Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment

Chen, Fang; Li, Shenghui; Guo, Ruochun; Song, Fanghua; Zhang, Yue; Wang, Xifan; Huo, Xiaokui; Lv, Qingbo; Ullah, Hayan; Wang, Guangyang; Ma, Yufang; Yan, Qiulong; Ma, Xiaochi

doi:10.1016/j.jare.2022.09.012

Cited by 20 publications

(18 citation statements)

References 55 publications

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“…We curated fecal metagenomes from three independent cohorts, including the CRC cohort (comprising 480 CRC patients, 182 adenoma patients, and 492 healthy controls from 8 studies from European, USA, and Japan populations) 39 , the IBD cohort (88 CD patients,76 UC patients, and 56 controls from the USA) 40 , and a newly-recruited cohort comprising 73 SLE patients and 116 controls from China (Supplementary Table 5), to validate the reliability of gut viral signatures. Using these large cohorts, we quantified the relative abundances of 7,161 disease-associated vOTUs and compared them between cases and controls in new cohorts.…”

Section: Resultsmentioning

confidence: 99%

“…We performed an integrated homology- and feature-based pipeline to identify viral sequences based on our previously developed methodologies 7, 39, 60, 61 . In brief, we first removed assembled contigs whose prokaryotic genes were over half of their genes and ten times greater than the number of viral genes based on CheckV (v0.7.0) 22 assessment.…”

Section: Methodsmentioning

confidence: 99%

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Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases

Li¹,

Yan

Wang³

et al. 2022

Preprint

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The gut viral community has been linked to human physiology and health, but our knowledge of its genetic and functional contents and disease dependence is far from complete. Here, we collected 11,327 bulk or viral metagenomes from fecal samples from large-scale Chinese populations to establish a Chinese gut virus catalogue (cnGVC) comprising 67,096 nonredundant viral genomes. This catalogue included ~70% of novel viruses that are not represented in existing gut viral databases, and allowed us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we 1) profiled the gut virome in large-scale populations and evaluated their sex- and age-related variations, 2) investigated the diversity and compositional patterns of the gut virome across common diseases by analyzing 6,314 bulk metagenomes spanning 28 disease or unhealthy statuses, and 3) identified a large number of universal viral signatures of diseases and validated their predictive ability for health status. Overall, our resources and results would contribute to the grand effort of expanding the knowledge of the human gut virome and addressing a full picture of the associations between viruses and common diseases.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases

Li¹,

Yan

Wang³

et al. 2022

Preprint

Self Cite

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“…For example, Chen F. et al (2022) compared the gut virome of colorectal cancer patients and healthy subjects. The authors found that the virome was drastically altered, identifying viruses that were only present in cancer patients [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Human virome: Implications in cancer

Tamayo-Trujillo

Guevara-Ramírez

Cadena-Ullauri

et al. 2023

Heliyon

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“…Recently, the rapid development of metagenomics sequencing and analyzing technology has already characterized a vast array of novel phages that cannot be identified with the traditional culturing-based approaches [ 7 ]. Several evaluating strategies have been explored to optimize the amplifying, sequencing, and assembling methods for metavirome investigations, and metagenomic next-generation sequencing (mNGS) technology has been broadly applied for the clinical diagnostics of infectious diseases and the precise surveillance of newly emerged pathogenic viruses [ 8 , 9 , 10 , 11 ]. Benler et al identified 3738 complete phage genomes which represented 451 putative genera and thousands of previously unknown phage taxa by searching the circular contigs that encoded phage hallmark genes in human gut metagenomes [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris)

Wang

et al. 2023

Viruses

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Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.

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Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment

Cited by 20 publications

References 55 publications

Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases

Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases

Human virome: Implications in cancer

Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris)

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