bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Long-Term Starvation on the Survival, Recovery, and Carbon Utilization Profiles of a Bovine Escherichia coli O157:H7 Isolate from New Zealand
Authors: Xavier Ron N. , Morgan Hugh W. , McDonald Ian R. , Withers Helen 
Published: May 2014

ABSTRACT

The ability to maintain a dual lifestyle of colonizing the ruminant gut and surviving in nonhost environments once shed is key to the success of
Escherichia coli
O157:H7 as a zoonotic pathogen. Both physical and biological conditions encountered by the bacteria are likely to change during the transition between host and nonhost environments. In this study, carbon starvation at suboptimal temperatures in nonhost environments was simulated by starving a New Zealand bovine
E. coli
O157:H7 isolate in phosphate-buffered saline at 4 and 15°C for 84 days. Recovery of starved cells on media with different nutrient availabilities was monitored under aerobic and anaerobic conditions. We found that the New Zealand bovine
E. coli
O157:H7 isolate was able to maintain membrane integrity and viability over 84 days and that the level of recovery depended on the nutrient level of the recovery medium as well as the starvation temperature. In addition, a significant difference in carbon utilization was observed between starved and nonstarved cells.
Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes
Authors: Lie Alle A. Y. , Liu Zhenfeng , Hu Sarah K. , Jones Adriane C. , Kim Diane Y. , Countway Peter D. , Amaral-Zettler Linda A. , Cary S. Craig , Sherr Evelyn B. , Sherr Barry F. , Gast Rebecca J. , Caron David A. 
Published: May 2014

ABSTRACT
Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.
Analysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota
Authors: Aksoy Emre , Telleria Erich L. , Echodu Richard , Wu Yineng , Okedi Loyce M. , Weiss Brian L. , Aksoy Serap , Caccone Adalgisa 
Published: May 2014

ABSTRACT

The invertebrate microbiome contributes to multiple aspects of host physiology, including nutrient supplementation and immune maturation processes. We identified and compared gut microbial abundance and diversity in natural tsetse flies from Uganda using five genetically distinct populations of
Glossina fuscipes fuscipes
and multiple tsetse species (
Glossina morsitans morsitans
,
G. f. fuscipes
, and
Glossina pallidipes
) that occur in sympatry in one location. We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals. Our results show extremely limited diversity in field flies of different tsetse species. The obligate endosymbiont
Wigglesworthia
dominated all samples (>99%), but we also observed wide prevalence of low-density
Sodalis
(tsetse's commensal endosymbiont) infections (<0.05%). There were also several individuals (22%) with high
Sodalis
density, which also carried coinfections with
Serratia
. Albeit in low density, we noted differences in microbiota composition among the genetically distinct
G. f. fuscipes
flies and between different sympatric species. Interestingly,
Wigglesworthia
density varied in different species (10
4
to 10
6
normalized genomes), with
G. f. fuscipes
having the highest levels. We describe the factors that may be responsible for the reduced diversity of tsetse's gut microbiota compared to those of other insects. Additionally, we discuss the implications of
Wigglesworthia
and
Sodalis
density variations as they relate to trypanosome transmission dynamics and vector competence variations associated with different tsetse species.
Abiotic Stress Resistance, a Novel Moonlighting Function of Ribosomal Protein RPL44 in the Halophilic Fungus Aspergillus glaucus
Authors: Liu Xiao-Dan , Xie Lixia , Wei Yi , Zhou Xiaoyang , Jia Baolei , Liu Jinliang , Zhang Shihong 
Published: May 2014

