Review article: the human intestinal virome in health and disease.

S R Carding,L Hoyles,N Davis

doi:10.1111/apt.14280

S R Carding, L Hoyles + Show 1 more

Open Access

https://doi.org/10.1111/apt.14280

Copy DOI

Abstract

SummaryBackgroundThe human virome consists of animal‐cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High‐throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus‐like particles make to the human virome, and in particular the intestinal virome.AimTo review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases.MethodsRelevant virome‐related articles were selected for review following extensive language‐ and date‐unrestricted, electronic searches of the literature.ResultsThe human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively.ConclusionsOur understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome‐disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.

Highlights

Recent improvements in recovery methods give the potential to characterise human-associated virus-like particles (VLPs) assemblages at the molecular level in greater detail than ever before (Table 2). These methods have yet to be compared with one another directly, and the issue of which DNA extraction method or kit is best for use with gut virome samples has not been addressed
Phage(s); source KLPN1a; caecal effluent Phage tail-like particle; Clostridium difficile HMC114 ɸAPCEc01, ɸAPCEc02, ɸAPCEc03; faeces PM16a; faeces aPhage isolated from same sample as host strain
Using co-occurrence profiling, crAssphage was identified in publicly available metagenomes, and by clustered regularly interspaced short palindromic repeats (CRISPRs) analysis and co-occurrence profiling predicted to infect Bacteroides or Prevotella spp.[22]

Summary

Age Lifestyle Medication Immune status Environment

Diverse microbiota Intact intestinal barrier (epithelial cells and mucin) ‘Bacteriophage adherence to mucus’ model of protection Controlled activation of immune system. A protocol involving homogenisation of faeces in buffer, centrifugation (to remove cell debris), tangential flow filtration (TFF) (to concentrate large-volume samples and isolate VLPs), ultracentrifugation and metagenomic reconstruction was used to characterise the first human faecal virome.[19] recent improvements in recovery methods give the potential to characterise human-associated VLP assemblages at the molecular level in greater detail than ever before (Table 2). These methods have yet to be compared with one another directly, and the issue of which DNA extraction method or kit is best for use with gut virome samples has not been addressed.

Erwinia Escherichia Hamiltonella Helicobacter

Findings

SUPPORTING INFORMATION