The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

Abstract

The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any ''disease'' effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

“…Importantly, these results indicate that virome studies that employ metagenome-mining techniques should be interpreted differently than VLP-enriched viromes, echoed by recent analysis by Gregory et al (2020). We also similarly report an increased number of VCs identified in the whole metagenome with a decreased average contig length when comparing paired samples.…”

“…Samples sequenced multiple times to assess phage-spikein loads were also analyzed to evaluate reproducibility; these reads were then merged for subsequent analyses. Bacterial contamination and viral content were assessed by aligning reads to the cpn60 database (ultra-sensitive mode) (Vancuren and Hill, 2019), the Gut Virome Database (Gregory et al, 2020), known crAssphages (Guerin et al, 2018), and all viral genomes available on the NCBI Viral Genomes Resource (Brister et al, 2015) as of May 11, 2020 (12,194 genomes). Host-removed, whole metagenomic sequencing reads were aligned to a database of all non-redundant sequences using DIAMOND 0.9.2 (Buchfink et al, 2014) and annotated using MEGAN 6.18.3 (Huson et al, 2016).…”

“…Aligning virome sequencing reads to viral databases further corroborated the removal of host and bacterial DNA. An average of 76.6% of virome reads aligned to 10,673 of 33,242 viral sequences in the Gut Virome Database (66.2-87.5%) (Gregory et al, 2020), though decreasing to 41.7% (11.0-86.5%) after applying a 75% breadth of coverage filter (372 viral sequences). Thus, a significant portion of virome sequencing reads in FIGURE 1 | Mapping of metagenome and virome sequencing reads to human, bacterial, and viral databases.…”

“…Recent advances in the study of the human virome include virus-like particle (VLP) purification protocols optimized for stool (Hayes et al, 2017;Shkoporov et al, 2018) and improved bioinformatic tools and databases (Roux et al, 2015;Ren et al, 2017;Gregory et al, 2020). These tools have enabled the study of the gut virome in inflammatory bowel disease (Norman et al, 2014;Clooney et al, 2019), its temporal stability in healthy adults , and its development during infancy (McCann et al, 2018;Liang et al, 2020) and into senescence (Gregory et al, 2020). However, nearly all studies profiled stool samples, which overlook the complex biogeography of the gastrointestinal tract (Martinez-Guryn et al, 2019).…”

“…We also compare our virome sequencing efforts with the viral signals identified in whole metagenomic sequencing. Combining both methods has been hypothesized to "improve de novo viral recovery" (Gregory et al, 2020).…”