bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium
Authors: Stanborough Tamsyn , Fegan Narelle , Powell Shane M. , Tamplin Mark , Chandry P. Scott 
Published: December 2016

ABSTRACTBrochothrix thermosphactais a dominant but poorly studied meat spoilage organism. It is a close relative of the foodborne pathogenListeria monocytogenes, andBrochothrixconstitutes the second genus in theListeriaceaefamily. Here, the genomes of 12B. thermosphactastrains were sequenced, assembled into draft genomes, characterized, and compared with the genomes ofBrochothrix campestrisandL. monocytogenes. Phenotypic properties including biogenic amine production and antibiotic and heavy metal susceptibilities were tested. Comparative genomic analyses revealed a high degree of similarity among theB. thermosphactastrains, with bacteriophage genes constituting a significant proportion of the accessory genome. Genes for the production of the malodorous compounds acetate, acetoin, butanediol, and fatty acids were found, as were stress response regulatory genes, which likely play important roles in the spoilage process. Amino acid decarboxylases were not identified in the genomes, and phenotypic testing confirmed their absence. Orthologs ofListeriavirulence proteins involved in virulence regulation, intracellular survival, and surface protein anchoring were found; however, key virulence genes were absent. Analysis of antibiotic susceptibility showed that strains were sensitive to the four tested antibiotics, except for one tetracycline-resistant isolate with plasmid-mediated tetracycline resistance genes. Strains tolerated higher levels of copper and cobalt than of cadmium although not at concentrations high enough to categorize the strains as being resistant. This study provides insight into theBrochothrixgenome, links previous phenotypic data and data provided here to the gene inventory, and identifies genes that may contribute to the persistence of this organism in the food chain.IMPORTANCEDespite increasing knowledge and advances in food preservation techniques, microbial spoilage of foods causes substantial losses, with negative social and economic consequences. To better control the contamination and microbial spoilage of foods, fundamental knowledge of the biology of key spoilage bacteria is crucial. As a common meat spoilage organism,B. thermosphactacontributes substantially to spoilage-associated losses. Nonetheless, this organism and particularly its genome remain largely unstudied. This study contributes to improving our knowledge of theBrochothrixgenus. Spoilage-relevant pathways and genes that may play a role in the survival of this organism in a food processing environment were identified, linking previous phenotypic data and data provided here to the gene inventory ofBrochothrixand establishing parallels to and differences from the closely related foodborne pathogenL. monocytogenes.
Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils
Authors: Ben Tekaya Seifeddine , Ganesan Abirama Sundari , Guerra Trina , Dawson Jeffrey O. , Forstner Michael R. J. , Hahn Dittmar 
Published: December 2016

ABSTRACT

The nodule-forming actinobacterial genus
Frankia
can generally be divided into 4 taxonomic clusters, with clusters 1, 2, and 3 representing nitrogen-fixing strains of different host infection groups and cluster 4 representing atypical, generally non-nitrogen-fixing strains. Recently, quantitative PCR (qPCR)-based quantification methods have been developed for frankiae of clusters 1 and 3; however, similar approaches for clusters 2 and 4 were missing. We amended a database of partial 23S rRNA gene sequences of
Frankia
strains belonging to clusters 1 and 3 with sequences of frankiae representing clusters 2 and 4. The alignment allowed us to design primers and probes for the specific detection and quantification of these
Frankia
clusters by either Sybr Green- or TaqMan-based qPCR. Analyses of frankiae in different soils, all obtained from the same region in Illinois, USA, provided similar results, independent of the qPCR method applied, with abundance estimates of 10 × 10
5
to 15 × 10
5
cells (g soil)
−1
depending on the soil. Diversity was higher in prairie soils (native, restored, and cultivated), with frankiae of all 4 clusters detected and those of cluster 4 dominating, while diversity in soils under
Alnus glutinosa
, a host plant for cluster 1 frankiae, or
Betula nigra
, a related nonhost plant, was restricted to cluster 1 and 3 frankiae and generally members of subgroup 1b were dominating. These results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.