ABSTRACT

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily involved in the translation of mRNA leading to protein synthesis. However, certain ribosomal proteins moonlight in the development and differentiation of organisms. In this study, the ribosomal protein L44 (RPL44), associated with salt resistance, was screened from the halophilic fungus
Aspergillus glaucus
(AgRPL44), and its activity was investigated in
Saccharomyces cerevisiae
and
Nicotiana tabacum
. Sequence alignment revealed that AgRPL44 is one of the proteins of the large ribosomal subunit 60S. Expression of
AgRPL44
was upregulated via treatment with salt, sorbitol, or heavy metals to demonstrate its response to osmotic stress. A homologous sequence from the model fungus
Magnaporthe oryzae
, MoRPL44, was cloned and compared with
AgRPL44
in a yeast expression system. The results indicated that yeast cells with overexpressed
AgRPL44
were more resistant to salt, drought, and heavy metals than were yeast cells expressing
MoRPL44
at a similar level of stress. When
AgRPL44
was introduced into
M. oryzae
, the transformants displayed obviously enhanced tolerance to salt and drought, indicating the potential value of
AgRPL44
for genetic applications. To verify the value of its application in plants, tobacco was transformed with
AgRPL44
, and the results were similar. Taken together, we conclude that
AgRPL44
supports abiotic stress resistance and may have value for genetic application.
Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread
Authors: Volkova Victoriya V. , Lu Zhao , Besser Thomas , Gröhn Yrjö T. 
Published: May 2014

ABSTRACT

Animal-associated bacterial communities are infected by bacteriophages, although the dynamics of these infections are poorly understood. Transduction by bacteriophages may contribute to transfer of antimicrobial resistance genes, but the relative importance of transduction among other gene transfer mechanisms is unknown. We therefore developed a candidate deterministic mathematical model of the infection dynamics of enteric coliphages in commensal
Escherichia coli
in the large intestine of cattle. We assumed the phages were associated with the intestine and were predominantly temperate. Model simulations demonstrated how, given the bacterial ecology and infection dynamics, most (>90%) commensal enteric
E. coli
bacteria may become lysogens of enteric coliphages during intestinal transit. Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits (“worst-case scenario”) of gene transfer through specialized and generalized transduction in
E. coli
by enteric coliphages when the transduced genetic segment is picked at random. The estimates were consistent with a relatively small contribution of transduction to lateral gene spread; for example, generalized transduction delivered the chromosomal resistance gene to up to 8
E. coli
bacteria/hour within the population of 1.47 × 10
8
E. coli
bacteria/liter luminal contents. In comparison, the plasmidic
bla
CMY-2
gene carried by ∼2% of enteric
E. coli
was transferred by conjugation at a rate at least 1.4 × 10
3
times greater than our generalized transduction estimate. The estimated numbers of transductants varied nonlinearly depending on the ecology of bacteria available for phages to infect, that is, on the assumed rates of turnover and replication of enteric
E. coli
.
A Tailored
galK
Counterselection System for Efficient Markerless Gene Deletion and Chromosomal Tagging in Magnetospirillum gryphiswaldense
Authors: Raschdorf Oliver , Plitzko Jürgen M. , Schüler Dirk , Müller Frank D. 
Published: May 2014

ABSTRACT

Magnetotactic bacteria have emerged as excellent model systems to study bacterial cell biology, biomineralization, vesicle formation, and protein targeting because of their ability to synthesize single-domain magnetite crystals within unique organelles (magnetosomes). However, only few species are amenable to genetic manipulation, and the limited methods for site-specific mutagenesis are tedious and time-consuming. Here, we report the adaptation and application of a fast and convenient technique for markerless chromosomal manipulation of
Magnetospirillum gryphiswaldense
using a single antibiotic resistance cassette and
galK
-based counterselection for marker recycling. We demonstrate the potential of this technique by genomic excision of the
phbCAB
operon, encoding enzymes for polyhydroxyalkanoate (PHA) synthesis, followed by chromosomal fusion of magnetosome-associated proteins to fluorescent proteins. Because of the absence of interfering PHA particles, these engineered strains are particularly suitable for microscopic analyses of cell biology and magnetosome biosynthesis.
Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing
Authors: Crauwels Sam , Zhu Bo , Steensels Jan , Busschaert Pieter , De Samblanx Gorik , Marchal Kathleen , Willems Kris A. , Verstrepen Kevin J. , Lievens Bart 
Published: May 2014

