Bacterial sequences. Medical search. Frequent questions

Genomic and transcriptomic sequencing analyses were performed with phenotypic validation to investigate its adaptation in SARS-CoV-2 infected environment. (frontiersin.org)
However, linking the possession of mobile genetic elements and their associated antibiotic resistance genes to a specific strain in the mixed bacterial community is often lost due to the fragmentation of genomic DNA during normal metagenomic sequencing protocols. (edu.au)
These findings warrant a close genomic monitoring of MPXV to get a better picture of the genetic micro-evolution and mutational patterns of this virus , and a close clinical monitoring of skin bacterial superinfection in monkeypox patients . (bvsalud.org)
Each participant's microbiome was assessed with genomic sequencing with sequences aligned to a bacterial database. (medscape.com)
The Viral Diseases Branch of Walter Reed Army Institute of Research apply advanced next-generation sequencing technologies and bioinformatics analyses to support genomic surveillance of COVID-19 in Military Health System beneficiaries. (health.mil)
Additionally, iSKIM has been used to scan hundreds of thousands of publicly available raw genomic sequencing datasets to explore the emergence patterns of key SARS-CoV-2 mutations. (health.mil)

This list of sequenced eubacterial genomes contains most of the eubacteria known to have publicly available complete genome sequences. (wikipedia.org)
For the genomes of archaea see list of sequenced archaeal genomes. (wikipedia.org)
Through start-up support from the Advanced Molecular Detection (AMD) program, StrepLab now sequences whole genomes of group A strep and other bacteria. (cdc.gov)
They applied their approach to individual bacteria and the mouse gut genome, as well as demonstrate a method for nanopore sequencing-based methylation binning of metagenomic contigs, associating mobile genetic elements with their host genomes, and identifying misassembled metagenomic contigs. (genomeweb.com)
SNPsaurus is now offering Illumina PE 150 sequencing of bacterial genomes: library prep, sequencing to 60X read depth, assembly, annotation, and alignment to a reference with variant calling--starting at $69/sample. (seqanswers.com)
However, easy and … automated construction of high-quality bacterial genomes using nanopore reads remains challenging. (workflowhub.eu)
Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. (workflowhub.eu)
Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection. (bvsalud.org)
Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)

The bacterial species Streptococcus pyogenes , or group A strep, is known for causing strep throat. (cdc.gov)
While they identified over 2,000 distinct bacterial species, further analysis revealed that 79 species tended to classify samples into their respective cohorts. (genomeweb.com)
In particular, the authors were "surprised to find a relatively high prevalence of clinically important bacterial species and antibiotic-resistance genes" in outpatient samples, despite not being on antibiotics at the time. (genomeweb.com)
By contrast, metagenomic sequencing was a "single diagnostic test with precise and clear quantitative detection of clinically important species and antibiotic-resistance genes of MDR bacteria relative to the abundance of all other species and antibiotic-resistance genes within the gut microbiota. (genomeweb.com)
They also find that nanopore sequencing signals display complex heterogeneity across methylation events of the same type, which suggests that detection methods are best developed using a diverse collection of species. (genomeweb.com)
To enable nanopore sequencing for broad methylation discovery, they generated a training dataset from an assortment of bacterial species and develop a technique that combines the identification and fine mapping of the three forms of methylation into a multi-label classification framework. (genomeweb.com)
In 2002, an ad hoc committee for the reevaluation of species definition in bacteriology ( 24 ) advised that all new bacterial species descriptions include an rRNA sequence from the type strain, and in 2001, Bergey's Trust published a revised higher-order taxonomy attempting to reconcile bacterial taxonomy with rRNA-based phylogeny ( 12 , 13 ). (asm.org)
Their ability to capture DNA and to spread within and between bacterial species by conjugation facilitates the rapid dissemination of potentially beneficial genes through a bacterial population. (cdc.gov)
We conclude that the bacterial survivability and species richness in each stage could be used as bioindicators to monitor the level of pollution and appropriate functioning of a CETP. (scitechnol.com)
These primers, because of their high degree of conservation, could also be used for cloning these genes from other bacterial species. (mcmaster.ca)
A conserved insert in F. succinogenes Hsp60 that is commonly present in all bacterial species, except various Gram-positive bacteria, Deinococcus-Thermus groups and green non-sulphur bacteria, provides evidence that F. succinogenes does not belong to these taxa. (mcmaster.ca)
The taxonomic status of all species of the genus Elizabethkingia was re-evaluated by comparative genomics based on whole-genome sequencing. (microbiologyresearch.org)
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. (microbiologyresearch.org)
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (microbiologyresearch.org)
The main objectives of this study are to identify the bacterial species present in wounds and to evaluate and compare the results obtained using conventional biochemical analysis and 16S rDNA sequencing. (um.edu.my)
However, by 16S rDNA sequencing only 19 (35.2) isolates were identified at species level and 35 (64.8) were identified at the genus or family level. (um.edu.my)
16S rDNA sequencing however provided a better view on the phylogenetic relationships of bacterial species present in wounds. (um.edu.my)
Among NYC firefighters enrolled in the randomized FIREHOUSE (Food Intake Restriction for Health Outcome Support and Education) study who took part in a microbiome substudy, those who followed a low-calorie, Mediterranean-style diet had higher levels in stools samples at 6 months of Bacteroides ovatus , a bacterial species associated with protection against bowel inflammation. (medscape.com)
Overall, we found that in our validation cohort, Bacteroides ovatus was increased in the LoCalMed arm after 6 months, and this bacterial species is associated with fewer negative health effects," she said. (medscape.com)
The number and diversity of bacterial species in each sample were determined with the Chao1 Index and Shannon Index, respectively. (medscape.com)
Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. (cdc.gov)
In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. (cdc.gov)
16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)

