[HTML][HTML] The human virome: assembly, composition and host interactions

G Liang, FD Bushman - Nature Reviews Microbiology, 2021 - nature.com
The human body hosts vast microbial communities, termed the microbiome. Less well
known is the fact that the human body also hosts vast numbers of different viruses …

Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

[HTML][HTML] Emergence of methicillin resistance predates the clinical use of antibiotics

J Larsen, CL Raisen, X Ba, NJ Sadgrove… - Nature, 2022 - nature.com
The discovery of antibiotics more than 80 years ago has led to considerable improvements
in human and animal health. Although antibiotic resistance in environmental bacteria is …

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 …

[HTML][HTML] VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

J Guo, B Bolduc, AA Zayed, A Varsani… - Microbiome, 2021 - Springer
Background Viruses are a significant player in many biosphere and human ecosystems, but
most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to …

[HTML][HTML] 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 …

Enterococcus peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy

ME Griffin, J Espinosa, JL Becker, JD Luo, TS Carroll… - Science, 2021 - science.org
The antitumor efficacy of cancer immunotherapy can correlate with the presence of certain
bacterial species within the gut microbiome. However, many of the molecular mechanisms …

[HTML][HTML] Combination of pre-adapted bacteriophage therapy and antibiotics for treatment of fracture-related infection due to pandrug-resistant Klebsiella pneumoniae

A Eskenazi, C Lood, J Wubbolts, M Hites… - Nature …, 2022 - nature.com
A 30-year-old bombing victim with a fracture-related pandrug-resistant Klebsiella
pneumoniae infection after long-term (> 700 days) antibiotic therapy is treated with a pre …

[HTML][HTML] Direct activation of a bacterial innate immune system by a viral capsid protein

T Zhang, H Tamman, K Coppieters't Wallant, T Kurata… - Nature, 2022 - nature.com
Bacteria have evolved diverse immunity mechanisms to protect themselves against the
constant onslaught of bacteriophages,–. Similar to how eukaryotic innate immune systems …

[HTML][HTML] VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

K Kieft, Z Zhou, K Anantharaman - Microbiome, 2020 - Springer
Background Viruses are central to microbial community structure in all environments. The
ability to generate large metagenomic assemblies of mixed microbial and viral sequences …