• Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. (biomedcentral.com)
  • We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. (biomedcentral.com)
  • The price and time for whole genome sequencing will soon be in the same range as the traditional typing methods mentioned above. (biomedcentral.com)
  • In recent years, advances in sequencing technology have led to what is known as "next-generation sequencing" becoming much more affordable and available, paving the way to whole genome sequencing of bacterial isolates as a more cost-effective means than MLST for comparing isolates of the same species, and this is now our preferred approach, for a number of different reasons. (rapidmicrobiology.com)
  • In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. (cdc.gov)
  • METHODS: We identified outbreak-associated listeriosis cases using whole-genome sequencing (WGS), product testing results, and epidemiologic linkage to cases in the same Kansas hospital. (cdc.gov)
  • The investigation began with two environmental L. monocytogenes isolates recovered from Manufacturer A, primarily a processor of frozen onions, that were a match by whole genome sequencing (WGS) to eight clinical isolates and historical onion isolates with limited collection details. (cdc.gov)
  • Furthermore, average nucleotide identity (ANI) estimation, single nucleotide polymorphism (SNP), and core gene multilocus sequence typing (cgMLST) were applied to characterize the molecular profile of isolates based on whole genome sequencing. (biomedcentral.com)
  • We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). (peerj.com)
  • These factors caused phylogenetics to enter an era of multi-locus analysis and is facilitated by availability of whole-genome sequencing [ 3 ]. (biomedcentral.com)
  • To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid. (biomedcentral.com)
  • Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. (biomedcentral.com)
  • Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. (biomedcentral.com)
  • Genome analysis revealed that 2 bacterial isolates represent a potential new species of Brucella . (cdc.gov)
  • The new isolates formed a distinct clade, which was most closely related to Leptospira borgpetersenii, in multilocus sequence analysis using concatenated sequences of the genes rpoB, recA, fusA, gyrB, leuS and sucA. (nih.gov)
  • Analysis of average nucleotide identity and genome-to-genome distances, which have recently been proposed as reliable substitutes for classical DNA-DNA hybridization, further confirmed that these isolates should be classified as representatives of a novel species. (nih.gov)
  • If several different strains are present in a manufacturing facility - and this could easily be the case with many of the more common environmental isolates - investigation results may be misleading or inconclusive if strain typing and comparison have not been undertaken. (rapidmicrobiology.com)
  • 16S sequencing is quite a flexible approach and sequencing the full 16S gene, rather than just the first 500 bp, provides additional data that is sometimes required for accurate species-level identification, but can also be useful for highlighting differences between bacterial isolates. (rapidmicrobiology.com)
  • MLST uses the sequences of internal fragments of seven essential, single-copy, housekeeping genes - i.e. genes required for processes that are essential for cell operation - to characterise isolates. (rapidmicrobiology.com)
  • It is generally undertaken by Sanger sequencing - in other words, the same sequencing technology used for 16S microbial identification of isolates. (rapidmicrobiology.com)
  • We investigated whether machine learning approaches applied to wgMLST allele call data could assist in attribution analysis of food source of L. monocytogenes isolates. (cdc.gov)
  • We compiled isolates with a known source from five food categories (dairy, fruit, meat, seafood, and vegetable) using the metadata of L. monocytogenes isolates in PulseNet, deduplicated closely genetically related isolates, and developed random forest models to predict the food sources of isolates. (cdc.gov)
  • Isolates from 4 patients and Company A products were closely related by WGS, and the 4 patients with known exposures had consumed milkshakes made with Company A ice cream while hospitalized. (cdc.gov)
  • these isolates were closely related by WGS to those from 5 patients in 3 other states. (cdc.gov)
  • To resolve phylogenetic relationships among ries of bacterial clonal complexes by using concatenated isolates, we sequenced 68 isolates from Europe and North sequences of housekeeping genes when within-loci and America at 1 chromosomal locus (16S-23S ribosomal RNA between-loci recombinations are infrequent ( 5 ). (cdc.gov)