1 Bacterial samples collected over the course of an outbreak might only be "near" identical because bacteria pick up genome mutations over time. (cdc.gov)
NEW YORK (GenomeWeb) - Researchers with Cincinnati Children's Hospital have developed a metagenomic sequencing protocol for fecal samples to detect bacteria resistant to multiple drugs, in order to prevent the spread of infection with such bugs. (genomeweb.com)
The researchers sequenced the fecal microbiomes of 17 inpatient samples, who were deemed at a higher risk to becoming infected with drug resistant bacteria due to prolonged hospital stays, as well as 11 outpatient samples, who were deemed at a lower risk. (genomeweb.com)
An approach for using nanopore sequencing to discover different types of DNA methylation from bacteria and the microbiome is described by a Mount Sinai-led team in this week's Nature Methods . (genomeweb.com)
Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals. (cdc.gov)
These bacteria were often absent from gram stain smears of patients with other bacterial morphotypes. (cdc.gov)
This document specifies the minimum requirements for generating and analysing whole genome sequencing (WGS) data of bacteria obtained from the food chain. (iso.org)
The phylogenetic placement of the rumen bacterium Fibrobacter succinogenes was determined using a signature sequence approach that allows determination of the relative branching order of the major divisions among Bacteria [Gupta, R. S. (2000) FEMS Microbiol Rev 24, 367-402]. (mcmaster.ca)
We determined whether Gram-negative bacterial molecules are associated with Alzheimer disease (AD) neuropathology given that previous studies demonstrate Gram-negative Escherichia coli bacteria can form extracellular amyloid and Gram-negative bacteria have been reported as the predominant bacteria found in normal human brains. (neurology.org)
Culture analysis and 16S rDNA sequencing both revealed that the most prevalent bacteria in wounds are Staphylococcus spp. (um.edu.my)
Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)
The procedure's high sequence depth allows for these amplicons to be analysed separetely so different bacteria from the same sample can be identified. (folkhalsomyndigheten.se)
For bacterial mycetoma (actinomycetoma) treatment relies on long-term treatment with a combination of antibiotics, tailored to the type of bacteria involved. (who.int)
has been identified as the 2nd most consensus (ERIC) sequences which · 60 environmental samples were tak- frequent organism causing ventilator- are common to Gram-negative enteric en throughout the ICU, including associated pneumonia, the 4th most bacteria [11,12]. (who.int)

Participating ABCs sites then send patients' bacterial strains to CDC's StrepLab. (cdc.gov)
Genome sequence information allows scientists to track new strains and antibiotic resistance trends. (cdc.gov)
Before genome sequencing, scientists only knew the type of group A strep strains, not if they were identical or near identical. (cdc.gov)
Antimicrobial drug resistance is a global challenge for the 21st century with the emergence of resistant bacterial strains worldwide. (cdc.gov)
The virus was sequenced at the Institut Pasteur's Mutualized Platform for Microbiology (P2M), which performs genome sequencing on bacterial, viral, fungal and parasite strains received by National Reference Centers and World Health Organization Collaborating Centers for the purpose of infectious disease surveillance. (pasteur.fr)
We propose a more rapid identification scheme on the basis of an in silico PCR assay derived from comparative genomics of whole-genome sequences (WGS) from 29 well-curated strains. (microbiologyresearch.org)
Some of the enzymes which generate aromatic radicals that break down most prominent bacterial strains found were isolated and tax- the complex linkages present in lignin to compounds of lower onomically identified using 16S ribosomal RNA (rRNA) se- molecular weight. (lu.se)

Metagenomics provides in-depth information about the microbiome in a specific sample, including bacterial composition, metabolic capacity, carriage of antibiotic resistance genes, plasmids, phage, and other mobile genetic elements. (edu.au)
Here, we performed DNA metagenomics using next-generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV-infected patients diagnosed between June and July 2022. (bvsalud.org)

Metagenomic sequencing was performed on the Illumina HiSeq 2500. (genomeweb.com)
See http://www.snpsaurus.com/illumina-bacterial-assembly/ for details and pricing for your project size. (seqanswers.com)
In our experience, the largest contigs from Illumina sequencing and assembly will be hundreds of kilobases to a megabase in length. (seqanswers.com)
microPIPE was developed to automate high-quality complete bacterial genome assembly using Oxford Nanopore Sequencing in combination with Illumina sequencing. (workflowhub.eu)
Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing. (workflowhub.eu)

When comparing the sequencing method to culture, the researchers found that the culture missed several drug-resistance genes and was "cumbersome and required additional testing given the growth of isolates not intended to be selected on all types of screening media. (genomeweb.com)
We aim to optimise the proximity ligation with shotgun sequencing protocol for the purpose of linking antibiotic resistance genes and plasmids with their bacterial hosts within mixed population communities. (edu.au)
For this purpose, segments of the Hsp60 (groEL), Hsp70 (dnaK), CTP synthase and alanyl-tRNA synthetase genes, which are known to contain signature sequences that are useful for phylogenetic deterministic purposes, were cloned. (mcmaster.ca)
Using degenerate oligonucleotide primers for highly conserved regions in these proteins, 1.4 kb, 0.75 kb, 401 bp and 171 bp fragments of the Hsp70, Hsp60, CTP synthase and alanyl-tRNA synthetase genes respectively were amplified by PCR, and these fragments were cloned and sequenced. (mcmaster.ca)
Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)

Sequencing the genome of pathogens is crucial for the development of specific diagnostic tests and the identification of potential treatment options," explains Sylvie van der Werf, Director of the National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur. (pasteur.fr)
The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. (cdc.gov)
In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)

The MDH Public Health Laboratory obtained potentially outbreak-related isolates, performed additional testing, and shared these isolates with StrepLab for sequencing and analysis. (cdc.gov)
The workflow below summarises the different steps of the pipeline (with each selected tool) and the approximate run time (using GPU basecalling, averaged over 12 E. coli isolates sequenced on a R9.4 MinION flow cell). (workflowhub.eu)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)
Bacterial metabolism selected lignin model compounds (vanillin, vanillate, 4- hydroxybenzoate, p-coumarate, benzoate, and ferulate) was carried out with three of the Pseudomonas isolates and in addition with the strain Pseudomonas putida KT2440 from a Introduction culture collection. (lu.se)

Today, rRNA-based analysis remains a central method in microbiology, used not only to explore microbial diversity but also as a day-to-day method for bacterial identification. (asm.org)

