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Challenges and opportunities in sharing microbiome data and analyses
Microbiome data, metadata and analytical workflows have become ‘big’ in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary a...
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Open AccessScreening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes
Understanding the myriad pathways by which antimicrobial-resistance genes (ARGs) spread across biomes is necessary to counteract the global menace of antimicrobial resistance. We screened 17939 assembled metag...
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Open AccessA mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
The human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically...
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Open AccessPublisher Correction: A catalogue of 1,167 genomes from the human gut archaeome
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Open AccessA catalogue of 1,167 genomes from the human gut archaeome
The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report the analysis of 1,167 nonredundant archaeal genomes (608 high-...
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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic derm...
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Reporting guidelines for human microbiome research: the STORMS checklist
The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a ch...
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Open AccessR2DT is a framework for predicting and visualising RNA secondary structure using templates
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few autom...
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Open AccessAn inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities
Despite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiom...
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Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data
Recovering genomes from shotgun metagenomic sequence data allows detailed taxonomic and functional characterization of individual species or strains in a microbial community. Retrieving these metagenome-assemb...
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Open AccessA unified catalog of 204,938 reference genomes from the human gut microbiome
Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) coll...
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Open AccessEstimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the curre...
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Open AccessCOVID-19 pandemic reveals the peril of ignoring metadata standards
Efficient response to the pandemic through the mobilization of the larger scientific community is challenged by the limited reusability of the available primary genomic data. Here, the Genomic Standards Consor...
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Open AccessPhylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli
The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we ex...
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Open AccessMicrobial community drivers of PK/NRP gene diversity in selected global soils
The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natu...
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Open AccessA new genomic blueprint of the human gut microbiota
The composition of the human gut microbiota is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological roles. Despite extensive culturing and sequenci...
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Open AccessMicrobial abundance, activity and population genomic profiling with mOTUs2
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, whic...
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Open AccessA human gut bacterial genome and culture collection for improved metagenomic analyses
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We prese...
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Open AccessShould the poultry red mite Dermanyssus gallinae be of wider concern for veterinary and medical science?
The poultry red mite Dermanyssus gallinae is best known as a threat to the laying-hen industry; adversely affecting production and hen health and welfare throughout the globe, both directly and through its role a...
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Open AccessStructure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis
CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar ...
