Bacteriophages in natural and artificial environments

S Batinovic, F Wassef, SA Knowler, DTF Rice… - Pathogens, 2019 - mdpi.com
Bacteriophages (phages) are biological entities that have attracted a great deal of attention
in recent years. They have been reported as the most abundant biological entities on the …

Viruses in soil ecosystems: an unknown quantity within an unexplored territory

KE Williamson, JJ Fuhrmann… - Annual review of …, 2017 - annualreviews.org
Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion
per gram in wetlands. Abundance appears to be strongly influenced by water availability …

INfrastructure for a PHAge REference database: identification of large-scale biases in the current collection of cultured phage genomes

R Cook, N Brown, T Redgwell, B Rihtman, M Barnes… - Phage, 2021 - liebertpub.com
Background: With advances in sequencing technology and decreasing costs, the number of
phage genomes that have been sequenced has increased markedly in the past decade …

PhaTYP: predicting the lifestyle for bacteriophages using BERT

J Shang, X Tang, Y Sun - Briefings in Bioinformatics, 2023 - academic.oup.com
Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and
temperate. Predicting the lifestyle of phages helps decipher their interactions with their …

Bacteriophage evolution differs by host, lifestyle and genome

TN Mavrich, GF Hatfull - Nature Microbiology, 2017 - nature.com
Bacteriophages play key roles in microbial evolution 1, 2, marine nutrient cycling 3 and
human disease 4. Phages are genetically diverse, and their genome architectures are …

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

MC Gazitúa, DR Vik, S Roux, AC Gregory… - The ISME …, 2021 - academic.oup.com
Viruses play an important role in the ecology and biogeochemistry of marine ecosystems.
Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during …

Bacteriophage classification for assembled contigs using graph convolutional network

J Shang, J Jiang, Y Sun - Bioinformatics, 2021 - academic.oup.com
Motivation Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the
biology of microbes. As the most abundant biological entities on the planet, the number of …

Phage therapy with a focus on the human microbiota

S Divya Ganeshan, Z Hosseinidoust - Antibiotics, 2019 - mdpi.com
Bacteriophages are viruses that infect bacteria. After their discovery in the early 1900s,
bacteriophages were a primary cure against infectious disease for almost 25 years, before …

Underexplored viral auxiliary metabolic genes in soil: diversity and eco‐evolutionary significance

M Sun, S Yuan, R Xia, M Ye… - Environmental …, 2023 - Wiley Online Library
Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the
advent of metagenomics and viromics approaches, an ever‐increasing diversity of virus …

Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation

M Ellegaard, MRJ Clokie, T Czypionka… - Communications …, 2020 - nature.com
DNA can be preserved in marine and freshwater sediments both in bulk sediment and in
intact, viable resting stages. Here, we assess the potential for combined use of ancient …