Gut bacteriophage: current understanding and challenges

TDS Sutton, C Hill - Frontiers in endocrinology, 2019 - frontiersin.org
The gut microbiome is widely accepted to have a significant impact on human health yet,
despite years of research on this complex ecosystem, the contributions of different forces …

Viruses as winners in the game of life

AG Cobián Güemes, M Youle, VA Cantú… - Annual review of …, 2016 - annualreviews.org
Viruses are the most abundant and the most diverse life form. In this meta-analysis we
estimate that there are 4.80× 1031 phages on Earth. Further, 97% of viruses are in soil and …

[HTML][HTML] Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease

AG Clooney, TDS Sutton, AN Shkoporov, RK Holohan… - Cell host & …, 2019 - cell.com
The human gut virome is thought to significantly impact the microbiome and human health.
However, most virome analyses have been performed on a limited fraction of known viruses …

metaSPAdes: a new versatile metagenomic assembler

S Nurk, D Meleshko, A Korobeynikov… - Genome …, 2017 - genome.cshlp.org
While metagenomics has emerged as a technology of choice for analyzing bacterial
populations, the assembly of metagenomic data remains challenging, thus stifling biological …

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

S Roux, JB Emerson, EA Eloe-Fadrosh, MB Sullivan - PeerJ, 2017 - peerj.com
Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral
genomes, evaluate community diversity, and assess ecological hypotheses. While viromic …

Genome binning of viral entities from bulk metagenomics data

J Johansen, DR Plichta, JN Nissen… - Nature …, 2022 - nature.com
Despite the accelerating number of uncultivated virus sequences discovered in
metagenomics and their apparent importance for health and disease, the human gut virome …

Choice of assembly software has a critical impact on virome characterisation

TDS Sutton, AG Clooney, FJ Ryan, RP Ross, C Hill - Microbiome, 2019 - Springer
Background The viral component of microbial communities plays a vital role in driving
bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite …

Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages

AR Weinheimer, FO Aylward - The ISME Journal, 2022 - academic.oup.com
Recent research has underscored the immense diversity and key biogeochemical roles of
large DNA viruses in the ocean. Although they are important constituents of marine …

[HTML][HTML] Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence

X Liu, Y Liu, J Liu, H Zhang, C Shan… - Neural Regeneration …, 2024 - journals.lww.com
A growing body of evidence suggests that the gut microbiota contributes to the development
of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor …

The emerging role of the gut virome in health and inflammatory bowel disease: challenges, covariates and a viral imbalance

D Jansen, J Matthijnssens - Viruses, 2023 - mdpi.com
Virome research is a rapidly growing area in the microbiome field that is increasingly
associated with human diseases, such as inflammatory bowel disease (IBD). Although …