IMPORTANCE
Root nodule formation by the actinobacterium
Frankia
is host plant specific and largely, but not exclusively, correlates with assignments of strains to specific clusters within the genus. Due to the lack of adequate detection and quantification tools, studies on
Frankia
have been limited to clusters 1 and 3 and generally excluded clusters 2 and 4. We have developed tools for the detection and quantification of clusters 2 and 4, which can now be used in combination with those developed for clusters 1 and 3 to retrieve information on the ecology of all clusters delineated within the genus
Frankia
. Our initial results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.
Western Bats as a Reservoir of Novel Streptomyces Species with Antifungal Activity
Authors: Hamm Paris S. , Caimi Nicole A. , Northup Diana E. , Valdez Ernest W. , Buecher Debbie C. , Dunlap Christopher A. , Labeda David P. , Lueschow Shiloh , Porras-Alfaro Andrea 
Published: December 2016

ABSTRACTAt least two-thirds of commercial antibiotics today are derived fromActinobacteria, more specifically from the genusStreptomyces. Antibiotic resistance and new emerging diseases pose great challenges in the field of microbiology. Cave systems, in which actinobacteria are ubiquitous and abundant, represent new opportunities for the discovery of novel bacterial species and the study of their interactions with emergent pathogens. White-nose syndrome is an invasive bat disease caused by the fungusPseudogymnoascus destructans, which has killed more than six million bats in the last 7 years. In this study, we isolated naturally occurring actinobacteria from white-nose syndrome (WNS)-free bats from five cave systems and surface locations in the vicinity in New Mexico and Arizona, USA. We sequenced the 16S rRNA region and tested 632 isolates from 12 different bat species using a bilayer plate method to evaluate antifungal activity. Thirty-six actinobacteria inhibited or stopped the growth ofP. destructans, with 32 (88.9%) actinobacteria belonging to the genusStreptomyces. Isolates in the generaRhodococcus,Streptosporangium,Luteipulveratus, andNocardiopsisalso showed inhibition. Twenty-five of the isolates with antifungal activity againstP. destructansrepresent 15 novelStreptomycesspp. based on multilocus sequence analysis. Our results suggest that bats in western North America caves possess novel bacterial microbiota with the potential to inhibitP. destructans.IMPORTANCEThis study reports the largest collection of actinobacteria from bats with activity againstPseudogymnoascus destructans, the fungal causative agent of white-nose syndrome. Using multigene analysis, we discovered 15 potential novel species. This research demonstrates that bats and caves may serve as a rich reservoir for novelStreptomycesspecies with antimicrobial bioactive compounds.
Draft Genome Sequence of the Nonpathogenic, Thermotolerant, and Exopolysaccharide-Producing Bacillus anthracis Strain PFAB2 from Panifala Hot Water Spring in West Bengal, India
Authors: Banerjee Aparna , Halder Urmi , Chaudhry Vasvi , Varshney Rajeev K. , Mantri Shrikant , Bandopadhyay Rajib 
Published: December 2016

ABSTRACT

Bacillus anthracis
is the causative agent of fatal anthrax in both animals and humans. It is prevalently pathogenic. Here, we present a
Bacillus anthracis
PFAB2 strain from a relatively unexplored Panifala hot water spring in West Bengal, India. It is nonpathogenic, exopolysaccharide producing, and thermotolerant in nature.
Complete Genome Sequence of
Streptococcus
sp. Strain NPS 308
Authors: Kondo Yoshio , Ogura Yoshitoshi , Sato Keiko , Imamura Keigo , Hoshino Tomonori , Nishiguchi Miyuki , Hasuwa Tomoyuki , Moriuchi Hiroyuki , Hayashi Tetsuya , Fujiwara Taku 
Published: December 2016

ABSTRACT

Streptococcus
sp. strain NPS 308, isolated from an 8-year-old girl diagnosed with infective endocarditis, likely presents a novel species of
Streptococcus
. Here, we present a complete genome sequence of this species, which will contribute to better understanding of the pathogenesis of infective endocarditis.
Genome Sequences of a Novel Vietnamese Bat Bunyavirus
Authors: Oude Munnink Bas B. , Phan My V. T. , van der Hoek Lia , Kellam Paul , Cotten Matthew 
Published: December 2016

