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Article
Biochemistry & Molecular Biology
Nathalie Bonin et al.
Summary: Antimicrobial resistance is a critical threat to public health, and genomic/metagenomic investigations using high-throughput analysis have become increasingly important. MEGARes v3.0 is a comprehensive database of published antimicrobial resistance gene sequences, and AMR++ v3.0 is a customized bioinformatic pipeline designed for high-throughput analysis of metagenomic data.
NUCLEIC ACIDS RESEARCH
(2023)
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Biochemistry & Molecular Biology
Lorna Richardson et al.
Summary: The MGnify platform is a resource for analyzing and storing microbiome-derived nucleic acid sequences. It offers access to taxonomic assignments and functional annotations for a large number of datasets derived from different environments. The platform has expanded in terms of dataset quantity and analysis capabilities over the past three years, and includes a relational database for understanding the genomic context of proteins. Deep learning-based annotation methods have also been implemented to enhance functional annotations. Additionally, the platform's technology has been upgraded, and a Jupyter Lab environment has been introduced for downstream analysis of the data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ana Hernandez-Plaza et al.
Summary: The eggNOG database is a bioinformatics resource that provides orthology data and comprehensive functional information for organisms from all domains of life. The updated version 6.0 expands the number of covered organisms to 12,535 reference species, improves functional annotations, and introduces new functionality. It offers a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels and phylogenetic trees for all OGs.
NUCLEIC ACIDS RESEARCH
(2023)
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Biochemistry & Molecular Biology
Anthony Fullam et al.
Summary: The interpretation of 'omics data relies on well-annotated genomes. As the number of available microbial genomes increases, quality control and consistent annotation become crucial. proGenomes3 is a database containing 907,388 high-quality genomes with consistent annotation, including functional and taxonomic information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Alex Chklovski et al.
Summary: This work presents CheckM2, a machine learning-based tool for predicting the genome quality of isolated, single-cell, and metagenome-assembled genomes. CheckM2 outperforms existing tools in accuracy and computational speed, as demonstrated by synthetic and experimental data. CheckM2's database can be rapidly updated with new high-quality reference genomes, even for taxa represented by only a single genome. It accurately predicts the genome quality of MAGs from novel lineages, including those with reduced genome size.
Article
Multidisciplinary Sciences
Luis Pedro Coelho et al.
Summary: The majority of microbial genes are specific to a single habitat, with a small fraction found in multiple habitats enriched in antibiotic-resistance genes and markers for mobile genetic elements. A small fraction of protein families contain the majority of genes, with most genetic variability observed within the families being neutral or nearly neutral.
Article
Biochemistry & Molecular Biology
Die Dai et al.
Summary: GMrepo is a curated database of human gut metagenomes aimed at increasing data reusability and accessibility, and enabling cross-project and phenotype comparisons. The latest version, GMrepo v2, includes more projects and samples obtained through different sequencing methods. Various disease markers have been identified and compared across datasets to facilitate the discovery of consistent microbial markers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bo Liu et al.
Summary: The VFDB is a comprehensive knowledge base and analysis platform for bacterial virulence factors, which has recently undergone a reorganization based on extensive literature mining to make it more suitable for future analysis of bacterial virulence factors. Additionally, the web interface of VFDB has been redesigned to ensure global accessibility for users with various client settings.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Donovan H. Parks et al.
Summary: The Genome Taxonomy Database (GTDB) provides a phylogenetically consistent taxonomy for prokaryotic genomes sourced from the NCBI database. It includes a large number of bacterial and archaeal genomes, highlights the importance of metagenome-assembled genomes, and discusses improvements to the GTDB website and the procedure for updating species clusters.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Fernando Meyer et al.
Summary: This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis. The results show substantial improvements in assembly, but related strains and assembly quality still pose challenges. Taxon profilers and binners excel at higher bacterial ranks but underperform for viruses and Archaea. The need to improve reproducibility is emphasized by the clinical pathogen detection results.
Article
Biology
Chiara Vanni et al.
Summary: Genes of unknown function pose a major challenge in molecular biology, especially in microbial systems. This study presents a computational framework to bridge the gap between known and unknown genes, and provides valuable insights into the diversity and relevance of the unknown fraction. The findings highlight the importance of investigating unknown genes and their potential implications in various organisms and environments.
Article
Microbiology
Hans-Joachim Ruscheweyh et al.
Summary: We developed mOTUs3, a command line tool that enables accurate species-level profiling of metagenomes. It provides a more comprehensive view of prokaryotic community diversity, especially for underexplored microbiomes. The tool leverages the reconstruction of over 600,000 draft genomes, including metagenome-assembled genomes (MAGs), to address the lack of reference genomes for many microbial species. mOTUs3 is found to be more accurate and congruent with 16S rRNA gene-based methods, and it increases the resolution of microbial groups and identifies differentially abundant taxa in comparative metagenomic studies.
Article
Multidisciplinary Sciences
Lucas Paoli et al.
Summary: Natural microbial communities are diverse and offer great potential for the discovery of enzymes and biochemical compounds. However, studying this diversity and assigning the synthesis of compounds to their hosts is challenging. In this study, we integrated microbial genomes from various sources and discovered thousands of new biosynthetic gene clusters, including in previously unsuspected phylogenetic groups. We identified a lineage rich in biosynthetic gene clusters and characterized the structures and enzymology of bioactive compounds. This research demonstrates the value of microbiomics-driven strategies in exploring previously undescribed enzymes and natural products.
Article
Biochemical Research Methods
Pierre-Alain Chaumeil et al.
Summary: This study presents an updated version of GTDB-Tk that uses a divide-and-conquer approach to reduce memory requirements while minimizing classification impact.
Article
Microbiology
Christian Rinke et al.
Summary: The study proposes a standardized archaeal taxonomy derived from a 122-concatenated-protein phylogeny, resolving polyphyletic groups and normalizing ranks. This taxonomy is based on 2,392 archaeal genomes, identifying 16 archaeal phyla and reclassifying major monophyletic units. Rank normalization corrects for up to 30-fold substitution rate variations and addresses incomplete and uneven archaeal classifications through a genome-based approach.
NATURE MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Carlos P. Cantalapiedra et al.
Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Askarbek Orakov et al.
Summary: GUNC is a tool that accurately detects and quantifies genome chimerism based on lineage homogeneity of individual contigs, providing a fast and robust way to improve prokaryotic genome quality. It targets previously underdetected types of contamination and can substantially enhance genome quality.
Article
Biochemistry & Molecular Biology
I-Min A. Chen et al.
Summary: The Integrated Microbial Genomes & Microbiomes system at the DOE's Joint Genome Institute contains annotated genome datasets and metagenome bins, with advanced search functions and a new statistical analysis tool available in IMG v 6.0. The updated web user interface includes a Help page and webinar tutorials to assist users in understanding and utilizing various IMG functions and tools in their research. New datasets have been processed with an extended prokaryotic annotation pipeline v.5, featuring expanded protein family assignments.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Stephen Nayfach et al.
Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.
NATURE BIOTECHNOLOGY
(2021)
Correction
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(2020)
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ENVIRONMENTAL MICROBIOLOGY
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