The oral microbiome: diversity, biogeography and human health
The human oral microbiota is highly diverse and has a complex ecology, comprising
bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and …
bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and …
Innovations to culturing the uncultured microbial majority
Despite the surge of microbial genome data, experimental testing is important to confirm
inferences about the cell biology, ecological roles and evolution of microorganisms. As the …
inferences about the cell biology, ecological roles and evolution of microorganisms. As the …
Open graph benchmark: Datasets for machine learning on graphs
Abstract We present the Open Graph Benchmark (OGB), a diverse set of challenging and
realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine …
realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine …
DRAM for distilling microbial metabolism to automate the curation of microbiome function
M Shaffer, MA Borton, BB McGivern… - Nucleic acids …, 2020 - academic.oup.com
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the
specific reactions catalyzed by these biological engines are hard to decode due to the …
specific reactions catalyzed by these biological engines are hard to decode due to the …
A standardized archaeal taxonomy for the Genome Taxonomy Database
The accrual of genomic data from both cultured and uncultured microorganisms provides
new opportunities to develop systematic taxonomies based on evolutionary relationships …
new opportunities to develop systematic taxonomies based on evolutionary relationships …
Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major …
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of
bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although …
bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although …
A complete domain-to-species taxonomy for Bacteria and Archaea
Abstract The Genome Taxonomy Database is a phylogenetically consistent, genome-based
taxonomy that provides rank-normalized classifications for~ 150,000 bacterial and archaeal …
taxonomy that provides rank-normalized classifications for~ 150,000 bacterial and archaeal …
MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
Microbial communities are responsible for biological wastewater treatment, but our
knowledge of their diversity and function is still poor. Here, we sequence more than 5 million …
knowledge of their diversity and function is still poor. Here, we sequence more than 5 million …
Beyond horizontal gene transfer: the role of plasmids in bacterial evolution
J Rodríguez-Beltrán, J DelaFuente… - Nature Reviews …, 2021 - nature.com
Plasmids have a key role in bacterial ecology and evolution because they mobilize
accessory genes by horizontal gene transfer. However, recent studies have revealed that …
accessory genes by horizontal gene transfer. However, recent studies have revealed that …
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing
become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more …
become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more …