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A set of computational tools to de novo recognize plasmids in complex environments, like the human gut microbiome, and to organize them into evolutionarily cohesive units.
Automated and scalable designation of virus lineages based on a heuristic approach can help to determine and curate virus lineages from large genomic datasets and inform nomenclature.
Ocean viral proteome annotations are expanded by a machine learning approach that is not reliant on sequence homology and can annotate sequences not homologous to those seen in training.
Phylogenetics and convergence-based genome-wide association studies were used to analyse genomic variants across approximately 2,000 isolates from six Candida species to reveal how Candida fungal pathogens adapt to drugs and clinical environments.
A postnatal multiple micronutrient deficiency mouse model reveals shifts in bacterial, fungal and viral components of the gut microbiome with implications for microbiome-encoded intrinsic antibiotic resistance mechanisms.
Culture-independent CRISPR spacer screens enable the discovery of hundreds of viruses and mobile genetic elements infecting all known methanogenic lineages.
Systematic review and analysis of pre-pandemic coronavirus surveillance in bats identifies requirements for improvements to surveillance in the future.
A comprehensive survey of secondary metabolites encoded in bacteria identifies large differences in biosynthetic diversity among genera and pinpoints those that can be targeted for novel chemistries provisionally suitable as antimicrobials.
Large-scale gut microbiome analysis of a widely use mouse model of inflammatory bowel disease reveals that the gut microbiome is a driver of variability across genetically identical mice, in particular two species that are associated with variable treatment endpoints.
Phylogeography and phylogenomic analyses of E. coli isolates collected from humans and domesticated and wild animals across 99 households in Nairobi reveal strong intra-household, and lower but detectable inter-household and inter-host, strain-sharing patterns.
A systematic screen across hundreds of eukaryotes and thousands of viral taxa provides insights into the directionality and functionality of horizontal gene transfer in these organisms.
Quantification of gut bacterial strains after fecal microbiome transplantation using the Strainer algorithm delineates long-term stable engraftment that explains patient outcomes.