A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome

Li, Shenghui; Guo, Ruochun; Zhang, Yue; Li, Peng; Chen, Fang; Wang, Xifan; Li, Jing; Jie, Zhuye; Lv, Qingbo; Jin, Hao; Wang, Guangyang; Yan, Qiulong

doi:10.1016/j.isci.2022.104418

Cited by 31 publications

(38 citation statements)

References 81 publications

(83 reference statements)

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“…The resulting gut virus catalog contained the genome sequences of a total of 67,096 vOTUs with completeness > 50%, as estimated by CheckV ( Nayfach et al, 2021b ). Taxonomy annotation and prokaryotic host prediction of the vOTUs were performed according to the methods described in the previous studies ( Yan et al, 2021 ; Li et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Huang

Guo

et al. 2022

Front. Microbiol.

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BackgroundPolycystic ovary syndrome (PCOS) is a complex disease that afflicts women of reproductive age, and its pathological mechanism has not been well explained. The gut microbiota is believed to be closely related to the development of PCOS. Although an important component of the gut microbiome, the role of the gut virome in the development of PCOS is still unclear.MethodsIn this study, we profiled and compared the gut viral community of 50 patients with PCOS and 43 healthy women based on the analysis of their fecal whole-metagenome dataset.ResultsThe gut virome of PCOS patients exhibited a significant decrease in within-sample viral diversity and a remarkable alteration of the overall virome composition compared with that of healthy controls. At the family level, Siphoviridae was significantly depleted in the gut virome of patients, while Quimbyviridae was enriched. We identified 1,089 viral operational taxonomic units (vOTUs) that differed in relative abundance between the two groups, of which 455 vOTUs were enriched in PCOS patients (including numerous Bacteroidaceae phages) and 634 were enriched in controls (including numerous viruses predicted to infect Oscillospiraceae, Prevotellaceae, and Ruminococcaceae). Functional comparison of the PCOS-enriched and control-enriched vOTUs uncovered the viral functional signatures associated with PCOS. Furthermore, we demonstrated gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.938, demonstrating the potential of the gut virome in the prediction of PCOS.ConclusionOur findings reveal specific alterations in viral diversity and taxonomic and functional compositions of the gut virome of PCOS patients. Further studies on the etiology of PCOS and the gut viral community will offer new prospects for treating and preventing PCOS and its related diseases.

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Section: Methodsmentioning

confidence: 99%

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Huang

Guo

et al. 2022

Front. Microbiol.

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“…Referring to the clustering method provided by our prior study 60 vOTUs were predicted via Prodigal (v2.6.3) 65 with the parameter '-p meta', and were clustered into nearly 1.6 million nonredundant protein sequences using MMseqs2 (v12.113e3) easy-linclust mode 66 with the parameters '--min-seq-id 0.9 --cov-mode 1 -c 0.8 --kmer-per-seq 80'.…”

Section: Viral Clustering and Gene Predictionmentioning

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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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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“…Nodes are clustered together based on protein similarity and number of shared proteins. Previously identified SGA phages 23,40,41 were included in the network. Nodes are colored based on the predicted host of the phages or the SGA genome taxonomy.…”

Section: Resultsmentioning

confidence: 99%

“…To compare the putative SGA-infecting phages to reference phages and their predicted host bacteria, we constructed two protein-sharing networks using vContact2 74 (--rel-mode Diamond, -vcs-mode ClusterONE, --pcs-mode MCL). One network linked the proteomes of the putative SGA phages (including prophages) identified in this study, previously identified CPR phages 23,26,40,41 , and SGA bacteria. The second network linked the SGA phages identified in this study, the previously identified SGA phages, and non-SGA reference phages (--db 'ProkaryoticViralRefSeq201-Merged').…”

Section: Absconditabacteria Saccharibacteria and Gracilibacteria Phag...mentioning

confidence: 92%

“…Protein-sharing network of the putative SGA phages, where each node represents a phage and nodes are clustered together based on protein similarity and number of shared proteins. Non-CPR reference phages and previously identified SGA phages were included 23,40,41 in the network. Only reference phages with at least one neighboring SGA phage are displayed.…”

Section: Supplemental Figuresmentioning

confidence: 99%

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Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

Liu

Jaffe

Chen

et al. 2022

Preprint

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Within human microbiomes, Gracilibacteria, Absconditabacteria, and Saccharibacteria, members of Candidate Phyla Radiation (CPR), are increasingly correlated with human oral health and disease. We sought phages that are capable of infecting these bacteria, as these may prove effective for phage therapies to control oral microbiome composition. To do this we analyzed spacer inventories from CRISPR-Cas systems that themselves could be used for phage editing. Absconditabacteria and Gracilibacteria recode the typical TGA stop codon to glycine and are infected by phages that share their host's alternate genetic code. Unexpectedly, however, other predicted phages of Gracilibacteria and Absconditabacteria do not use an alternative genetic code. Some of these phages are predicted to infect both alternatively coded CPR bacteria and the standard code host bacteria upon which the CPR bacteria depend. These phages rely on other stop codons, and thus should be capable of producing viable gene products in either bacterial host type. Interestingly, we predict that phages of Saccharibacteria can replicate in Actinobacteria, which are likely the Saccharibacteria hosts. Overall, this broad host range behavior may be advantageous for the production of CPR phage therapy agents, as non-CPR bacteria are easier to cultivate than CPR bacteria. Absconditabacteria and Gracilibacteria phages may have avoided acquisition of in-frame stop codons to increase the diversity of bacteria in which they can replicate.

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A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome

Cited by 31 publications

References 81 publications

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

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

Host translation machinery is not a barrier to phages that infect both CPR and non-CPR bacteria

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