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 …

Agnostic sequencing for detection of viral pathogens

NPG Gauthier, SD Chorlton, M Krajden… - Clinical microbiology …, 2023 - Am Soc Microbiol
The advent of next-generation sequencing (NGS) technologies has expanded our ability to
detect and analyze microbial genomes and has yielded novel molecular approaches for …

[HTML][HTML] Multiscale analysis of independent Alzheimer's cohorts finds disruption of molecular, genetic, and clinical networks by human herpesvirus

B Readhead, JV Haure-Mirande, CC Funk… - Neuron, 2018 - cell.com
Investigators have long suspected that pathogenic microbes might contribute to the onset
and progression of Alzheimer's disease (AD) although definitive evidence has not been …

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

J Ren, NA Ahlgren, YY Lu, JA Fuhrman, F Sun - Microbiome, 2017 - Springer
Background Identifying viral sequences in mixed metagenomes containing both viral and
host contigs is a critical first step in analyzing the viral component of samples. Current tools …

Identifying viruses from metagenomic data using deep learning

J Ren, K Song, C Deng, NA Ahlgren… - Quantitative …, 2020 - Wiley Online Library
Background The recent development of metagenomic sequencing makes it possible to
massively sequence microbial genomes including viral genomes without the need for …

The human intestinal virome in health and disease

SR Carding, N Davis, L Hoyles - Alimentary pharmacology & …, 2017 - Wiley Online Library
Background The human virome consists of animal‐cell viruses causing transient infections,
bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and …

Beyond just bacteria: functional biomes in the gut ecosystem including virome, mycobiome, archaeome and helminths

R Vemuri, EM Shankar, M Chieppa, R Eri, K Kavanagh - Microorganisms, 2020 - mdpi.com
Gut microbiota refers to a complex network of microbes, which exerts a marked influence on
the host's health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or …

The gut virome: the 'missing link'between gut bacteria and host immunity?

I Mukhopadhya, JP Segal, SR Carding… - Therapeutic …, 2019 - journals.sagepub.com
The human gut virome includes a diverse collection of viruses that infect our own cells as
well as other commensal organisms, directly impacting on our well-being. Despite its …

Human virome and disease: high-throughput sequencing for virus discovery, identification of phage-bacteria dysbiosis and development of therapeutic approaches …

TM Santiago-Rodriguez, EB Hollister - Viruses, 2019 - mdpi.com
The virome is comprised of endogenous retroviruses, eukaryotic viruses, and
bacteriophages and is increasingly being recognized as an essential part of the human …

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria

MR Olm, N Bhattacharya, A Crits-Christoph… - Science …, 2019 - science.org
Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in
premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal …