Long-read gut phageome study in healthy Japanese adults
15 fecal samples from healthy Japanese adults were analyzed using long-read (PacBio) and short-read (MiSeq) metagenomic sequencing of the gut virome, in a cross-sectional study design. machine-written summary
15 samples · 25 runs · JP · Adult · 2021 · 5.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 75 sample values (age, collection date, country, sex, subject id) |
| ✓ Abstract / description | 15 sample values (health condition) |
| – Full text | no open-access full text linked · PMC8513251 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
longitudinal — not resolved
5 of 5 people sampled more than once (15 samples; median 3, up to 3 per person).
Genera, mean relative abundance over 5 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 15 | 100% | ||||
| country | 15 | 100% | 15 | |||
| health_condition | 15 | 100% | 15 | |||
| subject_id | 15 | 100% | 15 | |||
| age_at_collection_days | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| sex | 15 | 100% | 15 |
- Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads. 2021 PMID 34586399 PMC8513251 own_data
Archive description
Fecal samples of five healthy Japanese adults were collected (Kiguchi et al.). The DNA of viral-like particles (VLPs) were extracted and subjected to the multiple displacement amplification (MDA). The whole metagenomic sequencing of MDA-treated VLPs DNA was performed by MiSeq (Illumina) and Sequel (PacBio).
How this project entered the registry
Classified as human gut / stool mixed assays of adult by sonnet_x2 with confidence 0.65. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “Fecal samples of five healthy Japanese adults”
- life stage study.description · “five healthy Japanese adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00192913 | age_at_collection_days | 12043.2 | R1 | 0.85 | sample.attr.host_age | 33 |
| SAMD00192913 | collection_date | 2019-08-15 | R1 | 0.90 | biosample.attribute:collection_date | 2019-08-15 |
| SAMD00192913 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00192913 | health_condition | healthy_control | R4 | 0.50 | study.description | five healthy Japanese adults |
| SAMD00192913 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMD00192913 | subject_id | S1 | R1 | 0.85 | sample.attr.host_subject_id | S1 |
Sequencing
25 runs over 15 samples · mean 2.91 Gbp per run (median 2.54 Gbp, total 72.87 Gbp; 25 runs with a base count) · layout PAIRED 15, SINGLE 10 · platform ILLUMINA 15, PACBIO_SMRT 10 · models Illumina MiSeq (15), Sequel (10) · 40% of runs with a Sandpiper profile · first public 2021-12-03 – 2022-01-18
Authors (5)
Kiguchi Y first · Nishijima S · Kumar N · Hattori M · Suda W last
Downloads
PRJDB8956.csv.gz (1.3 KB) · parquet (69.8 KB) — all 15 samples, every field with route and confidence · PRJDB8956_determinations.csv.gz (1.1 KB) — 90 evidence rows