Gut metagenomes in Peutz-Jeghers syndrome, Guangzhou

Gut microbiome signatures in PJS

88 metagenome samples from Guangzhou, China, comparing colorectal adenoma (Peutz-Jeghers syndrome) patients (61) and healthy family members (27) in a case-control design examining gut microbiome functional changes. machine-written summary

88 samples · 88 runs · CN · Age unknown · 2023 · 6.80 Gbp / sample

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Sources

✓Sequence archive 704✓Abstract / description 88○Full text○Supplementary tables✓External resources 88–User contribution–Human verified

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

what each source gave

✓ Sequence archive	704 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
✓ Abstract / description	88 sample values (subject id)
○ Full text	read; no usable statement or table · PMC10101062
○ Supplementary tables	files read; no table could be matched to the samples
✓ External resources	88 sample values (antibiotic exposure) · from BugSigDB
– 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

unknown88

Condition

other_disease61

healthy_control27

Country

CN88

Body site

primary88

Sequencing depth per sample · this project all projects

Sampling design and relatedness

families — not resolved

61 PJS patients and 27 healthy family members (of 168/68 total cohort) who lived together; no individual dyad links in metadata..

How longitudinal and relatedness information is derived

Community composition

Phocaeicola 10.4%Faecalibacterium 10.3%Bacteroides 9.6%Roseburia 6.0%Prevotella 4.8%Escherichia 4.5%Bifidobacterium 4.3%Blautia_A 3.2%Streptococcus 3.0%Alistipes 2.8%Fusicatenibacter 2.7%Mediterraneibacter 1.8%not assigned to a genus 4.2%other genera 32.5%

Genera, mean relative abundance over 84 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	R2	R4
age_category	0	0%
country	88	100%	88
health_condition	88	100%	88
subject_id	88	100%			88
antibiotic_exposure	88	100%		88
collection_date	88	100%	88
detailed_location	88	100%
health_condition_detail	88	100%	88
latitude	88	100%	88
location_locality	88	100%	88
location_region	88	100%	88
longitude	88	100%	88

Papers (1)

Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome. 2023 PMID 36719190 PMC10101062 own_data

Details

Archive description

Here, we performed 16S rRNA sequencing on stools from 168 patients and 68 healthy family members who lived together to determine the gut microbiome composition of PJS patients. Metagenomics sequencing was further performed on the representative samples (61 PJS patients and 27 healthy family members) to analyze the functional changes.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.

host run.host_tax_id · “9606”
host run.scientific_name · “human gut metagenome”
body site study.description · “16S rRNA sequencing on stools”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN31955614	antibiotic_exposure	no	R2	0.60	external.bugsigdb source	Antibiotics exclusion: 3 months
SAMN31955614	collection_date	2020-09	R1	0.90	biosample.attribute:collection_date	2020-09
SAMN31955614	country	CN	R1	0.90	sample.attr.geo_loc_name	China:Guangzhou
SAMN31955614	health_condition	healthy_control	R1	0.70	sample.name_rule:alias	Normal_173
SAMN31955614	health_condition_detail	Normal	R1	0.70	sample.name_rule:alias	Normal_173
SAMN31955614	latitude	23.1300	R1	0.90	biosample.attribute:lat_lon	23.13 N 113.27 E
SAMN31955614	location_locality	Guangzhou	R1	0.85	biosample.attribute:geo_loc_name	China:Guangzhou
SAMN31955614	location_region	Guangdong	R1	0.60	biosample.attribute:lat_lon	23.13 N 113.27 E
SAMN31955614	longitude	113.2700	R1	0.90	biosample.attribute:lat_lon	23.13 N 113.27 E
SAMN31955614	subject_id	SAMN31955614	R4	0.60	design.one_sample_per_subject:description	Metagenomics sequencing was further performed on the representative samples (61 PJS patients and 27 healthy family members) to analyze the functional changes.

Sequencing

88 runs over 88 samples · mean 7.05 Gbp per run (median 6.80 Gbp, total 620.64 Gbp; 88 runs with a base count) · layout PAIRED 88 · platform ILLUMINA 88 · models Illumina NovaSeq 6000 (88) · 95% of runs with a Sandpiper profile · first public 2023-01-25

Authors (7)

Wang Z first · Liang L · Liu L · Wang Y · Yu Z · Wu B · Chen Y last

Downloads

PRJNA905444.csv.gz (3.2 KB) · parquet (74.4 KB) — all 88 samples, every field with route and confidence · PRJNA905444_determinations.csv.gz (7.2 KB) — 880 evidence rows

Samples (88 · every field this project has values for · hover a cell for its source)

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