Studying within-species variation has traditionally been limited to culturable bacterial
isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing …

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 …

Whole genome sequencing (WGS) provides the highest resolution for genome-based
species identification and can provide insight into the antimicrobial resistance and virulence …

An important fraction of microbial diversity is harbored in strain individuality, so identification
of conspecific bacterial strains is imperative for improved understanding of microbial …

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 …

Metagenomic sequencing is a powerful tool for examining the diversity and complexity of
microbial communities. Most widely used tools for taxonomic profiling of metagenomic …

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-
based, molecular methods as well as culture-based methods exist for population-scale …

Highlights•Analysis of massive NGS datasets poses difficult computational challenges.•Big
data algorithms are often adapted for NGS analysis.•HPC becomes pivotal as NGS …

Lactobacillus and Bifidobacterium spp. are best understood for their applications as
probiotics, which are often transient, but as commensals it is probable that stable …

Microbial communities are often composed by complex mixtures of multiple strains of the
same species, characterized by a wide genomic and phenotypic variability. Computational …