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 …

Four principles to establish a universal virus taxonomy

P Simmonds, EM Adriaenssens, FM Zerbini… - PLoS …, 2023 - journals.plos.org
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and
for communicating the complicated evolutionary relationships among viruses. However …

A roadmap for genome-based phage taxonomy

D Turner, AM Kropinski, EM Adriaenssens - Viruses, 2021 - mdpi.com
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago.
Genome sequencing has put pressure on the classification system and recent years have …

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

XQ Luo, P Wang, JL Li, M Ahmad, L Duan, LZ Yin… - Microbiome, 2022 - Springer
Background Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for
modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles …

PHROG: families of prokaryotic virus proteins clustered using remote homology

P Terzian, E Olo Ndela, C Galiez… - NAR Genomics and …, 2021 - academic.oup.com
Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both
in terms of the number of different protein families encountered and in the sequence …

Phage diversity, genomics and phylogeny

MB Dion, F Oechslin, S Moineau - Nature Reviews Microbiology, 2020 - nature.com
Recent advances in viral metagenomics have enabled the rapid discovery of an
unprecedented catalogue of phages in numerous environments, from the human gut to the …

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 …

Tara Oceans: towards global ocean ecosystems biology

S Sunagawa, SG Acinas, P Bork, C Bowler… - Nature Reviews …, 2020 - nature.com
A planetary-scale understanding of the ocean ecosystem, particularly in light of climate
change, is crucial. Here, we review the work of Tara Oceans, an international …

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information

B Gaborieau, H Vaysset, F Tesson, I Charachon… - Nature …, 2024 - nature.com
Predicting bacteriophage infection of specific bacterial strains promises advancements in
phage therapy and microbial ecology. Whether the dynamics of well-established phage …

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

H Bin Jang, B Bolduc, O Zablocki, JH Kuhn… - Nature …, 2019 - nature.com
Microbiomes from every environment contain a myriad of uncultivated archaeal and
bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable …