A practical guide to amplicon and metagenomic analysis of microbiome data
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …
field of microbiome research, and massive microbiome datasets are now being generated …
Metagenomics-enabled microbial surveillance
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential
for zoonoses and emerging infectious diseases that can adversely affect human health …
for zoonoses and emerging infectious diseases that can adversely affect human health …
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
Microbial genomes can be assembled from short-read sequencing data, but the assembly
contiguity of these metagenome-assembled genomes is constrained by repeat elements …
contiguity of these metagenome-assembled genomes is constrained by repeat elements …
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Characterizing complex microbial communities with single-cell resolution has been a long-
standing goal of microbiology. We present Microbe-seq, a high-throughput method that …
standing goal of microbiology. We present Microbe-seq, a high-throughput method that …
Perspectives and benefits of high-throughput long-read sequencing in microbial ecology
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important
insights into microbial ecology and function. Yet, in many instances short-read HTS …
insights into microbial ecology and function. Yet, in many instances short-read HTS …
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 …
[HTML][HTML] A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data
Metagenomic sequencing provides a culture-independent avenue to investigate the
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …
complex microbial communities by constructing metagenome-assembled genomes (MAGs) …
Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats
Many microbes in nature reside in dense, metabolically interdependent communities. We
investigated the nature and extent of microbe-virus interactions in relation to microbial …
investigated the nature and extent of microbe-virus interactions in relation to microbial …
A bioinformatic analysis of integrative mobile genetic elements highlights their role in bacterial adaptation
Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however,
high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a …
high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a …
A high-quality genome compendium of the human gut microbiome of Inner Mongolians
Metagenome-based resources have revealed the diversity and function of the human gut
microbiome, but further understanding is limited by insufficient genome quality and a lack of …
microbiome, but further understanding is limited by insufficient genome quality and a lack of …