Life and death in the soil microbiome: how ecological processes influence biogeochemistry

NW Sokol, E Slessarev, GL Marschmann… - Nature Reviews …, 2022 - nature.com
Soil microorganisms shape global element cycles in life and death. Living soil
microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil …

Soil viral diversity, ecology and climate change

JK Jansson, R Wu - Nature Reviews Microbiology, 2023 - nature.com
Soil viruses are highly abundant and have important roles in the regulation of host dynamics
and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems …

Proksee: in-depth characterization and visualization of bacterial genomes

JR Grant, E Enns, E Marinier, A Mandal… - Nucleic acids …, 2023 - academic.oup.com
Abstract Proksee (https://proksee. ca) provides users with a powerful, easy-to-use, and
feature-rich system for assembling, annotating, analysing, and visualizing bacterial …

Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2024 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

Profiling the human intestinal environment under physiological conditions

D Shalon, RN Culver, JA Grembi, J Folz, PV Treit, H Shi… - Nature, 2023 - nature.com
The spatiotemporal structure of the human microbiome,, proteome and metabolome, reflects
and determines regional intestinal physiology and may have implications for disease. Yet …

Systematic and quantitative view of the antiviral arsenal of prokaryotes

F Tesson, A Hervé, E Mordret, M Touchon… - Nature …, 2022 - nature.com
Bacteria and archaea have developed multiple antiviral mechanisms, and genomic
evidence indicates that several of these antiviral systems co-occur in the same strain. Here …

Pharokka: a fast scalable bacteriophage annotation tool

G Bouras, R Nepal, G Houtak, AJ Psaltis… - …, 2023 - academic.oup.com
In recent years, there has been an increasing interest in bacteriophages, which has led to
growing numbers of bacteriophage genomic sequences becoming available. Consequently …

Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome

MG Durrant, A Fanton, J Tycko, M Hinks… - Nature …, 2023 - nature.com
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific
integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as …

Wildfire-dependent changes in soil microbiome diversity and function

AR Nelson, AB Narrowe, CC Rhoades, TS Fegel… - Nature …, 2022 - nature.com
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and
rhizosphere processes. Wildfire season length, and the frequency and size of severe fires …

Interrogating the viral dark matter of the rumen ecosystem with a global virome database

M Yan, AA Pratama, S Somasundaram, Z Li… - Nature …, 2023 - nature.com
The diverse rumen virome can modulate the rumen microbiome, but it remains largely
unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create …