Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome

Wang, Guangyang; Li, Shenghui; Yan, Qiulong; Guo, Ruochun; Zhang, Yue; Chen, Fang; Tian, Xiangge; Lv, Qingbo; Jin, Hao; Ma, Xiaochi; Ma, Yufang

doi:10.1016/j.jare.2022.08.011

Cited by 16 publications

(15 citation statements)

References 70 publications

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“…4b). The substantial higher level of Microviridae viruses in the viral samples may because that the VLP technology is more inclined to target free viral particles, agreeing with the previous studies 6,35 .…”

Section: Gut Virome Profiling and Sex-and Age-related Variationssupporting

confidence: 90%

“…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: Gut Virome Profiling and Sex-and Age-related Variationssupporting

confidence: 90%

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

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“…Only contigs of ≥5 kb in length were used to identify viral sequences in each sample. The identification, decontamination, and dereplication of viral sequences were performed according to the prior studies ( 20 , 47 – 49 ). Briefly, the assembled contigs underwent a stringent quality assessment as follows: (i) contigs were classified as viral if their viral gene content surpassed that of microbial genes, as determined by CheckV v0.7.0 ( 25 ); (ii) contigs exhibiting a P value of less than 0.01 and a score exceeding 0.90 in DeepVirFinder v1.0 ( 50 ); and (iii) identification as viral sequences by VIBRANT v1.2.1 ( 51 ) using default settings.…”

Section: Methodsmentioning

confidence: 99%

Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia

Lv,

Wen,

Zhang

et al. 2024

mSphere

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Preeclampsia (PE), a pregnancy-specific syndrome, has been associated with the gut bacteriome. Here, to investigate the impact of the gut virome on the development of PE, we identified over 8,000 nonredundant viruses from the fecal metagenomes of 40 early-onset PE and 37 healthy pregnant women and profiled their abundances. Comparison and correlation analysis showed that PE-enriched viruses frequently connected to Blautia species enriched in PE. By contrast, bacteria linked to PE-depleted viruses were often the Bacteroidaceae members such as Bacteroides spp., Phocaeicola spp., Parabacteroides spp., and Alistipes shahii . In terms of viral function, PE-depleted viruses had auxiliary metabolic genes that participated in the metabolism of simple and complex polysaccharides, sulfur metabolism, lipopolysaccharide biosynthesis, and peptidoglycan biosynthesis, while PE-enriched viruses had a gene encoding cyclic pyranopterin monophosphate synthase, which seemed to be special, that participates in the biosynthesis of the molybdenum cofactor. Furthermore, the classification model based on gut viral signatures was developed to discriminate PE patients from healthy controls and showed an area under the receiver operating characteristic curve of 0.922 that was better than that of the bacterium-based model. This study opens up new avenues for further research, providing valuable insights into the PE gut virome and offering potential directions for future mechanistic and therapeutic investigations, with the ultimate goal of improving the diagnosis and management of PE. IMPORTANCE The importance of this study lies in its exploration of the previously overlooked but potentially critical role of the gut virome in preeclampsia (PE). While the association between PE and the gut bacteriome has been recognized, this research takes a pioneering step into understanding how the gut virome, represented by over 8,000 nonredundant viruses, contributes to this condition. The findings reveal intriguing connections between PE-enriched viruses and specific gut bacteria, such as the prevalence of Blautia species in individuals with PE, contrasting with bacteria linked to PE-depleted viruses, including members of the Bacteroidaceae family. These viral interactions and associations provide a deeper understanding of the complex dynamics at play in PE.

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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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Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome

Cited by 16 publications

References 70 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

Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia

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

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