI
was heterologously expressed in
Escherichia coli
, and the His-tagged enzyme was purified and biochemically characterized. The enzyme has a

K
m

and
k
cat
of 6.1 μM and 170 min
−1
, respectively, for MBC. Radiation-killed, freeze-dried SG-4G cells showed strong and stable MBC detoxification activity suitable for use in enzymatic bioremediation applications.
Phylogenetic Approach to the Variability of the Microsporidian
Enterocytozoon bieneusi
and Its Implications for Inter- and Intrahost Transmission
Authors: Henriques-Gil Nuno , Haro María , Izquierdo Fernando , Fenoy Soledad , del Águila Carmen 
Published: March 2010

ABSTRACT

Enterocytozoon bieneusi
is a microsporidian parasite that infects many vertebrate animals, including humans. The rDNA internal transcribed spacer (ITS) shows a hypervariable sequence; however, so far no clear information has been inferred about strain evolution in this species. We reviewed all the sequences described and performed a phylogenetic study. Four groups of sequences strongly differentiated from each other were detected, although most of the isolates (94%) corresponded to group I. The highly diverse sequences of this group were analyzed using median-joining networks. The host species (humans, pets, swine, cattle, birds, and wild animals) and the continents of origin of the isolates were considered. Central haplotypes in the network were obtained from very diverse hosts and geographical origins. The results show that although
E. bieneusi
has a broad host specificity, transmission is not completely free: some strains were able to circulate within a given host species and were only occasionally transmitted to another host. Additionally, while not relevant for swine or cattle hosts, geography seems to be a relevant factor for human infection by
E. bieneusi
.