Background Metagenomic next-generation sequencing (mNGS) has enabled the rapid,
unbiased detection and identification of microbes without pathogen-specific reagents …

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

Background Recent innovations in sequencing technologies have provided researchers
with the ability to rapidly characterize the microbial content of an environmental or clinical …

The amount of host DNA poses a major challenge to metagenome analysis. However, there
is no guidance on the levels of host DNA, nor on the depth of sequencing needed to acquire …

Background Microbial eukaryotes are found alongside bacteria and archaea in natural
microbial systems, including host-associated microbiomes. While microbial eukaryotes are …

Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize
the diversity and function of complex microbial communities. In this review, we highlight the …

Background Analysis of mixed microbial communities using metagenomic sequencing
experiments requires multiple preprocessing and analytical steps to interpret the microbial …

Understanding the regional pathogen landscape and surveillance of emerging pathogens is
key to mitigating epidemics. Challenges lie in resource-scarce settings, where outbreaks are …

Molecular approaches have long led to the assumption that the human gut microbiota is
dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and …

There is increasing interest in employing shotgun sequencing, rather than amplicon
sequencing, to analyze microbiome samples. Typical projects may involve hundreds of …