Single-cell long-read genomics of gut microbiome samples
15 human gut metagenome samples analyzed using CAP-seq, a single-microbe long-read genomics platform; no location, health condition, or intervention data reported. machine-written summary
15 samples · 24 runs · Age unknown · 2026 · 68.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 69 sample values (antibiotic exposure, collection date, intervention, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – 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 |
longitudinal
2 of 3 people sampled more than once (14 samples; median 7, up to 8 per person) · follow-up median 2 mo (max 2 mo) · median interval between samples 38 d (time from collection dates). Schedule stated by the source: “Samples collected Before FMT/Before Vancomycin treatment, Week 2, Week 4, with repeat sampling of same subjects”.
Each row is one person (2 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| intervention | 15 | 100% | 15 | |||
| timepoint_label | 15 | 100% | 15 | |||
| antibiotic_exposure | 9 | 60% | 9 |
- Large-scale single-cell long-read genomics enables high-resolution microbiome profiling 2024 own_data
Archive description
Microbial communities are extraordinarily diverse and play crucial roles in health and disease, yet current methods lack the resolution and scalability needed to dissect their genomic and ecological complexity at the single-cell level. Here, we present CAP-seq, a high-throughput single-microbe genomics platform that combines hydrogel-based semi-permeable encapsulation with minimal microfluidics to recover thousands of single-amplified genomes (SAGs) with long reads and high completeness at low sequencing depth.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD01712766 | antibiotic_exposure | no | R1 | 0.70 | sample.name_rule:sample_title | VAN-2_Before Vancomycin treatment |
| SAMD01712760 | collection_date | 2024-05-14 | R1 | 0.90 | biosample.attribute:collection_date | 2024-05-14 |
| SAMD01712760 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:sample_title | FMT-2_Before FMT |
| SAMD01712760 | subject_id | FMT-2 | R1 | 0.70 | sample.name_rule:sample_title | FMT-2 |
| SAMD01712760 | timepoint_label | Before FMT | R1 | 0.70 | sample.name_rule:sample_title | Before FMT |
Sequencing
24 runs over 15 samples · mean 47.82 Gbp per run (median 56.84 Gbp, total 1,147.62 Gbp; 24 runs with a base count) · layout SINGLE 24 · platform OXFORD_NANOPORE 24 · models PromethION (24) · 0% of runs with a Sandpiper profile · first public 2026-06-02
Authors (16)
Li M first · Li S · Liu H · Zhai X · Li J · Du Y · Li X · Tong J · Zhang J · Zhang R · Song Z · Ji Q · Luo Y · Zhang T · Wei W · Liu Y last
Downloads
PRJDB39536.csv.gz (1.3 KB) · parquet (69.8 KB) — all 15 samples, every field with route and confidence · PRJDB39536_determinations.csv.gz (1.1 KB) — 69 evidence rows