Oral/gut single-cell and metagenome study, Japan, cross-sectional
51 samples from adults and elderly in Japan (Tokyo, Saitama, Kanagawa, Chiba, Hyogo, Osaka), including IBS, ulcerative colitis, Crohn's disease, colorectal cancer, other cancer, and healthy controls, in a cross-sectional design. machine-written summary
51 samples · 51 runs · JP · Adult · 2023 · 7.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 459 sample values (age, collection date, country, health condition, health condition detail, location region, sex, smoking status) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11446047 |
| ○ 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 |
Genera, mean relative abundance over 15 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 | 51 | 100% | ||||
| country | 51 | 100% | 51 | |||
| health_condition | 51 | 100% | 51 | |||
| subject_id | 51 | 100% | 51 | |||
| age_at_collection_days | 51 | 100% | 51 | |||
| collection_date | 51 | 100% | 51 | |||
| detailed_location | 51 | 100% | ||||
| health_condition_detail | 51 | 100% | 51 | |||
| location_region | 51 | 100% | 51 | |||
| sex | 51 | 100% | 51 | |||
| smoking_status | 51 | 100% | 51 |
- A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome. 2024 PMID 39358771 PMC11446047 own_data
- Biome-specific genome catalogues reveal functional potential of shallow sequencing 2025 unsure
Archive description
The increase in metagenome-assembled genomes (MAGs) has significantly advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often mask heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs. We present the bbsag20 dataset, which encompasses 17,202 human-associated prokaryotic SAGs and 869 MAGs, spanning 647 gut and 312 oral bacterial species. The SAGs revealed diverse bacterial lineages and MGEs with a broad host range that were absent in the MAGs and traced the translocation of oral bacteria to the gut. Importantly, our SAGs linked individual mobilomes to resistomes and meticulously charted a dynamic network of antibiotic resistance genes (ARGs) on MGEs, pinpointing potential ARG reservoirs in the microbial community.
How this project entered the registry
Classified as human gut / stool / oral cavity / multiple sites shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site study.title · “human oral/gut microbiome”
- body site sample.attr.env_local_scale · “oral/gut (n=32/51)”
- life stage sample.attr.host_age · “51 (n=46/51)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN37920959 | age_at_collection_days | 13149.0 | R1 | 0.85 | sample.attr.host_age | 36 |
| SAMN37920959 | collection_date | 2020-12-09 | R1 | 0.90 | biosample.attribute:collection_date | 2020-12-09 |
| SAMN37920959 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan: Tokyo |
| SAMN37920959 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Able-bodied |
| SAMN37920959 | health_condition_detail | Able-bodied | R1 | 0.90 | sample.attr.host_disease | Able-bodied |
| SAMN37920959 | location_region | Tokyo | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan: Tokyo |
| SAMN37920959 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN37920959 | smoking_status | never | R1 | 0.80 | biosample.attribute:smoker | no |
| SAMN37920959 | subject_id | QLX001 | R1 | 0.85 | biosample.attribute:alias | QLX001 |
Sequencing
51 runs over 51 samples · mean 7.95 Gbp per run (median 7.77 Gbp, total 405.62 Gbp; 51 runs with a base count) · layout PAIRED 51 · platform ILLUMINA 51 · models NextSeq 2000 (51) · 82% of runs with a Sandpiper profile · first public 2023-12-24
Authors (15)
Kawano-Sugaya T first · Arikawa K · Saeki T · Endoh T · Kamata K · Matsuhashi A · Hosokawa M last · Escobar-Zepeda A first · Ruuskanen MO · Beracochea M · Lu J · Mongad D · Richardson L · Finn RD · Lahti L last
Downloads
PRJNA1030952.csv.gz (2.9 KB) · parquet (72.8 KB) — all 51 samples, every field with route and confidence · PRJNA1030952_determinations.csv.gz (4.5 KB) — 459 evidence rows