Mutualistic interplay between bacteriophages and bacteria in the human gut

AN Shkoporov, CJ Turkington, C Hill - Nature Reviews Microbiology, 2022 - nature.com
Bacteriophages (phages) are often described as obligate predators of their bacterial hosts,
and phage predation is one of the leading forces controlling the density and distribution of …

The logic of virus evolution

EV Koonin, VV Dolja, M Krupovic - Cell host & microbe, 2022 - cell.com
Viruses are obligate intracellular parasites. Despite their dependence on host cells, viruses
are evolutionarily autonomous, with their own genomes and evolutionary trajectories locked …

Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2023 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

S Nayfach, D Páez-Espino, L Call, SJ Low… - Nature …, 2021 - nature.com
Bacteriophages have important roles in the ecology of the human gut microbiome but are
under-represented in reference databases. To address this problem, we assembled the …

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] Expansion of the global RNA virome reveals diverse clades of bacteriophages

U Neri, YI Wolf, S Roux, AP Camargo, B Lee… - Cell, 2022 - cell.com
High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA
virome. Mining 5,150 diverse metatranscriptomes uncovered> 2.5 million RNA virus contigs …

Expanding known viral diversity in the healthy infant gut

SA Shah, L Deng, J Thorsen, AG Pedersen… - Nature …, 2023 - nature.com
The gut microbiome is shaped through infancy and impacts the maturation of the immune
system, thus protecting against chronic disease later in life. Phages, or viruses that infect …

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 …

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

S Benler, N Yutin, D Antipov, M Rayko, S Shmakov… - Microbiome, 2021 - Springer
Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in
structuring human gut microbiomes; yet, the gut virome is far from being fully characterized …

Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution

MD Ramos-Barbero, C Gómez-Gómez… - Nature …, 2023 - nature.com
Crassvirales (crAss-like phages) are an abundant group of human gut-specific
bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators …