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PRJNA824824 SRP368304

Ex vivo gut microbiome response to glycans (USA)

An ex vivo screening of community response to synthetic and reference glycans

324 samples from the USA were screened ex vivo for community response to synthetic and reference glycans; no age, health condition, or intervention details are specified. machine-written summary

324 samples · 324 runs · US · Age unknown · 2023 · 3.03 Gbp / sample

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Sources

✓Sequence archive 1,885–Abstract / description–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	1,885 sample values (collection date, country, latitude, longitude, subject id, timepoint)
– Abstract / description	no abstract or project description
– Full text	no open-access full text linked
– Supplementary tables	no supplementary tables available (or none open access)
– External resources	not covered by the external resources we ingest
– User contribution	nothing uploaded yet · share metadata
– 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 sampling locations · 1 country

Age

unknown324

Country

US324

Body site

primary324

Collected 2020–2021

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

22 of 22 people sampled more than once (324 samples; median 10, up to 36 per person) · follow-up median 7 mo (max 12 mo) · median interval between samples 2 mo (time from collection dates).

Each row is one person (11 shown of 22); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Bifidobacterium 11.4%Blautia_A 10.3%Faecalibacterium 6.7%Roseburia 6.2%Collinsella 4.1%Parabacteroides 3.7%Bacteroides 3.4%Phocaeicola 3.1%Escherichia 2.6%Dorea_A 2.2%Ruminococcoides 2.2%Streptococcus 1.9%not assigned to a genus 8.6%other genera 33.6%

Genera, mean relative abundance over 297 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
age_category	0	0%
country	324	100%	324
health_condition	0	0%
subject_id	324	100%	324
collection_date	324	100%	324
latitude	324	100%	324
longitude	324	100%	324
timepoint_label	265	82%	265

Details

Archive description

An ex vivo screening of community response to synthetic and reference glycans

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

host run.scientific_name · “human gut metagenome”
body site run.scientific_name · “human gut metagenome”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN27479446	collection_date	2020-11-22	R1	0.90	biosample.attribute:collection_date	2020-11-22
SAMN27479446	country	US	R1	0.90	sample.attr.geo_loc_name	USA
SAMN27479446	latitude	38.0400	R1	0.90	biosample.attribute:lat_lon	38.04 N 84.50 W
SAMN27479446	longitude	-84.5000	R1	0.90	biosample.attribute:lat_lon	38.04 N 84.50 W
SAMN27479446	subject_id	S02002ST	R1	0.85	biosample.attribute:community	S02002ST
SAMN27479505	timepoint_label	washout	R1	0.85	sample.attr.visit_name	washout

Sequencing

324 runs over 324 samples · mean 3.17 Gbp per run (median 3.03 Gbp, total 1,028.43 Gbp; 324 runs with a base count) · layout SINGLE 324 · platform ILLUMINA 324 · models NextSeq 500 (324) · 92% of runs with a Sandpiper profile · first public 2023-06-05

Authors (0)

No author record.

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

Downloads

PRJNA824824.csv.gz (8.3 KB) · parquet (80.6 KB) — all 324 samples, every field with route and confidence · PRJNA824824_determinations.csv.gz (10.3 KB) — 1,885 evidence rows

Samples (324 · every field this project has values for · hover a cell for its source)

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