Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies.

As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, 'Phylobook' was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis.

Genomic Islands Shape the Genetic Background of Both JP2 and Non-JP2 .

is a periodontal pathogen associated with periodontitis. This species exhibits substantial variations in gene content among different isolates and has different virulence potentials. This study examined the distribution of genomic islands and their insert sites among genetically diverse strains by comparative genomic analysis.

Cutibacterium recovered from deep specimens at the time of revision shoulder arthroplasty samples has increased biofilm-forming capacity and hemolytic activity compared with Cutibacterium skin isolates from normal subjects.

Background: Biofilm formation and hemolytic activity are factors that may correlate with the virulence of Cutibacterium. We sought to compare the prevalence of these potential markers of pathogenicity between Cutibacterium recovered from deep specimens obtained at the time of surgical revision for failed shoulder arthroplasty and Cutibacterium recovered from skin samples from normal subjects.

Methods: We compared 42 deep-tissue or explant isolates with 43 control Cutibacterium samples obtained from skin isolates from normal subjects.

Bacterial cyclic diguanylate signaling networks sense temperature.

Many bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, we identify a thermosensory diguanylate cyclase (TdcA) that modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogen Pseudomonas aeruginosa. TdcA synthesizes c-di-GMP with catalytic rates that increase more than a hundred-fold over a ten-degree Celsius change.

Cutibacterium subtype distribution on the skin of primary and revision shoulder arthroplasty patients.

Background: The skin of healthy shoulders is known to harbor multiple different subtypes of Cutibacterium (formerly Propionibacterium) acnes at the same time. C acnes can often be isolated from deep tissue and explant samples obtained during revision of a failed shoulder arthroplasty, presumably because the shoulder was inoculated with organisms from the patient's skin at the time of the index arthroplasty. It is possible that specific subtypes or distributions of subtypes may be associated with an increased pathogenic potential and that the skin of patients undergoing revision arthroplasty contains different distributions of the subtypes than in patients undergoing primary arthroplasty.

Transcriptomic Analysis of Core and Accessory Genes in Different Growth Conditions.

genome can be divided into an accessory gene pool (found in some but not all strains) and a core gene pool (found in all strains). The functions of the accessory genes (genomic islands and non-island accessory genes) are largely unknown. We hypothesize that accessory genes confer critical functions for in vivo.

Cutibacterium acnes Isolates from Deep Tissue Specimens Retrieved during Revision Shoulder Arthroplasty: Similar Colony Morphology Does Not Indicate Clonality.

is the most common bacterium associated with periprosthetic shoulder infections. Sequencing of has been proposed as a potential rapid diagnostic tool and a method of determining subtypes associated with pathogenicity and antibiotic resistance patterns. When multiple deep samples from the same surgery are culture positive for the same species and the isolates show the same culture phenotype, it is typically assumed that these isolates are clonal.

Temporal genetic association and temporal genetic causality methods for dissecting complex networks.

A large amount of panomic data has been generated in populations for understanding causal relationships in complex biological systems. Both genetic and temporal models can be used to establish causal relationships among molecular, cellular, or phenotypical traits, but with limitations. To fully utilize high-dimension temporal and genetic data, we develop a multivariate polynomial temporal genetic association (MPTGA) approach for detecting temporal genetic loci (teQTLs) of quantitative traits monitored over time in a population and a temporal genetic causality test (TGCT) for inferring causal relationships between traits linked to the locus.

Draft Genome Sequence of Clinical Isolate 9610.

We present here the draft genome sequence of 9610, a clinical isolate obtained from a periodontitis patient. The genome is composed of 79 scaffolds with 82 contigs, for a length of 3,201,941 bp and a G+C of 47.3%.

Human Serum-Specific Activation of Alternative Sigma Factors, the Stress Responders in Aggregatibacter actinomycetemcomitans.

Aggregatibacter actinomycetemcomitans, a known pathogen causing periodontal disease and infective endocarditis, is a survivor in the periodontal pocket and blood stream; both environments contain serum as a nutrient source. To screen for unknown virulence factors associated with this microorganism, A. actinomycetemcomitans was grown in serum-based media to simulate its in vivo environment.

Variable Nitrogen Fixation in Wild Populus.

The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings.

Draft Genome Sequence of Low-Passage Clinical Isolate Porphyromonas gingivalis MP4-504.

