Revolutionized Virome Research Using Systems Microbiology Approaches

Overview

Journal Exp Biol Med (Maywood)

Specialty Biology

Date 2022 Jun 20

PMID 35723062

Authors

Suwalak Chitcharoen

Pavaret Sivapornnukul

Sunchai Payungporn

Affiliations

Soon will be listed here.

Abstract

Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.

Citing Articles

The Diversity of Bacteriophages in the Human Gut.

Carroll-Portillo A, Lin D, Lin H Methods Mol Biol. 2023; 2738:17-30.

PMID: 37966590 DOI: 10.1007/978-1-0716-3549-0_2.

Insight into Oncogenic Viral Pathways as Drivers of Viral Cancers: Implication for Effective Therapy.

Elkhalifa A, Nabi S, Shah O, Bashir S, Muzaffer U, Ali S Curr Oncol. 2023; 30(2):1924-1944.

PMID: 36826111 PMC: 9955780. DOI: 10.3390/curroncol30020150.

Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases.

Clinton N, Hameed S, Agyei E, Jacob J, Oyebanji V, Jabea C J Immunol Res. 2022; 2022:7883945.

PMID: 36203793 PMC: 9532165. DOI: 10.1155/2022/7883945.

References

Chen X, Kost J, Sulovari A, Wong N, Liang W, Cao J . A virome-wide clonal integration analysis platform for discovering cancer viral etiology. Genome Res. 2019; 29(5):819-830. PMC: 6499315. DOI: 10.1101/gr.242529.118. View

Garretto A, Hatzopoulos T, Putonti C . virMine: automated detection of viral sequences from complex metagenomic samples. PeerJ. 2019; 7:e6695. PMC: 6462185. DOI: 10.7717/peerj.6695. View

Li N, Ma W, Pang M, Fan Q, Hua J . The Commensal Microbiota and Viral Infection: A Comprehensive Review. Front Immunol. 2019; 10:1551. PMC: 6620863. DOI: 10.3389/fimmu.2019.01551. View

Hirst J, Hutchinson E . Single-particle measurements of filamentous influenza virions reveal damage induced by freezing. J Gen Virol. 2019; 100(12):1631-1640. PMC: 6904231. DOI: 10.1099/jgv.0.001330. View

Kao D, Roach B, Silva M, Beck P, Rioux K, Kaplan G . Effect of Oral Capsule- vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection: A Randomized Clinical Trial. JAMA. 2017; 318(20):1985-1993. PMC: 5820695. DOI: 10.1001/jama.2017.17077. View

Shkoporov A, Ryan F, Draper L, Forde A, Stockdale S, Daly K . Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome. 2018; 6(1):68. PMC: 5892011. DOI: 10.1186/s40168-018-0446-z. View

Gumi B, Schelling E, Berg S, Firdessa R, Erenso G, Mekonnen W . Zoonotic transmission of tuberculosis between pastoralists and their livestock in South-East Ethiopia. Ecohealth. 2012; 9(2):139-49. PMC: 3415617. DOI: 10.1007/s10393-012-0754-x. View

Canakoglu A, Pinoli P, Bernasconi A, Alfonsi T, Melidis D, Ceri S . ViruSurf: an integrated database to investigate viral sequences. Nucleic Acids Res. 2020; 49(D1):D817-D824. PMC: 7778888. DOI: 10.1093/nar/gkaa846. View

Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory A, Allen M . Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ. 2019; 7:e6800. PMC: 6487183. DOI: 10.7717/peerj.6800. View

10.

Turin C, Ochoa T . The Role of Maternal Breast Milk in Preventing Infantile Diarrhea in the Developing World. Curr Trop Med Rep. 2014; 1(2):97-105. PMC: 4036098. DOI: 10.1007/s40475-014-0015-x. View

11.

Shkoporov A, Hill C . Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. Cell Host Microbe. 2019; 25(2):195-209. DOI: 10.1016/j.chom.2019.01.017. View

12.

Neu U, Mainou B . Virus interactions with bacteria: Partners in the infectious dance. PLoS Pathog. 2020; 16(2):e1008234. PMC: 7012391. DOI: 10.1371/journal.ppat.1008234. View

13.

Roux S, Tournayre J, Mahul A, Debroas D, Enault F . Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics. 2014; 15:76. PMC: 4002922. DOI: 10.1186/1471-2105-15-76. View

14.

Liang Y, Qiu K, Liao B, Zhu W, Huang X, Li L . Seeksv: an accurate tool for somatic structural variation and virus integration detection. Bioinformatics. 2016; 33(2):184-191. DOI: 10.1093/bioinformatics/btw591. View

15.

Kohl C, Wegener M, Nitsche A, Kurth A . Use of Preservation for Virome Sequencing in Outbreak Settings. Front Microbiol. 2017; 8:1888. PMC: 5623189. DOI: 10.3389/fmicb.2017.01888. View

16.

Granados A, Petrich A, McGeer A, Gubbay J . Measuring influenza RNA quantity after prolonged storage or multiple freeze/thaw cycles. J Virol Methods. 2017; 247:45-50. DOI: 10.1016/j.jviromet.2017.05.018. View

17.

Roux S, Adriaenssens E, Dutilh B, Koonin E, Kropinski A, Krupovic M . Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol. 2018; 37(1):29-37. PMC: 6871006. DOI: 10.1038/nbt.4306. View

18.

Callanan J, Stockdale S, Shkoporov A, Draper L, Ross R, Hill C . RNA Phage Biology in a Metagenomic Era. Viruses. 2018; 10(7). PMC: 6071253. DOI: 10.3390/v10070386. View

19.

Erickson A, Jesudhasan P, Mayer M, Narbad A, Winter S, Pfeiffer J . Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination. Cell Host Microbe. 2018; 23(1):77-88.e5. PMC: 5764776. DOI: 10.1016/j.chom.2017.11.007. View

20.

Brunse A, Deng L, Pan X, Hui Y, Castro-Mejia J, Kot W . Fecal filtrate transplantation protects against necrotizing enterocolitis. ISME J. 2021; 16(3):686-694. PMC: 8857206. DOI: 10.1038/s41396-021-01107-5. View