  • The genetic homogeneity of ospC -A isolates was confi rmed agent, Borrelia burgdorferi , a spirochete that parasitizes by sequences at 6 additional chromosomal housekeeping vertebrates, is transmitted by hard-bodied ticks through- loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)
  • Additional multilocus sequence analysis, including sequences of the housekeeping genes rpoA , recA , pyrH , gyrB and ftsZ , and DNA-DNA hybridization experiments indicated that the strains were distinct from currently known species of the genus Vibrio and confirmed the clustering of the three isolates. (microbiologyresearch.org)
  • The present study was taken up to explore 16S rRNA gene sequence to develop methods that can be used for preliminary identification and can supplement the existing methods for identification of clinically-relevant isolates of the genus Streptococcus . (biomedcentral.com)
  • Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns. (biomedcentral.com)
  • The Y. enterocolitica isolates were classified into 54 sequence types (STs) and 125 cgMLST types (CTs), with 4/O:3 being the dominant bioserotype in Ningxia. (biomedcentral.com)
  • Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment. (biomedcentral.com)
  • CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food. (biomedcentral.com)
  • Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. (peerj.com)
  • We examined the distribution of the pilus islet, using the presence of the rlrA gene as a marker for the locus, among a collection of invasive isolates recovered in Portugal and analyzed its association with capsular serotypes, clusters defined by the pulsed-field gel electrophoretic profiles (PFGE) and multilocus sequence types. (biomedcentral.com)
  • Analysis of rlrA negative isolates revealed heterogeneity in the genomic region downstream of the rfl gene, the region where the islet is found in other isolates, compatible with recent loss of the islet in some lineages. (biomedcentral.com)
  • Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. (biomedcentral.com)
  • Within L. monocytogenes , sequences homologous to gtcA were found in all serogroup 4 isolates but not in strains of any other serotypes. (asm.org)
  • Additionally, polymerase chain reaction ( PCR ) amplification of different DNA sequences can generate DNA barcodes, and analysis of the banding patterns can differentiate strains. (genengnews.com)
  • Rapid and reliable sub-typing of bacterial pathogens is important for identification of outbreaks and monitoring of trends in order to establish population structure and to study the evolution among bacterial genomes especially within and between the outbreak strains. (biomedcentral.com)
  • We performed a three-locus phylogenetic analysis of Fusarium strains presumably capable of trichothecene production, which were deposited in the Russian national collections. (actanaturae.ru)
  • Their comparative analysis demonstrated a relatively high level of intraspecific variability in F. graminearum and F. sporotrichioides, but no correlation between the sequence polymorphism and the geographic origin of the strains or their chemotype was found. (actanaturae.ru)
  • A group of strains representing species of the genus Leptospira, isolated from patients with leptospirosis in Mayotte (Indian Ocean), were previously found to be considerably divergent from other known species of the genus Leptospira. (nih.gov)
  • Draft genomes of the strains were also analysed to study the DNA relatedness with other species of the genus Leptospira. (nih.gov)
  • Strains are identified by comparing the sequence profiles obtained with previously published data. (rapidmicrobiology.com)
  • These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea . (frontiersin.org)
  • We used multilocus sequence analysis to estimate the genetic relatedness of 56 T. suavissima symbionts to 28 Ensifer reference strains. (usda.gov)
  • WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. (biomedcentral.com)
  • We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. (biomedcentral.com)
  • On the basis of 16S rRNA gene sequencing, the three strains formed a cluster within the genus Vibrio and were most closely related to Vibrio pectenicida DSM 19585 T (97.9 % similarity). (microbiologyresearch.org)
  • We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. (peerj.com)
  • Here we focus on the genotyping of Coccidioides strains from various origins by combining multiple studies in a meta-analysis and by using population genetics to clarify the causative agents of coccidioidomycosis. (blogspot.com)
  • Lyme disease is caused by spirochetal bacteria from the genus Borrelia , which has well over 300 known genomic strains. (newworldencyclopedia.org)
  • The recent development of second generation sequencing platforms (reviewed by Mardis [ 7 , 8 ] and Shendure [ 7 , 8 ]) offers an opportunity to change the direction of microbial genomics, enabling the rapid genome sequencing of large numbers of strains of both pathogenic and non-pathogenic strains. (biomedcentral.com)
  • Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. (bvsalud.org)
  • These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). (biomedcentral.com)
  • Further restriction fragment length polymorphism and DNA sequencing methods were used to identify the circulating strains in two selected geographical regions of Sri Lanka. (scielo.br)
  • The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. (omictools.com)
  • However, Brucella species can be clearly separated from each other by highly discriminating molecular techniques, such as multiplex PCR, multilocus sequencing typing, or multiple loci variable-number tandem repeat analysis. (cdc.gov)
  • This was inferred from sequence analysis of rrs (16S rRNA) and other genetic loci and suggests that they belong to a novel species. (nih.gov)
  • While Sanger technology is well suited to sequencing part, or all, of a single gene, when multiplied up to the requirement to sequence seven distinct loci, it does become a more expensive option. (rapidmicrobiology.com)
  • Sequence data was partitioned according to the replicons upon which the loci are located. (usda.gov)
  • Here we obtained a well-resolved polymorphism type of intergenic spacer (IGS) sequence phylogeny of B. burgdorferi sensu stricto clonal complexes (corresponding to the ospC- A and -B groups) is associated by using multilocus sequence typing at housekeeping loci with hematogenous dissemination in patients with early as well as loci under adaptive evolution. (cdc.gov)
  • The new "spider‐specific" probes were used to sequence UCE loci in 51 specimens. (researchgate.net)
  • Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. (biomedcentral.com)
  • An extensive reclassification of families and orders of the class based on a polyphasic analysis (including 16S rRNA gene analyses and 53-protein ribosomal protein concatamer analyses using the rMLST Multilocus sequence typing system) was published in 2017, that removed the order Hydrogenophilales from the class and into a novel class of the "Pseudomonadota", the Hydrogenophilalia. (wikipedia.org)
  • The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. (biomedcentral.com)
  • Mitochondrial DNA sequences consisting of 645 sites from the 12S rRNA and 16S rRNA genes were used to estimate the phylogeny of 15 of the 32 species of spiny-footed lizards Acanthodactylus. (lacerta.de)
  • This phylogeny indicates that the ancestor of existing Acanthodactylus probably originated in south-west Asia and that North Africa was invaded by more than one lineage of the genus. (lacerta.de)
  • We constructed a multilocus phylogeny, combining data from two mitochondrial (12S, cytb) and three nuclear (MC1R, ACM4, c-mos) markers for 302 individuals belonging to 36 known species, providing the first large-scale time-calibrated molecular phylogeny of the genus. (lacerta.de)
  • COI gene tree obtained by Maximum Likelihood and Bayesian have identical topologies agreeing with a multilocus phylogeny reconstructed in a previous work on Calisto and placing the new taxon as sister of C. hysius . (mapress.com)
  • Using sequence data from two mitochondrial and three nuclear genes and applying several phylogenetic methods and species delimitation approaches to an extensive dataset, we have reconstructed the phylogeny of the Podarcis wall lizards in the Balkans, and re-investigated the taxonomic status of the P. tauricus species subgroup. (gallotia.de)
  • Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. (gallotia.de)
  • The intra- and interspecific polymorphism of partial sequences of the translation elongation factor 1 alpha (TEF1α) gene and two genes from the trichothecene cluster TRI5 and TRI14 was studied. (actanaturae.ru)
  • Methods: The individual taxonomic microbiota composition of fecal samples from 90 NAFLD patients and 21 healthy controls was analyzed using 16S rRNA gene sequencing. (uni-frankfurt.de)
  • Furthermore, we used 16S ribosomal RNA gene sequencing to detect associations with different abundances of the gut microbiota with dietary patterns. (uni-frankfurt.de)
  • At NCIMB, our microbial identification identifies bacteria by sequencing the first 500 bp of the 16S rRNA gene and searching for matches using the MicroSEQ database. (rapidmicrobiology.com)
  • However, full 16S gene sequencing results are not always conclusive for this purpose. (rapidmicrobiology.com)
  • The seven fragments sequenced are each approximately 450 - 500 base pairs long - so around the same length as the section of the 16S gene that we sequence for identification purposes. (rapidmicrobiology.com)
  • The genus has been divided into different groups based on 16S rRNA gene sequence similarity. (biomedcentral.com)
  • The markers generated exploring 16S rRNA gene sequences provided useful tool that can be further used for identification of different species of the genus Streptococcus . (biomedcentral.com)
  • 16S rRNA gene sequencing has proved to be one of the most powerful tools for the classification of microorganisms [ 38 ] and has been used for identification of clinically relevant microbes [ 39 , 40 ]. (biomedcentral.com)
  • The genus consists of 2 genetically diverse species, C. immitis and C. posadasii , each of which contains 1 or more distinct populations with limited gene flow. (blogspot.com)
  • We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. (biomedcentral.com)
  • Traditional phylogenetic analyses that assume a bifurcating tree fails to model complicated evolutionary processes such as incomplete lineage sorting (ILS), gene flow, and horizontal gene transfer [ 1 ]. (biomedcentral.com)
  • Gene flow, or introgression, refers to alleles from one species entering a different (and usually closely related) species through migration and hybridization. (biomedcentral.com)
  • Analysis of gene flow must take ILS into account, because both processes generate gene trees that are incongruent with the species tree. (biomedcentral.com)
  • Among the earliest methods to detect gene flow are a homoplasy-based analysis that finds taxa that are intermediate between putative parent species [ 9 ], and a gene tree comparison that identifies locus divergence younger than the species' divergence [ 10 ]. (biomedcentral.com)
  • Shell morphology and anatomy of the reproductive organs were examined, and a fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene and the nuclear ribosomal Internal Transcribed Spacer 1 (ITS-1) were sequenced from 15 populations. (pensoft.net)
  • Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. (omictools.com)
  • Genome-wide transcript analysis showed that B. anthracis undergoes considerable changes in gene expression during growth in iron-depleted media, including the regulation of known and candidate virulence factors. (omictools.com)
  • Bayesian and maximum likelihood analyses based on the combined four-gene dataset resulted in a tree consisting of two major clades within the group. (e-algae.org)
  • For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes. (biomedcentral.com)
  • Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. (biomedcentral.com)
  • Identification of genes with different degrees of variation is important especially in trend analysis. (biomedcentral.com)
  • Today, the most widely used typing methods for bacterial genomes include multilocus sequence typing (MLST), pulsed field gel electrophoresis (PFGE), sequencing of 16S rRNA genes, and multilocus variable-number of tandem-repeat analysis (MLVA). (biomedcentral.com)
  • Conserved genes are present across bacterial genomes of the same species (or genus). (biomedcentral.com)
  • Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data. (biomedcentral.com)
  • Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium), two host restricted serotypes (Typhi [two genomes] and Paratyphi) and one host adapted serotype (Choleraesuis) were used to identify core genome genes that show evidence for recombination and positive selection. (biomedcentral.com)
  • The evolution of Salmonella Typhi towards a lifestyle characterized by systemic infection and transmission by excretion through the gall bladder rather than luminal gut colonization [ 4 ] involved a combination of acquisition events (e.g., acquisition of Vi capsule related genes), and deletion events (e.g., loss of virulence-associated genes, such as several genes in SPI-1, SPI-2, SPI-3, SPI-4 and SPI-5). (biomedcentral.com)
  • Later studies confirmed that the RlrA protein acted as a transcription factor recognizing several promoters within the rlrA islet and showed it to be essential for wild-type levels of expression of the pili structural genes and associated sortases [ 6 ]. (biomedcentral.com)
  • The deepest branching species in the genus, Y. ruckeri , causative agent of red mouth disease in fish, has the smallest genome (3.7 Mb), although it shares the same core set of approximately 2,500 genes as the other members of the species, whose genomes range in size from 4.3 to 4.8 Mb. (biomedcentral.com)
  • This work underscores the importance of the acquisition of horizontally transferred genes in the evolution of Y. pestis and points to virulence determinants that have been gained and lost on multiple occasions in the history of the genus. (biomedcentral.com)
  • For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. (bvsalud.org)