We present the draft genome ofPorphyromonas gingivalisMP4-504, a low-passage clinical isolate obtained from a periodontitis patient. The genome is composed of 92 contigs for a length of 2,373,453 bp and a G+C of 48.3%.

Propionibacterium in Shoulder Arthroplasty: What We Think We Know Today.

➤ Propionibacterium is a slow-growing gram-positive rod that is part of the normal skin microbiome but can be found on culture of specimens from a large number of patients having revision shoulder arthroplasty performed for pain, stiffness, and component loosening. ➤ Propionibacterium infections do not present with obvious signs of infection, such as swelling, erythema, drainage, or tenderness, but rather are of the so-called stealth type, presenting with unexplained pain, stiffness, or component loosening months to years after the index arthroplasty. ➤ Not all propionibacteria are the same: certain subtypes of Propionibacterium are enriched with virulence factors that may enhance deep infection.

High-Quality Draft Genome Sequence of Low-pH-Active Veillonella parvula Strain SHI-1, Isolated from Human Saliva within an In Vitro Oral Biofilm Model.

We announce here a draft genome sequence of Veillonella parvula strain SHI-1, obtained from healthy human saliva, discovered to be active at low pH using metatranscriptomics within an in vitro oral biofilm model. The genome is composed of 7 contigs, for a total of 2,200,064 bp.

Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont.

Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter strain XH001, isolated from the human oral cavity. Uniquely, it was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the first cultivated member of "Candidatus Saccharibacteria" (formerly candidate phylum TM7).

Digital detection of endonuclease mediated gene disruption in the HIV provirus.

Genome editing by designer nucleases is a rapidly evolving technology utilized in a highly diverse set of research fields. Among all fields, the T7 endonuclease mismatch cleavage assay, or Surveyor assay, is the most commonly used tool to assess genomic editing by designer nucleases. This assay, while relatively easy to perform, provides only a semi-quantitative measure of mutation efficiency that lacks sensitivity and accuracy.

Lack of viral control and development of combination antiretroviral therapy escape mutations in macaques after bone marrow transplantation.

Objective: We have previously demonstrated robust control of simian/human immunodeficiency virus (SHIV1157-ipd3N4) viremia following administration of combination antiretroviral therapy (cART) in pigtailed macaques. Here, we sought to determine the safety of hematopoietic stem cell transplantation (HSCT) in cART-suppressed and unsuppressed animals.

Design: We compared disease progression in animals challenged with SHIV 100 days post-transplant, to controls that underwent transplant following SHIV challenge and stable cART-dependent viral suppression.

Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.

Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing.

Resistance detected by pyrosequencing following zidovudine monotherapy for prevention of HIV-1 mother-to-child-transmission.

To prevent mother-to-child-transmission of HIV-1, the 2010 WHO guidelines recommended prenatal zidovudine (ZDV) monotherapy (option A). To determine if ZDV monotherapy selects for HIV resistance in antiretroviral-naive women during pregnancy, specimens from 50 individuals were examined using pyrosequencing. ZDV-resistance mutations were detected at delivery in seven women (14%, 95% confidence interval 6.

Comparative genomic analysis of seven Mycoplasma hyosynoviae strains.

Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly those aged 10 weeks or older. Strategies for controlling this pathogen are becoming increasingly important due to the rise in the number of cases of arthritis that have been attributed to infection in recent years. In order to begin to develop interventions to prevent arthritis caused by M.

Genome-Wide Association Studies of Virulent and Avirulent Haemophilus parasuis Serotype 4 Strains.

Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. However, in conjunction with stress and/or viral infections, or in immunocompromised animals, H. parasuis can transform into a pathogen causing Glasser's disease, which is typically characterized by fibrinous polyserositis, polyarthritis, meningitis, and sometimes acute pneumonia and septicemia.

Propionibacterium persists in the skin despite standard surgical preparation.

Background: Propionibacterium acnes, which normally resides in the skin, is known to play a role in surgical site infection in orthopaedic surgery. Studies have suggested a persistence of propionibacteria on the skin surface, with rates of positive cultures ranging from 7% to 29% after surgical preparation. However, as Propionibacterium organisms normally reside in the dermal layer, these studies may underestimate the true prevalence of propionibacteria after surgical skin preparation.

Genome sequences of porcine epidemic diarrhea virus: in vivo and in vitro phenotypes.

Since the outbreak of porcine epidemic diarrhea virus (PEDV) in May 2013, U.S. swine producers have lost almost five million baby pigs.