Prevotella diversity, niches and interactions with the human host
The genus Prevotella includes more than 50 characterized species that occur in varied
natural habitats, although most Prevotella spp. are associated with humans. In the human …
natural habitats, although most Prevotella spp. are associated with humans. In the human …
Machine learning for microbiologists
Abstract Machine learning is increasingly important in microbiology where it is used for tasks
such as predicting antibiotic resistance and associating human microbiome features with …
such as predicting antibiotic resistance and associating human microbiome features with …
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
Abstract The Genome Taxonomy Database (GTDB; https://gtdb. ecogenomic. org) provides a
phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic …
phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic …
RESCRIPt: Reproducible sequence taxonomy reference database management
Nucleotide sequence and taxonomy reference databases are critical resources for
widespread applications including marker-gene and metagenome sequencing for …
widespread applications including marker-gene and metagenome sequencing for …
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 …
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective
taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk …
taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk …
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
True fungi (Fungi) and fungus-like organisms (eg Mycetozoa, Oomycota) constitute the
second largest group of organisms based on global richness estimates, with around 3 …
second largest group of organisms based on global richness estimates, with around 3 …
VIRIDIC—A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses
C Moraru, A Varsani, AM Kropinski - Viruses, 2020 - mdpi.com
Nucleotide-based intergenomic similarities are useful to understand how viruses are related
with each other and to classify them. Here we have developed VIRIDIC, which implements …
with each other and to classify them. Here we have developed VIRIDIC, which implements …
[HTML][HTML] Elevated rates of horizontal gene transfer in the industrialized human microbiome
Industrialization has impacted the human gut ecosystem, resulting in altered microbiome
composition and diversity. Whether bacterial genomes may also adapt to the …
composition and diversity. Whether bacterial genomes may also adapt to the …
Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity
The average amino acid identity (AAI) is an index of pairwise genomic relatedness, and
multiple studies have proposed its application in prokaryotic taxonomy and related …
multiple studies have proposed its application in prokaryotic taxonomy and related …