Ancient gut metagenomes from Jomon-era Torihama coprolites, Japan
Shotgun metagenomic analysis of 4 coprolite samples excavated from the Torihama shell-mound site (Fukui, Japan), dated 7,000–5,500 years ago (Early Jomon period), examining ancient gut microbes, viruses, and food DNA; cross-sectional design. machine-written summary
4 samples · 4 runs · JP · Age unknown · 2024 · 188.79 Gbp / sample · cohort Metagenomic analyses of 7000 to 5500 years old cop
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 20 sample values (country, latitude, location region, location site, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10807776 |
| ✓ Supplementary tables | 4 sample values (collection date) |
| – 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 1 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 | 0 | 0% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| latitude | 4 | 100% | 4 | |||
| location_region | 4 | 100% | 4 | |||
| location_site | 4 | 100% | 4 | |||
| longitude | 4 | 100% | 4 |
- Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. 2024 PMID 38265980 PMC10807776 own_data
Archive description
Coprolites, contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, virus, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host study.description · “gut environment of ancient peoples”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00615088 | collection_date | 1975-07-26 | R2 | 0.85 | paper.supp.pone.0295924.s002.xlsx[S1 Table!Collection date] | Collection date: 1975-07-26 00:00:00 |
| SAMD00615088 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan:Fukui, Mikatakaminaka-gun, Wakasa-cho, Torihama shell mound ruins |
| SAMD00615088 | latitude | 35.5576 | R1 | 0.90 | biosample.attribute:lat_lon | 35.5576 N 135.898 E |
| SAMD00615088 | location_region | Fukui | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Fukui, Mikatakaminaka-gun, Wakasa-cho, Torihama shell mound ruins |
| SAMD00615088 | location_site | Torihama shell mound ruins | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Fukui, Mikatakaminaka-gun, Wakasa-cho, Torihama shell mound ruins |
| SAMD00615088 | longitude | 135.8980 | R1 | 0.90 | biosample.attribute:lat_lon | 35.5576 N 135.898 E |
Sequencing
4 runs over 4 samples · mean 185.42 Gbp per run (median 188.79 Gbp, total 741.69 Gbp; 4 runs with a base count) · layout PAIRED 4 · platform ILLUMINA 4 · models Illumina NovaSeq 6000 (4) · 25% of runs with a Sandpiper profile · first public 2024-01-27
Authors (12)
Nishimura L first · Tanino A · Ajimoto M · Katsumura T · Ogawa M · Koganebuchi K · Waku D · Kumagai M · Sugimoto R · Nakaoka H · Oota H · Inoue I last
Downloads
PRJDB15258.csv.gz (1020 B) · parquet (69.6 KB) — all 4 samples, every field with route and confidence · PRJDB15258_determinations.csv.gz (808 B) — 24 evidence rows