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

Abstract

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.

Alterations in the gut virome in patients with ankylosing spondylitis

“…To establish the composition of the gut viral community, we mapped clean reads of each sample to the cnGVC database, including 67,096 dereplicated vOTUs with high completeness ( 18 ). The rates of reads mapping to cnGVC ranged from 12.68% to 30.24% ( Figure 1A ), suggesting efficient capture of gut viral reads.…”

“…To analyze the composition of the gut viral community in metagenomic samples, we used a gut virus catalog comprising over 67,000 nonredundant viral operational taxonomic units (vOTUs) as the reference. This Chinese gut virus catalog (cnGVC) was constructed from over 10,000 publicly available fecal metagenomes from the Chinese population (including all samples used in the current study) ( 18 ). Briefly, the clean reads of each metagenomic sample were assembled into contigs using Megahit v1.2.9 ( 26 ).…”

“…The quality of viral sequences was estimated using CheckV v0.7.0 ( 28 ). Taxonomic classification, host prediction, and functional annotation of viral sequences were also performed according to our prior study ( 18 ).…”

“…Furthermore, evidence that the virome directly affects human health through the immune system has been found ( 16 , 17 ). More importantly, our previous study has preliminary showed significant changes in the gut virome associated with several immune diseases, including AS ( 18 ). Given these findings, it makes sense to investigate the association between AS and the virome in more detail.…”

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

“…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.…”