ABSTRACT
To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.
Whole-Genome Sequences of 26 Vibrio cholerae Isolates
Authors: Watve Samit S. , Chande Aroon T. , Rishishwar Lavanya , Mariño-Ramírez Leonardo , Jordan I. King , Hammer Brian K. 
Published: December 2016

ABSTRACT

The human pathogen
Vibrio cholerae
employs several adaptive mechanisms for environmental persistence, including natural transformation and type VI secretion, creating a reservoir for the spread of disease. Here, we report whole-genome sequences of 26 diverse
V. cholerae
isolates, significantly increasing the sequence diversity of publicly available
V. cholerae
genomes.
Genome Sequence of the Soviet/Russian Bacillus anthracis Vaccine Strain 55-VNIIVViM
Authors: Farlow Jason , Kotorashvili Adam 
Published: December 2016

ABSTRACT

Bacillus anthracis
strain 55-VNIIVViM is a live-attenuated nonencapsulated Soviet/Russian veterinary anthrax vaccine strain. We report here the genome of 55-VNIIVViM and confirm its phylogenetic placement in the global population structure of
B. anthracis
.
Complete Genome Sequences of Four Bordetella pertussis Vaccine Reference Strains from Serum Institute of India
Authors: Weigand Michael R. , Peng Yanhui , Loparev Vladimir , Johnson Taccara , Juieng Phalasy , Gairola Sunil , Kumar Rakesh , Shaligram Umesh , Gowrishankar Ramnath , Moura Hercules , Rees Jon , Schieltz David M. , Williamson Yulanda , Woolfitt Adrian , Barr John , Tondella M. Lucia , Williams Margaret M. 
Published: December 2016

ABSTRACT

Serum Institute of India is among the world's largest vaccine producers. Here, we report the complete genome sequences for four
Bordetella pertussis
strains used by Serum Institute of India in the production of whole-cell pertussis vaccines.
Complete Genome Sequence of a Novel Aquareovirus That Infects the Endangered Fountain Darter,
Etheostoma fonticola
Authors: Iwanowicz Luke R. , Iwanowicz Deborah D. , Adams Cynthia R. , Lewis Teresa D. , Brandt Thomas M. , Cornman Robert S. , Sanders Lakyn 
Published: December 2016

ABSTRACT

Here, we report the complete genome of a novel aquareovirus isolated from clinically normal fountain darters,
Etheostoma fonticola
, inhabiting the San Marcos River, Texas, USA. The complete genome consists of 23,958 bp consisting of 11 segments that range from 783 bp (S11) to 3,866 bp (S1).
Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV
Authors: Jia Nan , Ding Ming-Zhu , Du Yu-Zhang , Feng Shuai , Gao Feng , Yuan Ying-Jin 
Published: December 2016

ABSTRACT

Ketogulonicigenium vulgare
has been widely used in vitamin C two-step fermentation, which converts
l
-sorbose to 2-keto-
l
-gluonic acid. Here, the complete genome of
K. vulgare
SKV, which performs better fermentation production than
K. vulgare
Hbe602, is deciphered to understand the key differences in metabolism between
K. vulgare
strains SKV and Hbe602.
Complete Genome Sequence of a Mosaic NADC30-Like Porcine Reproductive and Respiratory Syndrome Virus in China
Authors: Wang Lin-jian , Guo Zhenhua , Qiao Songlin , Chen Xin-xin , Zhang Gaiping 
Published: December 2016

ABSTRACT
Here, we report the complete genome of an NADC30-like porcine reproductive and respiratory syndrome virus (PRRSV) strain, HNhx, which was isolated from Henan Province, China, in 2016 and was characterized by recombination with JXA1 strain (an epidemic highly pathogenic PRRSV strain in China) in Nsp4 to Nsp9.
Genome Sequence of the Acetogenic Bacterium Acetobacterium wieringae DSM 1911
T
Authors: Poehlein Anja , Bengelsdorf Frank Robert , Schiel-Bengelsdorf Bettina , Daniel Rolf , Dürre Peter 
Published: December 2016

