Groundwater viruses are less well studied. Here, using large-scale sequencing, the authors uncover extensive, largely uncharacterized viral diversity in groundwater, showing that viruses infect domina...

In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...

FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

Chitboonthavisuk et al. present PHAGEPACK, a CRISPRi-based screen that links host gene perturbations to phage fitness via a phage packaging-based readout. Applied in permissive and non-permissive E. c...

Human host-associated cellular products may act as induction agents for bacteriophages.

Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

Nature Reviews Genetics - In this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing...

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we anal...

Persistent and resistant infections caused by bacteria are increasing in numbers and pose a treatment challenge to the medical community and public health. However, solutions with new agents that will...

The widespread contamination of urban soils by airborne microplastics (MPs) is an emerging environmental concern, particularly in urban allotment gard…

Overcoming key hurdles for the development of next-generation anaerobic cultivation methods could have major impacts on microbial community research and applications.

The Department of Marine Microbiology and Biogeochemistry (MMB; principal investigator and PHYVIR project coordinator Prof. Dr. Corina Brussaard) of NIOZ is looking for a talented and dedicated Postdo

Nature Communications - Biller et al. use long-read sequencing of fractionated ocean nanoparticles, showing that extracellular vesicles and virus-like particles contain distinct pools of genetic...

Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. We quantified microbial warming response over seven ye...

A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.

Abstract. Although a large fraction of Earth's volume and most places beyond the planet lack life because physical and chemical conditions are too extreme,

Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines. - RyanCook94/inphared

Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

Existing microbiota databases are biased toward adults, hindering infant gut microbiome profiling. Peng et al. introduce the metagenome-assembled genome inventory for children (MAGIC), featuring 3,299 prokaryotic and 139,624 viral genomes. MAGIC enables characterization of early-life microbiome dynamics, identification of candidate keystone species, and strain-level study of target species.

Nature Communications - How climate change will impact microbial community growth is unclear. Here, the authors use a field experiment with varying global change factors, finding fungal growth more...