Examining horizontal gene transfer in microbial communities
IL Brito - Nature Reviews Microbiology, 2021 - nature.com
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables
an organism to rapidly adapt to changing environmental conditions, provides a competitive …
an organism to rapidly adapt to changing environmental conditions, provides a competitive …
[HTML][HTML] Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
We present two standards developed by the Genomic Standards Consortium (GSC) for
reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum …
reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum …
[HTML][HTML] Oxford Nanopore R10. 4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short …
Abstract Long-read Oxford Nanopore sequencing has democratized microbial genome
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
sequencing and enables the recovery of highly contiguous microbial genomes from isolates …
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
Coexisting microbial cells of the same species often exhibit genetic variation that can affect
phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a …
phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a …
[HTML][HTML] Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features
Empiric probiotics are commonly consumed by healthy individuals as means of life quality
improvement and disease prevention. However, evidence of probiotic gut mucosal …
improvement and disease prevention. However, evidence of probiotic gut mucosal …
[HTML][HTML] Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle
The body-wide human microbiome plays a role in health, but its full diversity remains
uncharacterized, particularly outside of the gut and in international populations. We …
uncharacterized, particularly outside of the gut and in international populations. We …
[HTML][HTML] Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT
Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and
related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut …
related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut …
[HTML][HTML] MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
Background The study of microbiomes using whole-metagenome shotgun sequencing
enables the analysis of uncultivated microbial populations that may have important roles in …
enables the analysis of uncultivated microbial populations that may have important roles in …
[HTML][HTML] Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …
available microbial genomes. This is being addressed by advances in sequencing …
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
The number of microbial genomes sequenced each year is expanding rapidly, in part due to
genome-resolved metagenomic studies that routinely recover hundreds of draft-quality …
genome-resolved metagenomic studies that routinely recover hundreds of draft-quality …