Incongruence in the phylogenomics era
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …
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 …
Profiling the human intestinal environment under physiological conditions
The spatiotemporal structure of the human microbiome,, proteome and metabolome, reflects
and determines regional intestinal physiology and may have implications for disease. Yet …
and determines regional intestinal physiology and may have implications for disease. Yet …
The person-to-person transmission landscape of the gut and oral microbiomes
The human microbiome is an integral component of the human body and a co-determinant
of several health conditions,. However, the extent to which interpersonal relations shape the …
of several health conditions,. However, the extent to which interpersonal relations shape the …
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 …
CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Advances in sequencing technologies and bioinformatics tools have dramatically increased
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …
Sequence modeling and design from molecular to genome scale with Evo
The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an
organism's function. We present Evo, a long-context genomic foundation model with a …
organism's function. We present Evo, a long-context genomic foundation model with a …
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 …
Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases
Fecal microbiota transplantation (FMT) is highly effective against recurrent Clostridioides
difficile infection and is considered a promising treatment for other microbiome-related …
difficile infection and is considered a promising treatment for other microbiome-related …
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 …