ABSTRACT

Here, we report the draft genome sequence of
Acetobacterium wieringae
DSM 1911
T
, an anaerobic, autotrophic, acetogenic,
d
,
l
-lactate-utilizing bacterium. The genome consists of a chromosome (3.88 Mb) and 3,620 predicted protein-encoding genes.
Draft Genome Sequence of
Kluyvera
intestini
Strain GT-16 Isolated from the Stomach of a Patient with Gastric Cancer
Authors: Tetz George , Tetz Victor 
Published: December 2016

ABSTRACT

Here, we report the complete genome sequence of the novel, non-spore-forming
Kluyvera intestini
strain GT-16, isolated from the stomach of a patient with gastric cancer. The genome is 5,868,299 bp in length with a G+C content of 53.0%. It possesses 5,350 predicted protein-coding genes encoding virulence factors and antibiotic resistance proteins.
Draft Whole-Genome Sequence of a Catalase-Negative Staphylococcus aureus subsp.
aureus
(Sequence Type 25) Strain Isolated from a Patient with Endocarditis and Septic Arthritis
Authors: Berenger Byron , Chen Justin , Bernier Anne-Marie , Bernard Kathryn 
Published: December 2016

ABSTRACT

Staphylococcus aureus
strains without catalase activity are rare, challenging to identify with conventional biochemical methods, and, despite a supposed decreased pathogenicity, can still cause disease. The first whole-genome sequence of a catalase-negative
S. aureus
isolate causing severe recurrent invasive infection with two novel missense mutations in the
katA
gene is reported here.
Quorum Sensing in a Methane-Oxidizing Bacterium
Authors: Puri Aaron W. , Schaefer Amy L. , Fu Yanfen , Beck David A. C. , Greenberg E. Peter , Lidstrom Mary E. 
Published: December 2016

ABSTRACT

Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Dissecting the molecular details of how these organisms interact in the environment may increase our understanding of how they perform this important ecological role. Many bacterial species use quorum sensing (QS) systems to regulate gene expression in a cell density-dependent manner. We have identified a QS system in the genome of
Methylobacter tundripaludum
, a dominant methane oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA). We determined that
M. tundripaludum
produces primarily
N
-3-hydroxydecanoyl-
l
-homoserine lactone (3-OH-C
10
-HSL) and that its production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by QS in this methane oxidizer using transcriptome sequencing (RNA-seq) and discovered that this system regulates the expression of a putative nonribosomal peptide synthetase biosynthetic gene cluster. Finally, we detected an extracellular factor that is produced by
M. tundripaludum
in a QS-dependent manner. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.

IMPORTANCE
Aerobic methanotrophs are critical for sequestering carbon from the potent greenhouse gas methane in the environment, yet the mechanistic details of chemical interactions in methane-oxidizing bacterial communities are not well understood. Understanding these interactions is important in order to maintain, and potentially optimize, the functional potential of the bacteria that perform this vital ecosystem function. In this work, we identify a quorum sensing system in the aerobic methanotroph
Methylobacter tundripaludum
and use both chemical and genetic methods to characterize this system at the molecular level.
Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System
Authors: Gibbons Sean M. , Scholz Monika , Hutchison Alan L. , Dinner Aaron R. , Gilbert Jack A. , Coleman Maureen L. 
Published: December 2016

ABSTRACT
Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.

IMPORTANCE
The diversity of microbial communities is linked to the functioning and stability of ecosystems. As humanity continues to impact ecosystems worldwide, and as diet and disease perturb our own commensal microbial communities, the ability to predict how microbial diversity will respond to disturbance is of critical importance. Using microbial microcosm experiments, we find that community diversity responds to different disturbance regimes in a reproducible and predictable way. Maximum diversity occurs when two communities, each suited to different environmental conditions, are mixed due to disturbance. This maximum diversity is transient except under specific regimes. Using a simple mathematical model, we show that transient unimodality is likely a common feature of microbial diversity-disturbance relationships in fluctuating environments.
Networked Chemoreceptors Benefit Bacterial Chemotaxis Performance
Authors: Frank Vered , Piñas Germán E. , Cohen Harel , Parkinson John S. , Vaknin Ady 
Published: December 2016