ABSTRACTBrettanomycesyeasts, with the speciesBrettanomyces(Dekkera)bruxellensisbeing the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However,B. bruxellensisis also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance,Brettanomycesyeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50Brettanomycesstrains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between theB. bruxellensisfingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate ofB. bruxellensis(VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminateBrettanomycesstrains and provides a first glimpse at the genetic diversity and genome plasticity ofB. bruxellensis.
Microbial Population Dynamics in the Hemolymph of Manduca sexta Infected with Xenorhabdus nematophila and the Entomopathogenic Nematode Steinernema carpocapsae
Authors: Singh Swati , Reese Jordan M. , Casanova-Torres Ángel M. , Goodrich-Blair Heidi , Forst Steven 
Published: May 2014

ABSTRACT

Xenorhabdus nematophila
engages in a mutualistic association with the nematode
Steinernema carpocapsae
. The nematode invades and traverses the gut of susceptible insects.
X. nematophila
is released in the insect blood (hemolymph), where it suppresses host immune responses and functions as a pathogen.
X. nematophila
produces diverse antimicrobials in laboratory cultures. The natural competitors that
X. nematophila
encounters in the hemolymph and the role of antimicrobials in interspecies competition in the host are poorly understood. We show that gut microbes translocate into the hemolymph when the nematode penetrates the insect intestine. During natural infection,
Staphylococcus saprophyticus
was initially present and subsequently disappeared from the hemolymph, while
Enterococcus faecalis
proliferated.
S. saprophyticus
was sensitive to
X. nematophila
antibiotics and was eliminated from the hemolymph when coinjected with
X. nematophila
. In contrast,
E. faecalis
was relatively resistant to
X. nematophila
antibiotics. When injected by itself,
E. faecalis
persisted (∼10
3
CFU/ml), but when coinjected with
X. nematophila
, it proliferated to ∼10
9
CFU/ml. Injection of
E. faecalis
into the insect caused the upregulation of an insect antimicrobial peptide, while the transcript levels were suppressed when
E. faecalis
was coinjected with
X. nematophila
. Its relative antibiotic resistance together with suppression of the host immune system by
X. nematophila
may account for the growth of
E. faecalis
. At higher injected levels (10
6
CFU/insect),
E. faecalis
could kill insects, suggesting that it may contribute to virulence in an
X. nematophila
infection. These findings provide new insights into the competitive events that occur early in infection after
S. carpocapsae
invades the host hemocoel.
Physiological and Transcriptional Responses of Anaerobic Chemostat Cultures of Saccharomyces cerevisiae Subjected to Diurnal Temperature Cycles
Authors: Hebly Marit , de Ridder Dick , de Hulster Erik A. F. , de la Torre Cortes Pilar , Pronk Jack T. , Daran-Lapujade Pascale 
Published: May 2014

ABSTRACT

Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of
Saccharomyces cerevisiae
. After three diurnal temperature cycles (DTC), concentrations of glucose and extracellular metabolites as well as CO
2
production rates showed regular, reproducible circadian rhythms. DTC also led to waves of transcriptional activation and repression, which involved one-sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to respond primarily to changes in the glucose concentration. Elimination of known glucose-responsive genes revealed an overrepresentation of previously identified temperature-responsive genes as well as genes involved in the cell cycle and
de novo
purine biosynthesis. In-depth analysis demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that the 24-h DTC was sufficiently slow to allow
S. cerevisiae
chemostat cultures to acclimate their transcriptome and physiology at the DTC temperature maximum and to approach acclimation at the DTC temperature minimum. Furthermore, this comparison and literature data on growth rate-dependent cell cycle phase distribution indicated that cell cycle synchronization was most likely an effect of imposed fluctuations of the relative growth rate (μ/μ
max
) rather than a direct effect of temperature.
Discovery of Bovine Digital Dermatitis-Associated Treponema spp. in the Dairy Herd Environment by a Targeted Deep-Sequencing Approach
Authors: Klitgaard Kirstine , Nielsen Martin W. , Ingerslev Hans-Christian , Boye Mette , Jensen Tim K. 
Published: May 2014

