The virome: a missing component of biological interaction networks in health and disease

Handley, Scott A.

doi:10.1186/s13073-016-0287-y

Cited by 47 publications

(32 citation statements)

References 10 publications

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“…Previous studies of the human virome have addressed the viral component of the gut flora [2–4] and skin [5–7], with particular attention to the very abundant bacteriophages [7, 8]. A thorough review has been published recently [9].…”

Section: Introductionmentioning

confidence: 99%

The blood DNA virome in 8,000 humans

Moustafa¹,

Xie²,

Kirkness³

et al. 2017

PLoS Pathog

267

258

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The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging.

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Section: Introductionmentioning

confidence: 99%

The blood DNA virome in 8,000 humans

Moustafa¹,

Xie²,

Kirkness³

et al. 2017

PLoS Pathog

267

258

View full text Add to dashboard Cite

show abstract

“…Metagenomic analysis suggests that the gut of healthy humans harbors commensal virus, including phages, DNA virus and RNA virus[18–22]. Virome (phages and other host viruses) play roles in intestinal physiology, enteric immune system, host health and disease[23, 24]. The dynamic balance between the virome and the intestinal immune system is finely regulated by cytokines secreted by immune cells[20, 25].…”

Section: Introductionmentioning

confidence: 99%

Profiling of Human Gut Virome with Oxford Nanopore Technology

Cao

Zhang

Dai

et al. 2020

Preprint

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AbstractHuman gut virome play critical roles in maintaining gut microbial composition and functionality, as well as host physiology and immunology. Yet, there are insufficient amount of studies on this topic mainly due to methodological limitations, including enrichment of viruses (phages and host viruses) as well as short read-length from current sequencing technology. Here we developed a full working protocol for analyzing human gut virome using physical enrichment, reverse transcription and random amplification, and eventually the state-of-art single-molecule real-time sequencing (SMRT) platform of Oxford Nanopore Technology (ONT). We demonstrate that sequencing viral DNA directly, or viral DNA/cDNA after amplification using ONT achieves much longer reads and provides more information regarding virome diversity, many of the virome sequences do not have match in current databases. Moreover, direct DNA sequencing of virome provides first insights into the epigenetic modifications on phages, where signals of methylations can be directly detected. Our study demonstrates that progressing sequencing technology and bioinformatic improvements will bring more knowledge into virome composition, diversity and potentially their important functions.HighlightsVirus-like particles were enriched from human stool samples;Viral nucleotides were sequenced with Oxford Nanopore Technology with and without amplification;Gut virome in humans showed highly individualized composition;Novel sequences and contigs were found to be the majority in the resulted sequences;Epigenetic modifications were detected directly on virus genomes.

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“…Again, by borrowing examples from other systems and hosts, we do know that bacteriophages can regulate bacterial communities (Obeng et al, 2016)being important drivers of the composition of bacterial communities in the human gut (Ogilvie & Jones, 2015) and even a three-way interaction among fungi, bacteria, and phages has been reported in soil (Pratama & van Elsas, 2018). Our knowledge regarding bacteriome-virome interactions in insects is limited to a few examples (see 'Viruses' section; Handley, 2016). The complexity of such interactions is exemplified in aphid-bacteria-phage interactions, in which the phage APSE infects its bacterial host H. defensa, and the bacterium then defends the aphid against its natural enemies (Oliver et al, 2009).…”

Section: Cross-kingdom Interactionsmentioning

confidence: 99%

The microbiome of pest insects: it is not just bacteria

Gurung

Wertheim

Salles

2019

Entomologia Exp Applicata

147

113

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Insects are associated with multiple microbes that have been reported to influence various aspects of their biology. Most studies in insects, including pest species, focus on the bacterial communities of the microbiome even though the microbiome consists of members of many more kingdoms, which can also have large influence on the life history of insects. In this review, we present some key examples of how the different members of the microbiome, such as bacteria, fungi, viruses, archaea, and protozoa, affect the fitness and behavior of pest insects. Moreover, we argue that interactions within and among microbial groups are abundant and of great importance, necessitating the use of a community approach to study microbial–host interactions. We propose that the restricted focus on bacteria very likely hampers our understanding of the functioning and impact of the microbiome on the biology of pest insects. We close our review by highlighting a few open questions that can provide an in‐depth understanding of how other components of the microbiome, in addition to bacteria, might influence host performance, thus contributing to pest insect ecology.

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The virome: a missing component of biological interaction networks in health and disease

Cited by 47 publications

References 10 publications

The blood DNA virome in 8,000 humans

The blood DNA virome in 8,000 humans

Profiling of Human Gut Virome with Oxford Nanopore Technology

The microbiome of pest insects: it is not just bacteria

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