  • Some members of the Betaproteobacteria can cause disease in various eukaryotic organisms, including in humans, such as members of the genus Neisseria: N. gonorrhoeae and N. meningitidis being primary examples, which cause gonorrhea and meningitis respectively, as well as Bordetella pertussis which causes whooping cough. (wikipedia.org)
  • In addition, the mycotoxins produced by members of the genus Fusarium pose a threat to human and animal health and also act as pathogenicity factors for plants [ 1 ]. (actanaturae.ru)
  • Trichothecene mycotoxins are produced not only by members of the genus Fusarium, but also by those from the genera Myrothecium, Trichoderma, Cephalosporium, Verticimonosporium, and Stachybotrys [ 2 ]. (actanaturae.ru)
  • Members of the genus Ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related genera, Medicago L., Melilotus Mill. (usda.gov)
  • This word is used as a prefix in this case, to reflect the smaller size of the fish compared to other members of the genus Brycon. (iloveaquarium.com)
  • Members of the genus Haemophilus are small, pleomorphic gammaproteobacteria that are characterized by their dependency on the blood factors haemin (X-factor) and/or nicotinamide adenine dinucleotide (V-factor) for growth [ 1 , 2 ]. (biomedcentral.com)
  • Human brucellosis is a zoonoses caused by bacteria of the genus Brucella . (cdc.gov)
  • Brucellosis is caused by gram-negative, facultative intracellular bacteria of the Brucella genus that can infect many organs and soft tissues. (cdc.gov)
  • The Betaproteobacteria are a class comprising over 75 genera and 400 species of bacteria. (wikipedia.org)
  • MALDI-TOF is known to be a reliable method for the identification of intact bacteria and yeast, and is more accurate than phenotypic systems, but not as accurate as sequence-based approaches. (genengnews.com)
  • The genus Streptococcus consists of spherical Gram positive bacteria belonging to the class Bacilli and the order Lactobacillales [ 1 ]. (biomedcentral.com)
  • It can be used with a set of predefined MacSyFinder models, "TXSScan," to identify all major secretion systems of diderm bacteria (i.e., with inner and LPS-containing outer membranes) as well as evolutionarily related cell appendages (pili and flagella). (bvsalud.org)
  • Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. (biomedcentral.com)
  • Currently there are more than a hundred bacterial species for which sufficient genomic data are available to estimate the species core-genome (that is, there are at least three genomes sequenced from the same species) [ 14 ]. (biomedcentral.com)
  • Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species. (peerj.com)
  • Here we describe the deployment of new sequencing technology to extensively sample eight genomes from the Yersinia genus of the family Enterobacteriaceae. (biomedcentral.com)
  • Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification. (frontiersin.org)
  • The aim of this study was to develop, refine and evaluate an alternative methodology, which enables better preservation of large numbers of individual schistosome larval stages and eggs collected in low resource endemic areas, to provide PCR-quality DNA for multi-locus genetic analysis. (imperial.ac.uk)
  • From the combined phylogenetic analysis of multi-locus sequence data of the Lecanoraceae including two nuclear protein-coding markers (RPB2 and RPB1), the internal transcribed spacer and a fragment of the mitochondrial small subunit, found that the originally monotypic eastern Asian genus Verseghya is positioned within the Verseghya-Lecidella-Pyrrhospora clade of the Lecanoraceae and includes one more taxon Verseghya thysanophora widely distributed in Northern Hemisphere. (akjournals.com)
  • Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. (mdpi.com)
  • Four ospC clonal complexes dence of genetic endemism, recent migration events, and (A, B, I, and K groups) were found to be more likely than recombinant genomic types. (cdc.gov)
  • Early work by O'Rourke & Stevens (1993) using electrophoretic analysis of enzymes of the pathogen and serological methods suggested that gonococci have a non-clonal sexual or panmictic population structure. (peerj.com)
  • To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. (omictools.com)
  • This refers to a particular nucleotide (or "base") in a DNA sequence that is variable within a species (or between related species). (panzea.org)
  • The aim of this study was to prove the reproducibility of published results and to provide a detailed overview of all findings in our NAFLD cohort using next generation sequencing methods. (uni-frankfurt.de)
  • Phylogenetic analyses using Maximum Likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g. (researchgate.net)
  • These markers have been useful in population genetics studies that compare genotypes among closely related fungal species or populations ( 17 , 20 - 23 ). (blogspot.com)
  • We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. (biomedcentral.com)
  • both from Korea), which were described from Korea and Japan more than one century ago and not recorded from that time), including diagnostic characters important for the present taxonomy of the genus Caloplaca s. l., are provided. (akjournals.com)
  • The Chilean Altiplano and the Atacama Desert in northern Chile harbor isolated hydrological systems or oases where it is possible to find minute aquatic snails of the genus Heleobia whose taxonomy is uncertain and where many populations remain unknown. (springeropen.com)
  • More recent studies have also suggested high rates of recombination within the Neisseria genus ( Didelot & Maiden, 2010 ). (peerj.com)
  • The genus has seldom undergone taxonomic revisions, and although there are a number of described species and species-groups, their boundaries as well as their interspecific relationships are largely unresolved. (lacerta.de)
  • The following are four considerations when choosing an appropriate identification or strain typing platform. (genengnews.com)
  • 4. Understand that not all strain typing systems are created equal. (genengnews.com)
  • nov. is proposed, with 200901116(T) ( = CIP 110703(T) = DSM 28999(T)) as the type strain. (nih.gov)
  • Central databases have been established, to which users can submit strain information and new allele sequences. (rapidmicrobiology.com)
  • nov. (type strain PP-203 T = CECT 7398 T = DSM 21433 T ) is proposed. (microbiologyresearch.org)
  • Although clinical microbiology typically relies on single-colony picks (which has the potential to underestimate species diversity and transmission events), within-host diversity of E. coli in the gut is crucial to our understanding of inter-strain competition and co-operation and also for accurate diagnosis and epidemiological analyses. (peerj.com)
  • Whole genomic comparison between strain SM2-FT and close relatives suggested a novel species of a novel genus. (academic-accelerator.com)
  • DNA-DNA hybridization and whole genomic comparison, mandatory to taxonomically separate strain 924/12T from the type strain of L. (academic-accelerator.com)
  • The genus Bythinella Moquin-Tandon, 1856 consists of minute (2-4 mm shell height), dioecious, oviparous freshwater snails inhabiting springs and subterranean waters across Europe and western Asia. (pensoft.net)
  • Multilocus analyses revealed that the aforementioned subgroup consists of five major clades, with P. melisellensis as its most basal taxon. (gallotia.de)
  • Mpn HPRT (MPN672) consists of 175 amino acids and shares 29% sequence identity to human HPRT. (bcl-2protein.com)
  • These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. (peerj.com)
  • The genus Lecidella forming the Lecidella-Glaucomaria subclade within the same Verseghya-Lecidella-Pyrrhospora clade of the Lecanoraceae found to have tendency to be polyphyletic after including the recently described eastern Asian taxon Lecidella mandshurica into phylogenetic analysis of the Lecanoraceae. (akjournals.com)
  • Clades II and III inhabit areas adjacent to clade I and were most closely related with the latter clade. (pensoft.net)
  • Phylogenetic analyses revealed five main mitochondrial DNA clades, which were partly confirmed by analyses of the ITS-1 sequences. (pensoft.net)
  • Molecular phylogenetic analysis consistently recovered five clades, one of which constitutes a cryptic species previously assigned to a species recognized in the area. (springeropen.com)
  • Four other clades contained sequences of one nominal species consistent with its type locality and at least two additional candidate species, which were corroborated by a particular penis morphology. (springeropen.com)
  • Additional sequences from eight previously studied populations were included in our analyses. (pensoft.net)
  • Furthermore, some morphological differences in penis morphology were observed in two Altiplano populations not resolved by the DNA sequences, providing support for two additional candidate species in the genus. (springeropen.com)
  • Reptilia: Lacertidae) using mitochondrial DNA sequence, with comments on their biogeography and evolution. (lacerta.de)
  • We use simulations to compare the statistical performance of Mongrail with that of an existing composite likelihood method (NewHybrids) and apply the method to analyze genome sequence data for hybridizing species of barred and spotted owls. (nfshost.com)
  • Similar to 16S rDNA sequencing, the development of this technique has been underpinned by online data sharing. (rapidmicrobiology.com)
  • Rapid high-quality draft sequencing was used successfully to compare pathogenic and non-pathogenic members of the Yersinia genus. (biomedcentral.com)
  • For a variety of reasons, most research effort has been focused on characterizing these pathogens, while their closely related non-pathogenic relatives have only been lightly studied. (biomedcentral.com)
  • All three human pathogens carry a 70-kb pYV virulence plasmid (also known as pCD), which carries the Ysc type III secretion system and Yops effectors [ 18 - 20 ], that is not detected in non-pathogenic species. (biomedcentral.com)
  • The objective of the present study was to assess the effect of a correct 3-step hand hygiene technique on reducing of potentially pathogenic microorganisms on hands related to the WHO five moments for hand hygiene. (bvsalud.org)
  • This study aims to analyze the ecological and molecular epidemiological characteristics of Y. enterocolitis in order to inform the public health intervention strategies for the contains of related diseases. (biomedcentral.com)
  • However, analysis of the banding patterns can be hindered by data quality. (genengnews.com)
  • To fill this gap, we developed GEFAAR-a generic framework for the analysis of antimicrobial resistance data. (bvsalud.org)
  • However, combined analysis of molecular and morphological data sets produces the same tree topology as DNA sequence alone. (lacerta.de)
  • Molecular data provide independent evidence that the differential weighting of morphological characters in past analyses was appropriate. (lacerta.de)
  • Specifically, PrioriTree provides a suite of functions to generate input files for-and summarize output from-BEAST analyses for performing robust Bayesian inference, data-cloning analyses and assessing the relative and absolute fit of candidate discrete-geographic (prior) models to empirical datasets. (nfshost.com)
  • This method is designed to be used on either one of two types of data: (1) sequence alignment where there is only one or a few samples per taxa, or (2) SNP data where the frequency of each allele in each population is known. (biomedcentral.com)
  • In this chapter, we describe a complete pipeline of analysis, starting from (i) the integration of information from a reference set of experimentally studied systems, (ii) the identification of conserved proteins and the construction of their HMM protein profiles, (iii) the definition and optimization of "macsy-models," and (iv) their use and online distribution as tools to search genomic data for secretion systems of interest. (bvsalud.org)
  • Recombinant Mpn HPRT was expressed as an N-terminal fusion protein with a 6 × histidine tag and a tobacco etch virus (TEV) cleavage site at the N-terminus, and was purified to >98% purity by metal affinity chromatography, see more as assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis (data not shown). (bcl-2protein.com)
  • However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)
  • Most organisms are chemolithoautotrophs with some methylotrophs and heterotrophs Rhodocyclales comprises the families Rhodocyclaceae (type family), Azonexaceae and Zoogloeaceae. (wikipedia.org)
  • 3. If you are confirming the identity of a QC organism, make sure the technology you are using can resolve organisms in that genus. (genengnews.com)
  • The phylum Apicomplexa contains organisms that shareapical specializations related to their polarized attachment and entry into host cells All extant lineages of the Apicomplexa are obligate intracellular para-sites. (pdfmedarticles.com)
  • Rather, its genotoxic effects are limited to indirect clastogenicity occurring in select cell types, and only when high dose and time thresholds are exceeded. (cdc.gov)
  • Moreover, our application offers an intuitive web-based user interface to visualize resistance trend analysis as well as advanced cluster analyses on species- or clinic/unit level to generate alerts of potential transmission events. (bvsalud.org)
  • The originally monotypic eastern Asian genus Sedelnikovaea forming a monophyletic branch within the Sedelnikovaea-Lecanoropsis subclade and being in out-position to the Rhizoplaca-Protoparmeliopsis s. str. (akjournals.com)
  • doi:10.1016/S0304-4017(03)00206-1 L. David Sibley / Veterinary Parasitology 115 (2003) 185-198 relationship is supported both by morphological comparisons (presence of sub-cortical alve-olar membranes) and by molecular analyses based on conserved protein sequences or smallsubunit (SSU) rRNA sequences. (pdfmedarticles.com)
  • Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs. (omictools.com)
  • In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. (springer.com)
  • We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. (omictools.com)
  • New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. (biomedcentral.com)
  • Acanthodactylus constitutes the most species-rich genus in the family Lacertidae, with over 40 recognized species inhabiting a wide variety of dry habitats. (lacerta.de)