Phages in the gut ecosystem

M Zuppi, HL Hendrickson, JM O'Sullivan… - Frontiers in cellular and …, 2022 - frontiersin.org
Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the
most abundant biological entities on earth found in every explored environment, from the …

Global overview and major challenges of host prediction methods for uncultivated phages

C Coclet, S Roux - Current Opinion in Virology, 2021 - Elsevier
Highlights•Global phage diversity is now primarily explored through cultivation-independent
metagenomics.•Metagenome-derived phages are typically linked to their host (s) via in silico …

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

S Roux, AP Camargo, FH Coutinho, SM Dabdoub… - PLoS …, 2023 - journals.plos.org
The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied
through metagenomics. While metagenomes enable high-throughput exploration of the viral …

IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

S Roux, D Páez-Espino, IMA Chen… - Nucleic acids …, 2021 - academic.oup.com
Viruses are integral components of all ecosystems and microbiomes on Earth. Through
pervasive infections of their cellular hosts, viruses can reshape microbial community …

[HTML][HTML] Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans

J Mayneris-Perxachs, A Castells-Nobau… - Cell Host & Microbe, 2022 - cell.com
Growing evidence implicates the gut microbiome in cognition. Viruses, the most abundant
life entities on the planet, are a commonly overlooked component of the gut virome …

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

S Medvedeva, J Sun, N Yutin, EV Koonin… - Nature …, 2022 - nature.com
Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to
represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard …

Genomes of six viruses that infect Asgard archaea from deep-sea sediments

IM Rambo, MV Langwig, P Leão, V De Anda… - Nature …, 2022 - nature.com
Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes;
however, viruses that infect these organisms have not been described. Here, using …

A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses

D Tamarit, EF Caceres, M Krupovic, R Nijland… - Nature …, 2022 - nature.com
Asgard archaea have recently been identified as the closest archaeal relatives of
eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled …

Lysogenic bacteriophages encoding arsenic resistance determinants promote bacterial community adaptation to arsenic toxicity

X Tang, L Zhong, L Tang, C Fan, B Zhang… - The ISME …, 2023 - academic.oup.com
Emerging evidence from genomics gives us a glimpse into the potential contribution of
lysogenic bacteriophages (phages) to the environmental adaptability of their hosts …

Digital phagograms: predicting phage infectivity through a multilayer machine learning approach

C Lood, D Boeckaerts, M Stock, B De Baets… - Current Opinion in …, 2022 - Elsevier
Machine learning has been broadly implemented to investigate biological systems. In this
regard, the field of phage biology has embraced machine learning to elucidate and predict …