Clinical metagenomics
CY Chiu, SA Miller - Nature Reviews Genetics, 2019 - nature.com
Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of
microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly …
microbial and host genetic material (DNA and RNA) in samples from patients, is rapidly …
Shotgun metagenomics, from sampling to analysis
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes
have crucial roles in the environment and in human health. However, microbes are …
have crucial roles in the environment and in human health. However, microbes are …
Binning metagenomic contigs by coverage and composition
Shotgun sequencing enables the reconstruction of genomes from complex microbial
communities, but because assembly does not reconstruct entire genomes, it is necessary to …
communities, but because assembly does not reconstruct entire genomes, it is necessary to …
Recent advances in understanding enteric pathogenic Escherichia coli
Although Escherichia coli can be an innocuous resident of the gastrointestinal tract, it also
has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases …
has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases …
Microbial strain-level population structure and genetic diversity from metagenomes
Among the human health conditions linked to microbial communities, phenotypes are often
associated with only a subset of strains within causal microbial groups. Although it has been …
associated with only a subset of strains within causal microbial groups. Although it has been …
Benchmarking metagenomics tools for taxonomic classification
HY Simon, KJ Siddle, DJ Park, PC Sabeti - Cell, 2019 - cell.com
Metagenomic sequencing is revolutionizing the detection and characterization of microbial
species, and a wide variety of software tools are available to perform taxonomic …
species, and a wide variety of software tools are available to perform taxonomic …
The Prevotella copri complex comprises four distinct clades underrepresented in westernized populations
Prevotella copri is a common human gut microbe that has been both positively and
negatively associated with host health. In a cross-continent meta-analysis exploiting> 6,500 …
negatively associated with host health. In a cross-continent meta-analysis exploiting> 6,500 …
Exploring the human microbiome: the potential future role of next-generation sequencing in disease diagnosis and treatment
The interaction between the human microbiome and immune system has an effect on
several human metabolic functions and impacts our well-being. Additionally, the interaction …
several human metabolic functions and impacts our well-being. Additionally, the interaction …
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
Abstract Characterization of microbiomes has been enabled by high-throughput
metagenomic sequencing. However, existing methods are not designed to combine reads …
metagenomic sequencing. However, existing methods are not designed to combine reads …
The use of next generation sequencing for improving food safety: Translation into practice
Abstract Next Generation Sequencing (NGS) combined with powerful bioinformatic
approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of …
approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of …