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PRJDB18854 DRP012824

Gut microbiota of healthy Japanese adults, Yamanashi

Gut microbiota of healthy Japanese adult

Cross-sectional shotgun metagenomic study of 112 gut microbiota samples from healthy adult, elderly, and adolescent residents of Chuo, Yamanashi, Japan. machine-written summary

112 samples · 112 runs · JP · Adult · 2025 · 7.26 Gbp / sample

One study deposited as 4 BioProjects (178 catalog samples together): PRJDB14457 · PRJDB18384 · PRJDB18387 · PRJDB18854 · show together

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Sources

✓Sequence archive 939✓Abstract / description 224○Full text○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	939 sample values (age, collection date, country, latitude, location locality, location region, longitude, sex)
✓ Abstract / description	224 sample values (health condition, health condition detail)
○ Full text	read; no usable statement or table · PMC12302451
○ 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

Samples at a glance

1 sampling locations · 1 country

Age

adult107

elderly3

adolescent2

Condition

healthy_control112

Sex

male78

female34

Country

JP112

Body site

primary112

Sequencing depth per sample · this project all projects

Community composition

Phocaeicola 16.5%Bacteroides 12.5%Prevotella 8.7%Bifidobacterium 6.4%Faecalibacterium 4.6%Blautia_A 4.0%Alistipes 2.8%Roseburia 2.6%Parabacteroides 2.6%Collinsella 2.2%Megamonas 1.8%Mediterraneibacter 1.7%not assigned to a genus 3.2%other genera 30.2%

Genera, mean relative abundance over 112 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R4
age_category	112	100%
country	112	100%	112
health_condition	112	100%		112
subject_id	112	100%	112
collection_date	112	100%	112
detailed_location	112	100%
health_condition_detail	112	100%		112
latitude	112	100%	112
location_locality	112	100%	112
location_region	112	100%	112
longitude	112	100%	112
sex	112	100%	112
age_at_collection_days	43	38%	43

Papers (1)

Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii. 2025 PMID 40721806 PMC12302451 own_data

Details

Archive description

Shotgun metagenomic sequence of gut microbiota of healthy Japanese adult living in Chuo, Yamanashi, Japan.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
body site study.title · “Gut microbiota of healthy”
body site study.description · “metagenomic sequence of gut microbiota of healthy”
life stage study.title · “of healthy Japanese adult”
life stage study.description · “of healthy Japanese adult living in Chuo,”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMD00596832	age_at_collection_days	19706.0	R1	0.85	sample.attr.host_age	54
SAMD00596828	collection_date	2018-10	R1	0.90	biosample.attribute:collection_date	2018-10
SAMD00596828	country	JP	R1	0.90	sample.attr.geo_loc_name	Japan:Yamanashi, Chuo
SAMD00596828	health_condition	healthy_control	R4	0.50	study.description	healthy Japanese adult
SAMD00596828	health_condition_detail	healthy adults	R4	0.50	study.description	healthy Japanese adult
SAMD00596828	latitude	35.6000	R1	0.90	biosample.attribute:lat_lon	35.60 N 138.52 E
SAMD00596828	location_locality	Chuo	R1	0.85	biosample.attribute:geo_loc_name	Japan:Yamanashi, Chuo
SAMD00596828	location_region	Yamanashi	R1	0.85	biosample.attribute:geo_loc_name	Japan:Yamanashi, Chuo
SAMD00596828	longitude	138.5200	R1	0.90	biosample.attribute:lat_lon	35.60 N 138.52 E
SAMD00596828	sex	male	R1	0.90	sample.attr.host_sex	male
SAMD00596828	subject_id	PN001288	R1	0.85	sample.attr.host_subject_id	PN001288

Sequencing

112 runs over 112 samples · mean 7.42 Gbp per run (median 7.26 Gbp, total 831.22 Gbp; 112 runs with a base count) · layout PAIRED 112 · platform ILLUMINA 112 · models Illumina NovaSeq 6000 (112) · 100% of runs with a Sandpiper profile · first public 2025-05-11

Authors (10)

Hosomi K first · Maruyama S · Matsuoka T · Furuta M · Tojima Y · Uchiyama K · Morita M · Kawashima H · Kobayashi T · Kunisawa J last

Downloads

PRJDB18854.csv.gz (4.4 KB) · parquet (76.1 KB) — all 112 samples, every field with route and confidence · PRJDB18854_determinations.csv.gz (8.1 KB) — 1,163 evidence rows

Samples (112 · every field this project has values for · hover a cell for its source)

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