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PRJNA947684 SRP428823

Paired mNGS/VLP fecal metagenomes, healthy adults, Wuhan

Metagenomic sequencing of human feces and enriched virus-like particles

40 fecal samples (paired bulk metagenome and VLP-enriched sequencing) from healthy volunteers in Wuhan, China, mostly adults with one adolescent; cross-sectional design used to search for human gut phages. machine-written summary

40 samples · 54 runs · CN · Adult · 2023 · 14.59 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 542○Abstract / description✓Full text 81○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	542 sample values (age, bmi, collection date, country, diet, diet detail, health condition detail, latitude)
○ Abstract / description	read; no usable statement
✓ Full text	81 sample values (antibiotic exposure, health condition, health condition detail) · PMC10269749
○ 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

adult39

adolescent1

Condition

healthy_control40

Sex

male22

female17

Country

CN40

Body site

primary40

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal — not resolved

12 of 28 people sampled more than once (24 samples; median 2, up to 2 per person).

How longitudinal and relatedness information is derived

Community composition

Faecalibacterium 30.6%Phocaeicola 12.5%Bacteroides 6.8%Romboutsia 5.5%Gemmiger 5.2%Ruminococcus_C 4.4%CAG-302 4.0%Ruminococcoides 3.5%Agathobaculum 2.2%Fimenecus 2.0%Lawsonibacter 1.9%CAG-274 1.6%not assigned to a genus 9.6%other genera 10.0%

Genera, mean relative abundance over 11 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	R3
age_category	40	100%
country	40	100%	40
health_condition	40	100%		40
subject_id	40	100%	40
antibiotic_exposure	40	100%		40
collection_date	40	100%	40
detailed_location	40	100%
diet	40	100%	40
diet_detail	40	100%	40
health_condition_detail	40	100%	52	1
latitude	40	100%	40
location_locality	40	100%	40
location_region	40	100%	40
longitude	40	100%	40
age_at_collection_days	39	98%	39
bmi	39	98%	52
sex	39	98%	39

Papers (1)

Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces. 2023 PMID 36995238 PMC10269749 own_data

Details

Archive description

Bulk metagenome (mNGS) and VLP-enriched (vNGS) sequencing data of healthy Chinese volunteers. The mNGS and vNGS samples were paired. The data were used in the study of "Enrichment culture but not metagenomic sequencing identified a highly prevalent phage infecting Lactiplantibacillus plantarum in human feces"

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_adult_only”
body site study.title · “sequencing of human feces and enriched virus-like”
body site study.description · “plantarum in human feces "”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
life stage study.description · “of healthy Chinese volunteers . The mNGS”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN28109099	age_at_collection_days	6574.5	R1	0.90	sample.attr.host_age	18
SAMN28109099	antibiotic_exposure	no	R3	0.70	paper.fulltext.methods	use of antibiotics within 2 months
SAMN28109094	bmi	20.96	R1	0.90	sample.attr.host_body_mass_index	20.9566
SAMN28109099	collection_date	2020-10-01	R1	0.90	biosample.attribute:collection_date	2020-10-01
SAMN28109099	country	CN	R1	0.90	sample.attr.geo_loc_name	China: Wuhan
SAMN28109099	diet	omnivore	R1	0.70	biosample.attribute:host_diet	Normal diet
SAMN28109099	diet_detail	Normal diet	R1	0.70	biosample.attribute:host_diet	Normal diet
SAMN28109099	health_condition	healthy_control	R3	0.70	paper.fulltext.methods	Thirty-five healthy Chinese nationals as volunteers
SAMN28109094	health_condition_detail	No	R1	0.90	sample.attr.liver_disorder	No
SAMN28109273	health_condition_detail	healthy Chinese nationals as volunteers	R3	0.70	paper.fulltext.methods	Thirty-five healthy Chinese nationals as volunteers
SAMN28109099	latitude	30.5200	R1	0.90	biosample.attribute:lat_lon	30.52 N 114.42 E
SAMN28109099	location_locality	Wuhan	R1	0.85	biosample.attribute:geo_loc_name	China: Wuhan
SAMN28109099	location_region	Hubei	R1	0.60	biosample.attribute:lat_lon	30.52 N 114.42 E
SAMN28109099	longitude	114.4200	R1	0.90	biosample.attribute:lat_lon	30.52 N 114.42 E
SAMN28109099	sex	male	R1	0.90	sample.attr.host_sex	male
SAMN28109099	subject_id	09	R1	0.70	sample.name_rule:sample_alias	vH09

Sequencing

54 runs over 54 samples · mean 16.26 Gbp per run (median 14.59 Gbp, total 878.04 Gbp; 54 runs with a base count) · layout PAIRED 54 · platform DNBSEQ 27, ILLUMINA 27 · models DNBSEQ-T7 (27), Illumina NovaSeq 6000 (27) · 44% of runs with a Sandpiper profile · first public 2023-03-28

Authors (9)

Zhao X first · Sun C · Jin M · Chen J · Xing L · Yan J · Wang H · Liu Z · Chen WH last

Downloads

PRJNA947684.csv.gz (2.3 KB) · parquet (73.1 KB) — all 40 samples, every field with route and confidence · PRJNA947684_determinations.csv.gz (5.8 KB) — 623 evidence rows

Samples (40 · every field this project has values for · hover a cell for its source)

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