QnAs with Graham F. Hatfull

Abstract. Taxonomic classification underlies all biological science and is the basis for comparative analysis of biological organisms and therefore our und

Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is

ALT: a man walking in a field with an umbrella

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

Protist microbiomes are poorly understood. Here, the authors analysed single protist cells to profile their microbiomes and viromes showing that these tiny eukaryotes serve as environmental hubs for h...

Metabolic strategies of cave microorganisms are poorly studied. Here, the authors show that cave microbes use atmospheric trace gases hydrogen, carbon monoxide and methane as energy and carbon sources...

Mathematical representations of overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification recapitulate dynamics in co-cultures of Prochlorococcus and eight heterotrophic bacteria.

Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...

AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Read alignment statistics for metagenomics. Contribute to wwood/CoverM development by creating an account on GitHub.

Roles of viruses in deep-sea ecosystems are poorly understood. Here, the authors use metagenomics and metatranscriptomics to profile DNA and RNA viruses in deep-sea sediments showing that these viruse...

Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies this to previously studied soil data to reveal hundreds of novel linkages.

Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer micr...

Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.