1,721,097 research outputs found
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
Full text linkMetagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1X. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples
Large scale genome reconstructions illuminate Wolbachia evolution
Full text linkWolbachia is an iconic example of a successful intracellular bacterium. Despite its importance
as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied
from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over
30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling
over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our
phylogenies based on both core-genome and gene content provide a robust reference for
future studies, support new strains in model organisms, and reveal recent horizontal transfers
amongst distantly related hosts. We find various instances of gene function gains and losses
in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence
Dating the impossible: the origin and divergence of the largest infection on Earth
Full text linkWolbachia are common intracellular bacteria of many arthropod and nematode species; they are
responsible for likely the most widespread and evolutionary significant infection on Earth. Wolbachia
are generally acquired by maternal transmission, but they often move across species boundaries,
impairing the use of host divergences as independent calibration to infer their evolutionary history.
Here we present a first systematic effort to estimate the origin and the divergence of the Wolbachia
infection by coupling the molecular clock analysis of a genomic and an MLST data sets with three
types of disputed calibration priors: a root prior for splits within Proteobacteria, the recently proposed
Nomada host-symbiont co-divergence, and an adjusted mutation rate gathered from Drosophila
melanogaster and Nasonia species. We first perform a hierarchical based model comparison on the
MLST data set to select the best clock, replacement, and tree priors; we then used the best prior
combination to calibrate both the genomic and the MLST data sets using different combinations of
calibrations. Although divergence estimates are characterized by a high degree of uncertainty and
strongly depend on the use of certain calibrations, most results point towards a pre-Cambrian origin of
Wolbachia (its split from Ehrlichia). Diversification of Wolbachia supergroups is more recent, from
the late Paleozoic to the Mesozoic: this is compatible with a long-fuse model of evolution, and
suggests a co-radiation with holometabolan insects. Our results provide a comprehensive first effort to
date Wolbachia evolution: results are model, prior, and data set dependent and reveal the difficulties
embedded in the molecular dating of such elusive bacteria characterized by the absence of reliable
calibration priors and a clear evolutionary histor
Draft genome sequence of the cadmium-resistant strain JJU2, belonging to the family Hapalosiphonaceae of the cyanobacteria
Full text linkHere, we report the genome of strain JJU2, a cyanobacterium of the family Hapalosiphonaceae known to be resistant to high cadmium levels, assembled from a nonaxenic, unialgal culture from Marinduque, Philippines. The draft genome is 7.1 Mb long with a GC content of 40.05% and contains 5,625 protein-coding gene
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Large scale reconstruction of over a thousand Wolbachia genomes sheds light on its co-evolution
No full textWolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics and population biology have been poorly studied from a genomic viewpoint, mainly because of a paucity of available genomes. To expand the number of Wolbachia genomes across host phylogenies, we screened over 30,000 publicly available shotgun sequencing samples (>70TB of data) from more than 500 arthropods and nematodes species using metagenomic and phylogenomic approaches. By assembling over a thousand of high quality genomes, we provide the largest collection of Wolbachia genomes to date and a substantial increase in host representation. Our Wolbachia phylogenies based on both core-genome alignment and gene content provide a robust reference for future studies, support new strains in model organisms like Drosophila and economically relevant pest species, and reveal novel affinities including recent horizontal transfers amongst distantly related hosts. We found various instances of gene function gains and losses in different super-groups, particularly in Cytoplasmic Incompatibility inducing strains. Our intra-specific Wolbachia-host cophylogenies indicate striking heterogeneity of coevolutionary dynamics and show that horizontal transfer is widespread not only at the intraspecific, but also population interspecific level. Our work reveals new patterns of Wolbachia evolution and indicates that our strain-level metagenomic analysis of host sequencing projects is an effective method to recover endosymbiont genomes for downstream analyses
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Clinical populations of Pseudomonas aeruginosa isolated from acute infections show a wide virulence range partially correlated with population structure and virulence gene expression
No full textPseudomonas aeruginosa is a ubiquitous environmental bacterium responsible for a variety of infections in humans, as well as in animal hosts. While the evolution of virulence in P. aeruginosa strains isolated from chronic lung infection in cystic fibrosis (CF) patients has been extensively studied, the virulence phenotype of P. aeruginosa isolated from other infection types or from the environment is currently not well characterized. Here we report an extensive analysis of the virulence of P. aeruginosa strains isolated from acute infections compared with population structure. Virulence profiles of individual strains were also compared with the expression levels of the rhlR gene, the transcriptional regulator of the rhl quorum-sensing system, and the gene encoding Crc, a global regulator controlling catabolite repression and carbon metabolism. Additionally, the presence/absence of the two mutually exclusive genes, exoU and exoS, encoding effectors of the type III secretion system, was assessed. In order to capture the widest range of genetic variability, a collection of 120 clinical strains was initially characterized by repetitive element-based PCR genotyping, and a selection of 27 strains belonging to different clonal lineages was subsequently tested using three different virulence assays, including two Dictyostelium discoideum assays on different growth media, and a Caenorhabditis elegans fastkilling assay. We show that the parallel application of virulence assays can be used to quantitatively assess this complex, multifactorial phenotypic trait. We observed a wide spectrum of virulence phenotypes ranging from weakly to highly aggressive, indicating that clinical strains isolated from acute infections can present a reduced or altered virulence phenotype. Genotypic associations only partially correlated with virulence profiles and virulence gene expression, whereas the presence of either exoU or exoS was not significantly correlated with virulence. Interestingly, the expression of rhlR showed a significant and positive correlation with the virulence profiles obtained with the three assays, while the expression of crc was either negatively or not correlated with virulence, depending on the assay. © 2012 SGM
- …
