Human gut metagenome, PacBio long-read, cross-sectional
Cross-sectional study of 13 human faecal samples using PacBio long-read metagenomic sequencing to characterize extrachromosomal mobile genetic elements (plasmids and bacteriophages) and DNA methylation patterns in the gut microbiome; no country or health condition specified. machine-written summary
13 samples · 256 runs · JP · Age unknown · 2019 · 20.32 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 9 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 13 sample values (country) · PMC6712665 |
| ✓ Supplementary tables | 30 sample values (age, sex, subject id) |
| – 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 |
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 | 12 | 92% | ||||
| country | 13 | 100% | 13 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 13 | 100% | 7 | 6 | ||
| age_at_collection_days | 12 | 92% | 12 | |||
| sex | 12 | 92% | 12 | |||
| timepoint_label | 2 | 15% | 2 |
- Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. 2019 PMID 31455406 PMC6712665 own_data
- viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data. 2022 PMID 35189932 PMC8862349 own_data
Archive description
Uncover the diversity of “metamobilome”, a set of complete mobile genetic elements, and the “metamethylome”, a set of DNA methylation motifs and their methylation levels, in microbiomes as well as the diversity of metagenome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “human gut metagenome PacBio”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06241973 | age_at_collection_days | 7305 | R2 | 0.85 | paper.supp.40168_2019_737_MOESM2_ESM.xlsx[S1!Age] | 20 |
| SAMN06241973 | country | JP | R3 | 0.70 | paper.fulltext.methods | We recruited 12 Japanese volunteers |
| SAMN06241973 | sex | female | R2 | 0.85 | paper.supp.40168_2019_737_MOESM2_ESM.xlsx[S1!Sex] | female |
| SAMN06241979 | subject_id | ES | R1 | 0.70 | sample.name_rule:alias | alias: ES1-2 |
| SAMN06241973 | subject_id | apr34 | R2 | 0.75 | paper.body.text[Results] | three subjects (apr34, FAKO03, and FAKO05) |
| SAMN06241979 | timepoint_label | biological replicate 1 | R1 | 0.85 | biosample.attribute:replicate | replicate: biological replicate 1 |
Sequencing
256 runs over 13 samples · mean 1.22 Gbp per run (median 1.12 Gbp, total 312.71 Gbp; 256 runs with a base count) · layout SINGLE 256 · platform PACBIO_SMRT 249, ILLUMINA 7 · models PacBio RS II (249), Illumina MiSeq (7) · 2% of runs with a Sandpiper profile · first public 2019-10-02 – 2020-04-14
Authors (31)
Suzuki Y first · Nishijima S · Furuta Y · Yoshimura J · Suda W · Oshima K · Hattori M · Morishita S last · Antipov D first · Rayko M · Kolmogorov M · Pevzner PA last · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last
Downloads
PRJNA362284.csv.gz (1.3 KB) · parquet (69.7 KB) — all 13 samples, every field with route and confidence · PRJNA362284_determinations.csv.gz (1.3 KB) — 52 evidence rows