ABSTRACT

Motile bacteria use large receptor arrays to detect and follow chemical gradients in their environment. Extended receptor arrays, composed of networked signaling complexes, promote cooperative stimulus control of their associated signaling kinases. Here, we used structural lesions at the communication interface between core complexes to create an
Escherichia coli
strain with functional but dispersed signaling complexes. This strain allowed us to directly study how networking of signaling complexes affects chemotactic signaling and gradient-tracking performance. We demonstrate that networking of receptor complexes provides bacterial cells with about 10-fold-heightened detection sensitivity to attractants while maintaining a wide dynamic range over which receptor adaptational modifications can tune response sensitivity. These advantages proved especially critical for chemotaxis toward an attractant source under conditions in which bacteria are unable to alter the attractant gradient.

IMPORTANCE
Chemoreceptor arrays are found in many motile bacteria. However, although our understanding of bacterial chemotaxis is quite detailed, the signaling and behavioral advantages of networked receptor arrays had not been directly studied in cells. We have recently shown that lesions in a key interface of the
E. coli
receptor array diminish physical connections and functional coupling between core signaling complexes while maintaining their basic signaling capacity. In this study, we exploited an interface 2 mutant to show, for the first time, that coupling between core complexes substantially enhances stimulus detection and chemotaxis performance.
Cytochrome
bd
-Dependent Bioenergetics and Antinitrosative Defenses in
Salmonella
Pathogenesis
Authors: Jones-Carson Jessica , Husain Maroof , Liu Lin , Orlicky David J. , Vázquez-Torres Andrés 
Published: December 2016

ABSTRACT

In the course of an infection,
Salmonella enterica
occupies diverse anatomical sites with various concentrations of oxygen (O
2
) and nitric oxide (NO). These diatomic gases compete for binding to catalytic metal groups of quinol oxidases.
Enterobacteriaceae
express two evolutionarily distinct classes of quinol oxidases that differ in affinity for O
2
and NO as well as stoichiometry of H
+
translocated across the cytoplasmic membrane. The investigations presented here show that the dual function of bacterial cytochrome
bd
in bioenergetics and antinitrosative defense enhances
Salmonella
virulence. The high affinity of cytochrome
bd
for O
2
optimizes respiratory rates in hypoxic cultures, and thus, this quinol oxidase maximizes bacterial growth under O
2
-limiting conditions. Our investigations also indicate that cytochrome
bd
, rather than cytochrome
bo
, is an intrinsic component of the adaptive antinitrosative toolbox of
Salmonella
. Accordingly, induction of cytochrome
bd
helps
Salmonella
grow and respire in the presence of inhibitory NO. The combined antinitrosative defenses of cytochrome
bd
and the flavohemoglobin Hmp account for a great part of the adaptations that help
Salmonella
recover from the antimicrobial activity of NO. Moreover, the antinitrosative defenses of cytochrome
bd
and flavohemoglobin Hmp synergize to promote
Salmonella
growth in systemic tissues. Collectively, our investigations indicate that cytochrome
bd
is a critical means by which
Salmonella
resists the nitrosative stress that is engendered in the innate response of mammalian hosts while it concomitantly allows for proper O
2
utilization in tissue hypoxia.

IMPORTANCE
It is becoming quite apparent that metabolism is critically important to the virulence potential of pathogenic microorganisms. Bacterial cells use a variety of terminal electron acceptors to power electron transport chains and metabolic processes. Of all the electron acceptors available to bacteria, utilization of O
2
yields the most energy while diversifying the type of substrates that a pathogen can use. Recent investigations have demonstrated important roles for
bd
-type quinol oxidases with high affinity for O
2
in bacterial pathogenesis. The investigations presented here have revealed that cytochrome
bd
potentiates virulence of a clinically relevant bacterial pathogen by fueling bioenergetics of prokaryotic cells while protecting the respiratory chain against NO toxicity. The adaptive antinitrosative defenses afforded by cytochrome
bd
synergize with other NO-detoxifying systems to preserve cellular bioenergetics, thereby promoting bacterial virulence in tissue hypoxia.