Hypervariable loci in the human gut virome
12 samples from adults, studying hypervariable loci in the human gut virome. No location, health condition, or design details were provided. machine-written summary
12 samples · 12 runs · US · Adult · 2016 · 2.60 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 36 sample values (country, health condition, health condition detail) |
| ✓ Abstract / description | 12 sample values (subject id) |
| – Full text | no open-access full text linked · PMC3309749 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| health_condition_detail | 12 | 100% | 12 |
- Hypervariable loci in the human gut virome. 2012 PMID 22355105 PMC3309749 own_data
Archive description
Genetic variation is critical in microbial immune evasion and drug resistance, but variation has rarely been studied in complex heterogeneous communities such as the human microbiome. To begin to study natural variation, we analyzed DNA viruses present in the lower gastrointestinal tract of 12 human volunteers by determining 48 billion bases of viral DNA sequence. Viral genomes mostly showed low variation, but 51 loci of ∼100 bp showed extremely high variation, so that up to 96% of the viral genomes encoded unique amino acid sequences. Some hotspots of hypervariation were in genes homologous to the bacteriophage BPP-1 viral tail-fiber gene, which is known to be hypermutagenized by a unique reverse-transcriptase (RT)-based mechanism. Unexpectedly, other hypervariable loci in our data were in previously undescribed gene types, including genes encoding predicted Ig-superfamily proteins. Most of the hypervariable loci were linked to genes encoding RTs of a single clade, which we find is the most abundant clade among gut viruses but only a minor component of bacterial RT populations. Hypervariation was targeted to 5′-AAY-3′ asparagine codons, which allows maximal chemical diversification of the encoded amino acids while avoiding formation of stop codons. These findings document widespread targeted hypervariation in the human gut virome, identify previously undescribed types of genes targeted for hypervariation, clarify association with RT gene clades, and motivate studies of hypervariation in the full human microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “human gut virome”
- body site study.description · “lower gastrointestinal tract of 12 human volunteers”
- life stage study.description · “12 human volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06117578 | country | US | R1 | 0.85 | biosample.attribute:population | USA |
| SAMN06117578 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:health_state | healthy |
| SAMN06117578 | health_condition_detail | healthy | R1 | 0.85 | biosample.attribute:health_state | healthy |
| SAMN06117578 | subject_id | SAMN06117578 | R4 | 0.60 | design.one_sample_per_subject:abstract | DNA viruses present in the lower gastrointestinal tract of 12 human volunteers |
Sequencing
12 runs over 12 samples · mean 2.94 Gbp per run (median 2.60 Gbp, total 35.25 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina HiSeq 2000 (12) · 0% of runs with a Sandpiper profile · first public 2016-12-12
Authors (0)
No author record.
Downloads
PRJNA356544.csv.gz (1.2 KB) · parquet (69.3 KB) — all 12 samples, every field with route and confidence · PRJNA356544_determinations.csv.gz (842 B) — 48 evidence rows