Ménage à trois in the human gut: interactions between host, bacteria and phages

MK Mirzaei, CF Maurice - Nature Reviews Microbiology, 2017 - nature.com
The human gut is host to one of the densest microbial communities known, the gut
microbiota, which contains bacteria, archaea, viruses, fungi and other microbial eukaryotes …

Viruses defined by the position of the virosphere within the replicator space

EV Koonin, VV Dolja, M Krupovic… - … and Molecular Biology …, 2021 - journals.asm.org
Originally, viruses were defined as miniscule infectious agents that passed through filters
that retain even the smallest cells. Subsequently, viruses were considered obligate …

Healthy human gut phageome

P Manrique, B Bolduc, ST Walk, J van der Oost… - Proceedings of the …, 2016 - pnas.org
The role of bacteriophages in influencing the structure and function of the healthy human gut
microbiome is unknown. With few exceptions, previous studies have found a high level of …

Studying the gut virome in the metagenomic era: challenges and perspectives

S Garmaeva, T Sinha, A Kurilshikov, J Fu, C Wijmenga… - BMC biology, 2019 - Springer
The human gut harbors a complex ecosystem of microorganisms, including bacteria and
viruses. With the rise of next-generation sequencing technologies, we have seen a quantum …

Unraveling the viral dark matter through viral metagenomics

TM Santiago-Rodriguez, EB Hollister - Frontiers in immunology, 2022 - frontiersin.org
Viruses are part of the microbiome and have essential roles in immunology, evolution,
biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of …

A network-based integrated framework for predicting virus–prokaryote interactions

W Wang, J Ren, K Tang, E Dart… - NAR genomics and …, 2020 - academic.oup.com
Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences;
however, it remains challenging to identify the host (s) of these new viruses. We developed …

Virus diversity and interactions with hosts in deep-sea hydrothermal vents

R Cheng, X Li, L Jiang, L Gong, C Geslin, Z Shao - Microbiome, 2022 - Springer
Background The deep sea harbors many viruses, yet their diversity and interactions with
hosts in hydrothermal ecosystems are largely unknown. Here, we analyzed the viral …

The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization

S Sutela, M Forgia, EJ Vainio, M Chiapello… - Virus …, 2020 - academic.oup.com
Mutualistic plant-associated fungi are recognized as important drivers in plant evolution,
diversity, and health. The discovery that mycoviruses can take part and play important roles …

Expanding the marine virosphere using metagenomics

CM Mizuno, F Rodriguez-Valera, NE Kimes… - PLoS genetics, 2013 - journals.plos.org
Viruses infecting prokaryotic cells (phages) are the most abundant entities of the biosphere
and contain a largely uncharted wealth of genomic diversity. They play a critical role in the …

Past, present, and future of arenavirus taxonomy

SR Radoshitzky, Y Bào, MJ Buchmeier, RN Charrel… - 2015 - Springer
Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been
known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The …