Gut enterotype metagenome in healthy Chinese volunteers

Prevotella enterotype related metagenome sequencing

Shotgun metagenomic sequencing of 2 fecal samples from healthy, antibiotic-free Chinese volunteers (aged 10-38) collected to study Bacteroides and Prevotella gut enterotypes, China. machine-written summary

2 samples · 2 runs · CN · Age unknown · 2017 · 16.59 Gbp / sample

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Sources

✓Sequence archive 2○Abstract / description✓Full text 6✓Supplementary tables 10–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	2 sample values (country)
○ Abstract / description	read; no usable statement
✓ Full text	6 sample values (antibiotic exposure, health condition, health condition detail) · PMC5554170
✓ Supplementary tables	10 sample values (age, collection date, sex, subject id, timepoint)
– 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

Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance

1 country

Age

adult2

Condition

healthy_control2

Sex

female1

male1

Country

CN2

Body site

primary2

Sequencing depth per sample · this project all projects

Community composition

No Sandpiper profile for this project's samples yet.

Field coverage

field	samples	coverage	R1	R2	R3
age_category	2	100%
country	2	100%	2
health_condition	2	100%			2
subject_id	2	100%		2
age_at_collection_days	2	100%		2
antibiotic_exposure	2	100%			2
collection_date	2	100%		2
health_condition_detail	2	100%			2
sex	2	100%		2
timepoint_label	2	100%		2

Papers (1)

Investigation into the stability and culturability of Chinese enterotypes. 2017 PMID 28801639 PMC5554170 own_data

Details

Archive description

Investigation on the stability and culturable of Chinese Enterotypes

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.55. Assay shotgun_dna.

host runs.scientific_name · “human gut metagenome”
host papers[0].abstract · “fecal samples from 13 healthy Chinese volunteers”
body site runs.scientific_name · “human gut metagenome”
body site papers[0].abstract · “fecal samples from 13 healthy Chinese volunteers”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN05786335	age_at_collection_days	9029.0	R2	0.75	paper.supp.41598_2017_8478_MOESM1_ESM.pdf[Table S1!Date of birth]	N2 1990.09 ... 20150605
SAMN05786335	antibiotic_exposure	no	R3	0.70	paper.body.methods	Exclusion criteria included recent antibiotic treatment, frequent gastrointestinal disorders, and metabolic disease
SAMN05786335	collection_date	2015-06-05	R2	0.75	paper.supp.41598_2017_8478_MOESM1_ESM.pdf[Table S1!Sample collection time]	20150605 (T2) CXX20150605
SAMN05786335	country	CN	R1	0.90	sample.attr.geo_loc_name	China:Hangzhou
SAMN05786335	health_condition	healthy_control	R3	0.70	paper.body.methods	fecal samples from 13 healthy Chinese volunteers were collected and subjected to next-generation sequencing
SAMN05786335	health_condition_detail	healthy human volunteers	R3	0.70	paper.body.methods	fecal samples from 13 healthy Chinese volunteers were collected and subjected to next-generation sequencing
SAMN05786335	sex	female	R2	0.80	paper.supp.41598_2017_8478_MOESM1_ESM.pdf[Table S1!Sex]	N2 1990.09 F Hangzhou
SAMN05786335	subject_id	N2	R2	0.75	paper.supp.41598_2017_8478_MOESM1_ESM.pdf[Table S1!Volunteers]	N2 1990.09 F Hangzhou CXX
SAMN05786335	timepoint_label	T2	R2	0.75	paper.supp.41598_2017_8478_MOESM1_ESM.pdf[Table S1!Sample collection time]	20150605 (T2) CXX20150605

Sequencing

2 runs over 2 samples · mean 16.59 Gbp per run (median 16.59 Gbp, total 33.18 Gbp; 2 runs with a base count) · layout PAIRED 2 · platform ILLUMINA 2 · models Illumina HiSeq 4000 (2) · 100% of runs with a Sandpiper profile · first public 2017-11-07

Authors (10)

Yin Y first · Fan B · Liu W · Ren R · Chen H · Bai S · Zhu L · Sun G · Yang Y · Wang X last

Downloads

PRJNA336061.csv.gz (953 B) · parquet (69.9 KB) — all 2 samples, every field with route and confidence · PRJNA336061_determinations.csv.gz (1.1 KB) — 18 evidence rows

Samples (2 · every field this project has values for · hover a cell for its source)

Loading the sample table…