The gut microbiome and hypertension
A large body of evidence has emerged in the past decade supporting a role for the gut
microbiome in the regulation of blood pressure. The field has moved from association to …
microbiome in the regulation of blood pressure. The field has moved from association to …
Phylum Gemmatimonadota and its role in the environment
Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental
microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant …
microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant …
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …
can only capture few abundant organisms from most metagenomes. Here we present …
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
Abstract Summary The Genome Taxonomy Database (GTDB) and associated taxonomic
classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community …
classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community …
Identification of mobile genetic elements with geNomad
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …
understanding their diversity, ecology, biotechnological applications and impact on public …
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool
Abstract The Interactive Tree Of Life (https://itol. embl. de) is an online tool for the
management, display, annotation and manipulation of phylogenetic and other trees. It is …
management, display, annotation and manipulation of phylogenetic and other trees. It is …
Greengenes2 unifies microbial data in a single reference tree
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …
attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that …
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
AP Camargo, S Nayfach, IMA Chen… - Nucleic acids …, 2023 - academic.oup.com
Viruses are widely recognized as critical members of all microbiomes. Metagenomics
enables large-scale exploration of the global virosphere, progressively revealing the …
enables large-scale exploration of the global virosphere, progressively revealing the …
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
through metagenomics. While metagenomes enable high-throughput exploration of the viral …
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
AD Yates, J Allen, RM Amode, AG Azov… - Nucleic acids …, 2022 - academic.oup.com
Abstract Ensembl Genomes (https://www. ensemblgenomes. org) provides access to non-
vertebrate genomes and analysis complementing vertebrate resources developed by the …
vertebrate genomes and analysis complementing vertebrate resources developed by the …