The Active Bacterial Core surveillance (ABCs) system collects clinical and demographic information about patients with bacterial infections. (cdc.gov)
StrepLab scientists realized they could also use genome sequences to find connections between invasive group A strep infections. (cdc.gov)
Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). (microbialcell.com)
Introduction Previous studies found conflicting results regarding associations between urogenital Chlamydia trachomatis infections and ethnicity or urogenital symptoms among at-risk populations using either ompA- based genotyping or high-resolution multilocus sequence typing (MLST). (bmj.com)
RÉSUMÉ L'émergence et la propagation rapide des souches de Klebsiella pneumoniae résistantes aux antibiotiques et porteuses du gène blaKPC codant la production de carbapénèmases ont compliqué la prise en charge des infections des patients. (who.int)

Fariq A, Yasmin A, Blazier JC, Jannat S (2021) Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing. (pensoft.net)
A study reported the microbial diversity of three hot springs from Neuquén, Argentina, by using molecular based high-throughput amplicon sequencing technique. (pensoft.net)
Creative Biolabs has established the high-throughput SuPrecision™ platform for large-scale sequencing services. (seqanswers.com)
The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. (routledge.com)
The fecal samples were then analyzed using high-throughput sequencing of 16S rRNA V3-V4 amplicons. (hindawi.com)
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)

Whole-genome sequence of Burkholderia sp. (pacb.com)
For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)

The investigators note that existing methods for detecting DNA modification from nanopore sequencing data cannot effectively characterize unknown bacterial methylomes without previous knowledge. (genomeweb.com)
BACKGROUND: Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. (workflowhub.eu)

By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. (osti.gov)

To understand the structure and composition of such microbial communities, culture-independent bacterial diversity was characterised for two extreme sites in Pakistan, Khewra salt range and Murtazaabad hot spring. (pensoft.net)
Barcoded amplicon sequencing technique was used to study the microbial communities. (pensoft.net)

Outbreaks are caused by spreading the same bacterial strain from person-to-person. (cdc.gov)
The resulting "cluster detection tool" accurately and efficiently identifies outbreaks of the same bacterial strain. (cdc.gov)
In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. (asm.org)
therefore, dissemination has been attributed to conjugative plasmids rather than to clonal expansion of a bacterial host strain ( 13 ). (cdc.gov)
All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. (workflowhub.eu)
strain RPE67, a bacterial gut symbiont of the bean bug Riptortus pedestris. (pacb.com)
strain RPE67 is a bacterial symbiont isolated from a field-collected bean bug, Riptortus pedestris. (pacb.com)
To understand the genetic basis of the insect-microbe symbiosis, we performed whole-genome sequencing of the Burkholderia strain, revealing an 8.69-Mb genome consisting of three chromosomes and three plasmids. (pacb.com)

Bacterial and fungal profiling requires use of multiple reagents and informatics solutions to gain insightful results. (qiagen.com)
Mycetoma has two distinct etiologies: fungal and bacterial. (who.int)

The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. (pensoft.net)
2012. Time series analysis of two hydrothermal plumes at 9˚50'N East Pacific Rise reveals distinct, heterogeneous bacterial populations. (bco-dmo.org)

In contrast to the signal sequences of exported proteins, the bacterial SRP signal sequences are more hydrophobic and are mostly "uncleaved signal sequences" present in membrane proteins that remain in the final protein-chain as transmembrane anchor sequences. (nature.com)
The increase of the hydrophobicity in the signal sequences of E. coli presecretory proteins makes it possible to re-route the SecA dependent preproteins into the SRP targeting cycle 17 . (nature.com)
The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacterium-Bacteroides division The GenBank accession numbers for the sequences reported in this paper are AY017380, AY017381, AY017382 and AY017383. (mcmaster.ca)