ABSTRACT

The bacteria associated with the infectious claw disease bovine digital dermatitis (DD) are spirochetes of the genus
Treponema
; however, their environmental reservoir remains unknown. To our knowledge, the current study is the first report of the discovery and phylogenetic characterization of rRNA gene sequences from DD-associated treponemes in the dairy herd environment. Although the spread of DD appears to be facilitated by wet floors covered with slurry, no DD-associated treponemes have been isolated from this environment previously. Consequently, there is a lack of knowledge about the spread of this disease among cows within a herd as well as between herds. To address the issue of DD infection reservoirs, we searched for evidence of DD-associated treponemes in fresh feces, in slurry, and in hoof lesions by deep sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene coupled with identification at the operational-taxonomic-unit level. Using treponeme-specific primers in this high-throughput approach, we identified small amounts of DNA (on average 0.6% of the total amount of sequence reads) from DD-associated treponemes in 43 of 64 samples from slurry and cow feces collected from six geographically dispersed dairy herds. Species belonging to the
Treponema denticola
/
Treponema pedis
-like and
Treponema phagedenis
-like phylogenetic clusters were among the most prevalent treponemes in both the dairy herd environment and the DD lesions. By the high-throughput approach presented here, we have demonstrated that cow feces and environmental slurry are possible reservoirs of DD-associated treponemes. This method should enable further clarification of the etiopathogenesis of DD.
Functional Heterologous Production of Reductive Dehalogenases from Desulfitobacterium hafniense Strains
Authors: Mac Nelly Anita , Kai Marco , Svatoš Aleš , Diekert Gabriele , Schubert Torsten 
Published: May 2014

ABSTRACT

The anaerobic dehalogenation of organohalides is catalyzed by the reductive dehalogenase (RdhA) enzymes produced in phylogenetically diverse bacteria. These enzymes contain a cobamide cofactor at the active site and two iron-sulfur clusters. In this study, the tetrachloroethene (PCE) reductive dehalogenase (PceA) of the Gram-positive
Desulfitobacterium hafniense
strain Y51 was produced in a catalytically active form in the nondechlorinating, cobamide-producing bacterium
Shimwellia blattae
(ATCC 33430), a Gram-negative gammaproteobacterium. The formation of recombinant catalytically active PceA enzyme was significantly enhanced when its dedicated PceT chaperone was coproduced and when 5,6-dimethylbenzimidazole and hydroxocobalamin were added to the
S. blattae
cultures. The experiments were extended to
D. hafniense
DCB-2, a reductively dehalogenating bacterium harboring multiple
rdhA
genes. To elucidate the substrate spectrum of the
rdhA3
gene product of this organism, the recombinant enzyme was tested for the conversion of different dichlorophenols (DCP) in crude extracts of an RdhA3-producing
S. blattae
strain. 3,5-DCP, 2,3-DCP, and 2,4-DCP, but not 2,6-DCP and 3,4-DCP, were reductively dechlorinated by the recombinant RdhA3. In addition, this enzyme dechlorinated PCE to trichloroethene at low rates.
Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation
Authors: Wu Qun , Ling Jie , Xu Yan 
Published: May 2014

ABSTRACTSelection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified:Saccharomyces cerevisiae,Pichia membranaefaciens,Issatchenkia orientalis,Bacillus licheniformis, andBacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found thatS. cerevisiaewas positively correlated to nonanal, andB. licheniformiswas positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, whileI. orientaliswas positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. AlthoughP. membranaefaciensandB. amyloliquefacienswere not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor.
The Plasmid Complement of Lactococcus lactis UC509.9 Encodes Multiple Bacteriophage Resistance Systems
Authors: Ainsworth Stuart , Mahony Jennifer , van Sinderen Douwe 
Published: May 2014

ABSTRACT

Lactococcus lactis
subsp.
cremoris
strains are used globally for the production of fermented dairy products, particularly hard cheeses. Believed to be of plant origin,
L. lactis
strains that are used as starter cultures have undergone extensive adaptation to the dairy environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids that specify technologically important phenotypic traits. Here, we present a detailed analysis of the eight plasmids of
L. lactis
UC509.9, an Irish dairy starter strain. Key industrial phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified, including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed phage resistance of
L. lactis
UC509.9. AbiB escape mutants were generated for phage sk1, which were found to carry mutations in
orf6
, which encodes the major capsid protein of this phage.