TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.9b00714
Abstract: Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed… read more here.
Keywords: strain level; taxit iterative; classification; level ... See more keywords
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Sign Up to like & getrecommendations! Published in 2019 at "Nature Communications"
DOI: 10.1038/s41467-019-13036-1
Abstract: The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect. Here, we use in silico and sequence-based… read more here.
Keywords: analysis; 16s rrna; rrna gene; gene ... See more keywords
Effect of Tension Strain Level on Reinforcement Corrosion
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Materials in Civil Engineering"
DOI: 10.1061/(asce)mt.1943-5533.0002167
Abstract: AbstractReinforcement corrosion is a general problem about the reliability and durability of concrete structures. A lot of research about the issue of reinforcement corrosion has been done; however... read more here.
Keywords: effect tension; tension strain; corrosion; reinforcement corrosion ... See more keywords
Strain-level analysis of gut-resident pro-inflammatory viridans group Streptococci suppressed by long-term cotrimoxazole prophylaxis among HIV-positive children in Zimbabwe
Sign Up to like & getrecommendations! Published in 2020 at "Gut Microbes"
DOI: 10.1080/19490976.2020.1717299
Abstract: ABSTRACT Antimicrobials have become a mainstay of healthcare in the past century due to their activity against pathogens. More recently, it has become clear that they can also affect health via their impact on the… read more here.
Keywords: gut resident; cotrimoxazole prophylaxis; prophylaxis among; strain level ... See more keywords
Species- and strain-level assessment using rrn long-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects
Sign Up to like & getrecommendations! Published in 2022 at "Gut Microbes"
DOI: 10.1080/19490976.2022.2078621
Abstract: Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor’s… read more here.
Keywords: gut; microbiota; transference; rrn ... See more keywords
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
Sign Up to like & getrecommendations! Published in 2017 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkw837
Abstract: Metagenomic 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… read more here.
Keywords: level bacterial; bacterial typing; locus strain; multi locus ... See more keywords
Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling
Sign Up to like & getrecommendations! Published in 2017 at "mSystems"
DOI: 10.1128/msystems.00164-16
Abstract: Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission,… read more here.
Keywords: transmission; vertical transmission; infant microbiome; infant ... See more keywords
Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria
Sign Up to like & getrecommendations! Published in 2022 at "mSystems"
DOI: 10.1128/msystems.01488-21
Abstract: Candidate phylum radiation (CPR) bacteria comprise a poorly understood phylum that is estimated to encompass ∼26% of all diversity of domain bacteria. Among CPR bacteria, the Saccharibacteria lineage (TM7) is of particular interest, as it… read more here.
Keywords: cpr bacteria; host bacteria; host; strain level ... See more keywords
Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages
Sign Up to like & getrecommendations! Published in 2023 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.04551-22
Abstract: The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated… read more here.
Keywords: ecology; gut; atopic eczema; bacterial phages ... See more keywords
Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2022.823120
Abstract: IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of… read more here.
Keywords: potential probiotic; microbiology; application potential; irbt ... See more keywords
Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2022.828254
Abstract: Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have… read more here.
Keywords: level complexity; ultra deep; analysis; strain level ... See more keywords