Computer analysis of the HpcDNA revealed the presence of two strong potential bacterial promoters (alpha2PF and alpha2PS) located in the duplicated alpha2FS sequence. (rti.org)
The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. (asm.org)
Based on this advanced platform, we can provide the most comprehensive cancer WGS sequencing bioinformatics analysis for our global customers. (seqanswers.com)
This project seeks to establish this protocol at UQ to enable high-resolution analysis of mixed bacterial communities. (edu.au)
The sequencing run was completed by early evening on the Tuesday, and the scientists used data analysis to obtain the sequence of the whole genome in two of the first three confirmed cases in France. (pasteur.fr)
This proves the efficacy of the CNR's process of analysis based on viral sequencing," continues Vincent Enouf. (pasteur.fr)
In this case, it took just three days for the whole sequence to be determined: "We performed data analysis during the night from Tuesday to Wednesday, then corroborated the results on Wednesday with counter analysis," explains Vincent Enouf. (pasteur.fr)
Our analysis shows that S. tropica dedicates a large percentage of its genome ( approximately 9.9%) to natural product assembly, which is greater than previous Streptomyces genome sequences as well as other natural product-producing actinomycetes. (nih.gov)
In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). (microbialcell.com)
In this study, we investigated fecal 16S rRNA gene sequencing analysis of changes in the gut microbiota of rats with LDA-related intestinal injury. (hindawi.com)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)

Bacterial plasmids are key vectors of horizontal gene transfer, mediating the mobilization of genetic material from 1 bacterium to another. (cdc.gov)
To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. (frontiersin.org)

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). (asm.org)
Some unidentified sequences were also present at each taxonomic level. (pensoft.net)
Taxonomic reassessment of the genus Elizabethkingia using whole-genome sequencing: Elizabethkingia endophytica Kämpfer et al. (microbiologyresearch.org)

Dataset: Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at 9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise AT15-06 in July 2006. (bco-dmo.org)

Human brain samples were assessed for E coli DNA followed by DNA sequencing. (neurology.org)
DNA sequencing confirmed E coli DNA in human control and AD brains. (neurology.org)

A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
The development of molecular tools and the ability to isolate microbes in laboratory culture have revolutionised knowledge of bacterial diversity, which greatly exceeds that found in eukaryotes. (pensoft.net)
Modern metagenomic studies, like 16S rRNA sequencing, accurately characterise microbial diversity. (pensoft.net)

A proximity ligation sequencing assay for metagenomic samples has been developed to obtain complete microbiome assemblies by associating mobile genetic elements with their hosts, and has been successfully used to study microbiomes in environments such as wastewater and animal infection samples. (edu.au)
The two full sequences of the virus isolated in two of the first French cases were submitted to the Global Initiative on Sharing All Influenza Data (GISAID) platform, 1 which was initially developed to share sequences and monitor the genetic evolution of influenza viruses, a process that is vital to determine the composition of the influenza vaccine. (pasteur.fr)
Metagenomic sequencing engables a thorough mapping of the genetic material in the clinical sample, providing a broader understanding of the microbiological profile. (folkhalsomyndigheten.se)
By sequencing the entire genome, a comprehensive understanding of the genetic composition is obtained. (folkhalsomyndigheten.se)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. (asm.org)

In addition, the bacterial taxa showing significant differences between the control (NS) and APC groups were Firmicutes, Bacteroides, Verrucomicrobiaceae and Peptococcaceae. (hindawi.com)

Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). (microbialcell.com)

SRP at the ribosomal exit tunnel scans a nascent chain for bearing a hydrophobic SRP signal sequence 7 . (nature.com)

All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)
The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)

Providing nextRAD genotyping and PacBio sequencing services. (seqanswers.com)

The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community. (qub.ac.uk)

To further evaluate their biosynthetic potential, we sequenced the 5,183,331-bp S. tropica CNB-440 circular genome and analyzed all identifiable secondary natural product gene clusters. (nih.gov)

Running the genome sequences through the cluster detection tool at CDC showed the samples were near identical. (cdc.gov)
Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. (pensoft.net)
This project will establish in-house detailed molecular and bioinformatic protocols for the deployment of proximity ligation sequencing methodology in metagenomic samples, including determination of its accuracy and limit of detection. (edu.au)
Over the weekend of January 11-12, the Chinese authorities shared the full sequence of the coronavirus genome, as detected in samples taken from the first patients. (pasteur.fr)
That same Friday evening, scientists launched the process of sequencing the viral genome based on the samples. (pasteur.fr)
The sequences were identical in all our samples. (pasteur.fr)
The results indicated that the dominant bacterial phyla in the samples were Acidobacteriota , Proteobacteria , Actinobacteriota , Chloroflexi . (researchsquare.com)
The bacterial communities' structure of the samples treated with TC, g-C 3 N 4 or TC/g-C 3 N 4 were distinguishable. (researchsquare.com)
This study evaluated the use of a commercial stool storage kit for bacterial preservation in cow faecal samples compared to unpreserved stools placed into refrigeration at different time-points. (imperial.ac.uk)

The method has also been reported to perform well on problems similar to the classification of sequence data, such as the classification of text documents, that have a high-dimensional feature space and sparse data ( 16 ). (asm.org)
The sequence data were evaluated using the MG-RAST server, which revealed proteobacteria (4.3-34.6%) as predominant in all CETP stages. (scitechnol.com)
The data show that Gram-negative bacterial molecules are associated with AD neuropathology. (neurology.org)

The researchers noted that their next step would be to develop prediction models in order to better stratify patients according to their risk of developing a multi-drug resistance bacterial based on their metagenomic sequencing profile. (genomeweb.com)
The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, bla CTX-M-14 . (cdc.gov)

So, theV6 hyper-variable region of 16S rRNA gene was amplified and analysed using ion torrent PGM platform to explore the uncultivable bacterial community which are responsible for pollution reduction. (scitechnol.com)

By employing sediment traps for a time-series approach to sampling, the investigators show that bacterial community composition on plume particles changes on timescales much shorter than previously known. (bco-dmo.org)

Editor's note: This is the second article in a 7-part series that highlights the work of technicians and scientists in Military Health System laboratories who worked to identify COVID-19 variants using special sequencing technology. (health.mil)

This study examined the added value of whole genome sequencing (WGS) for investigating a non-point source outbreak of Salmonella ser. (who.int)

They also performed standard culturing methods to compare that to sequencing. (genomeweb.com)
The wound microbiotas obtained by bacterial culture methods followed by biochemical tests and 16S rDNA sequencing were compared. (um.edu.my)
Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. (folkhalsomyndigheten.se)

During PCR testing, Taq polymerase and DNA primers complementary to a unique sequence of target DNA were used to greatly amplify that region if the target was present in the sample. (cdc.gov)

On January 29, 2020, the Institut Pasteur, which is responsible for monitoring respiratory viruses in France, sequenced the whole genome of the coronavirus known as "2019-nCoV", becoming the first institution in Europe to sequence the virus since the start of the outbreak. (pasteur.fr)
A total of eight people from the CNR and two from the P2M sequencing platform have been working on the virus this week and will continue to monitor the outbreak in France. (pasteur.fr)
2 Whole genome sequencing (WGS) is a high-resolution typing method that can help foodborne disease investigators distinguish outbreak cases from non-outbreak cases. (who.int)

In general, the signal for insertion into the inner bacterial membrane is located in the first hydrophobic transmembrane domain and insertion is catalysed by the Sec translocase and/or YidC insertase. (nature.com)

Organisms6

Diseases2

Chemicals and Drugs4

Analytical, Diagnostic and Therapeutic Techniques and Equipment2

Phenomena and Processes8

Information Science6

Health Care1

Genomic6

Genomes11

Species23

Bacteria14

Strains7

Metagenomics2

Illumina5

Genes5

Pathogens3

Isolates4

Microbiology1

Infections5

High-throughput7

Genome sequence2

Nanopore2

Phylogenetic1

Microbial communities2

Strain8

Fungal2

Distinct2

Proteins3

Analysis12

Plasmids2

Taxonomic3

Dataset1

Coli2

Diversity3

Genetic5

RRNA gene sequence1

Bacteroides1

Transcriptome1

Ribosomal1

Clinical2

PacBio1

Metagenomes1

Biosynthetic1

Samples9

Data3

Resistance2

Uncultivable1

Composition1

Variants1

Salmonella1

Methods3

Primers1

Outbreak3

Membrane1