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PRJNA645402 SRP273495

Gut microbiome in US norovirus challenge study adults

Human gut microbiome Raw sequence reads

33 gut metagenome samples from adult participants (USA) in a norovirus human challenge study, comparing asymptomatic and symptomatic infection outcomes in an intervention design. machine-written summary

33 samples · 33 runs · US · Adult · 2020 · 3.49 Gbp / sample

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Sources

✓Sequence archive 165○Abstract / description○Full text✓Supplementary tables 153✓External resources 66–User contribution–Human verified

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

what each source gave

✓ Sequence archive	165 sample values (collection date, country, latitude, location region, longitude)
○ Abstract / description	read; no usable statement
○ Full text	read; no usable statement or table · PMC7683401
✓ Supplementary tables	153 sample values (age, intervention, sex, subject id, timepoint)
✓ External resources	66 sample values (health condition, health condition detail) · from GMrepo v3
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Interventions

Other administered intervention (see intervention_detail) · population gi_infection_or_diarrhoea · Human norovirus challenge study (experimental infection)

“subjects enrolled in a norovirus challenge study” — abstract:33203758 (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 sampling locations · 1 country

Age

adult33

Condition

gi_infection_or_diarrhoea33

Sex

male23

female10

Country

US33

Body site

primary33

Collected 2008–2009

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

9 of 9 people sampled more than once (33 samples; median 3, up to 7 per person) · follow-up median 30 d (max 30 d) · median interval between samples 30 d (time from collection months (month precision)). Schedule stated by the source: “Stool day before norovirus challenge (day 0); 3 symptomatic subjects re-sampled at variable intervals (1-8 days) up to 33 days postchallenge”; stated follow-up 33 d.

Each row is one person (1 shown of 9); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 17.1%Phocaeicola 10.6%Faecalibacterium 5.1%Roseburia 4.8%Alistipes 3.7%Blautia_A 3.0%Prevotella 2.8%Bifidobacterium 2.7%Gemmiger 2.2%Parabacteroides 2.2%Cryptobacteroides 2.1%Fimenecus 1.8%not assigned to a genus 6.2%other genera 35.6%

Genera, mean relative abundance over 32 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
age_category	33	100%
country	33	100%	33
health_condition	33	100%		33
subject_id	33	100%		33
age_at_collection_days	33	100%		33
collection_date	33	100%	33
detailed_location	33	100%
health_condition_detail	33	100%		33
latitude	33	100%	33
location_region	33	100%	33
longitude	33	100%	33
sex	33	100%		33
timepoint_label	33	100%		33
intervention	21	64%		21

Papers (1)

The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study. 2020 PMID 33203758 PMC7683401 own_data

Details

Archive description

Human gut metagenomes from patients enrolled in a Norovirus challenge study.

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 · “Human gut microbiome Raw sequence”
body site study.description · “Human gut metagenomes from patients”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN15502673	age_at_collection_days	6940	R2	0.85	paper.supp.mBio.02634-20-st001.xlsx[TableS1!Age]	19
SAMN15502673	collection_date	2008-09	R1	0.90	biosample.attribute:collection_date	2008-09
SAMN15502673	country	US	R1	0.90	sample.attr.geo_loc_name	USA
SAMN15502673	health_condition	gi_infection_or_diarrhoea	R2	0.75	external.gmrepo source	phenotype: Caliciviridae Infections
SAMN15502673	health_condition_detail	Caliciviridae Infections	R2	0.75	external.gmrepo source	phenotype: Caliciviridae Infections
SAMN15502691	intervention	other_intervention	R2	0.85	paper.supp.mBio.02634-20-st001.xlsx[TableS1!group]	S
SAMN15502673	latitude	33.7971	R1	0.90	biosample.attribute:lat_lon	33.7971368 N 84.32224 W
SAMN15502673	location_region	Georgia	R1	0.60	biosample.attribute:lat_lon	33.7971368 N 84.32224 W
SAMN15502673	longitude	-84.3222	R1	0.90	biosample.attribute:lat_lon	33.7971368 N 84.32224 W
SAMN15502673	sex	female	R2	0.85	paper.supp.mBio.02634-20-st001.xlsx[TableS1!Sex]	F
SAMN15502673	subject_id	13	R2	0.85	paper.supp.mBio.02634-20-st001.xlsx[TableS1!Individual]	13
SAMN15502673	timepoint_label	0	R2	0.85	paper.supp.mBio.02634-20-st001.xlsx[TableS1!Day]	0

Sequencing

33 runs over 33 samples · mean 3.37 Gbp per run (median 3.49 Gbp, total 111.11 Gbp; 33 runs with a base count) · layout PAIRED 33 · platform ILLUMINA 33 · models Illumina HiSeq 2500 (33) · 97% of runs with a Sandpiper profile · first public 2020-07-26

Authors (6)

Patin NV first · Peña-Gonzalez A · Hatt JK · Moe C · Kirby A · Konstantinidis KT last

Downloads

PRJNA645402.csv.gz (1.9 KB) · parquet (72.2 KB) — all 33 samples, every field with route and confidence · PRJNA645402_determinations.csv.gz (3.5 KB) — 384 evidence rows

Samples (33 · every field this project has values for · hover a cell for its source)

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