Diversity within species: interpreting strains in microbiomes
Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …
Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient
populations in hospitals around the world. Intensive care unit (ICU) patients are particularly …
populations in hospitals around the world. Intensive care unit (ICU) patients are particularly …
Environment dominates over host genetics in shaping human gut microbiota
Human gut microbiome composition is shaped by multiple factors but the relative
contribution of host genetics remains elusive. Here we examine genotype and microbiome …
contribution of host genetics remains elusive. Here we examine genotype and microbiome …
[HTML][HTML] Integrated omics endotyping of infants with respiratory syncytial virus bronchiolitis and risk of childhood asthma
Respiratory syncytial virus (RSV) bronchiolitis is not only the leading cause of hospitalization
in US infants, but also a major risk factor for asthma development. While emerging evidence …
in US infants, but also a major risk factor for asthma development. While emerging evidence …
Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis: supplementary issue: bioinformatics methods and applications for big …
V Aguiar-Pulido, W Huang… - Evolutionary …, 2016 - journals.sagepub.com
Microbiomes are ubiquitous and are found in the ocean, the soil, and in/on other living
organisms. Changes in the microbiome can impact the health of the environmental niche in …
organisms. Changes in the microbiome can impact the health of the environmental niche in …
[HTML][HTML] Metagenomics: the next culture-independent game changer
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories
is at a crossroads with the ability of public health agencies to perform their basic mandate of …
is at a crossroads with the ability of public health agencies to perform their basic mandate of …
[HTML][HTML] Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part
of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and …
of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and …
Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare
Whole metagenome analysis has the potential to reveal functional triggers of skin diseases,
but issues of cost, robustness and sampling efficacy have limited its application. Here, we …
but issues of cost, robustness and sampling efficacy have limited its application. Here, we …
[HTML][HTML] Strain-level epidemiology of microbial communities and the human microbiome
The biological importance and varied metabolic capabilities of specific microbial strains
have long been established in the scientific community. Strains have, in the past, been …
have long been established in the scientific community. Strains have, in the past, been …
ConStrains identifies microbial strains in metagenomic datasets
An important fraction of microbial diversity is harbored in strain individuality, so identification
of conspecific bacterial strains is imperative for improved understanding of microbial …
of conspecific bacterial strains is imperative for improved understanding of microbial …