Gut metagenome in pediatric HCT patients, Durham, NC

The gut metagenome during hematopoietic cell transplantation in children

1009 longitudinal fecal metagenome samples from children (<18 years) undergoing hematopoietic cell transplantation at Duke University, Durham, North Carolina, collected serially between 2015 and 2020. machine-written summary

1,009 samples · 1,009 runs · US · Mixed ages · 2023 · 3.00 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 8,272✓Abstract / description 1,818○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	8,272 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
✓ Abstract / description	1,818 sample values (collection date, location site)
○ Full text	read; no usable statement or table · PMC13562672
○ 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

child1,009

Condition

transplant_or_immunocompromised1,009

Country

US1,009

Body site

primary1,009

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal — not resolved

99 of 100 people sampled more than once (1,008 samples; median 9, up to 21 per person). Schedule stated by the source: “Serial fecal sample collection per patient during HCT, exact schedule/timepoints not specified in dossier”.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 10.7%Phocaeicola 6.5%Escherichia 5.3%Enterococcus_B 5.3%Enterococcus 4.9%Enterocloster 4.1%Bifidobacterium 3.9%Klebsiella 3.5%Streptococcus 3.4%Mediterraneibacter 3.1%Parabacteroides 2.9%Alistipes 2.3%not assigned to a genus 5.9%other genera 38.2%

Genera, mean relative abundance over 846 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	R4
age_category	1,009	100%
country	1,009	100%	1,009
health_condition	1,009	100%	1,009
subject_id	1,009	100%	1,009
collection_date	1,009	100%	200	809
detailed_location	1,009	100%
health_condition_detail	1,009	100%	1,009
latitude	1,009	100%	1,009
location_locality	1,009	100%	1,009
location_region	1,009	100%	1,009
location_site	1,009	100%		1,009
longitude	1,009	100%	1,009

Papers (1)

Commensal bacteria inhibit viral infections via a tryptophan metabolite. 2026 PMID 42722642 PMC13562672 unsure

Details

Archive description

Due to cytotoxic chemotherapy and broad-spectrum antibiotic exposure, children undergoing hematopoietic cell transplantation (HCT) experience significant alterations to their gut microbiomes. We performed shotgun metagenomic sequencing of serially collected fecal samples from children (<18 years) undergoing hematopoietic cell transplantation at Duke University between 2015 and 2020. These data support ongoing analyses to determine the impact of the gut microbiome on clinical outcomes after HCT in children.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child and adolescent by opus_adjudicated with confidence 0.60. Assay shotgun_dna.

host run.host_tax_id · “9606”
body site study.description · “serially collected fecal samples”
life stage study.description · “children (<18 years)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN40174364	collection_date	2015/2020	R1	0.90	biosample.attribute:collection_date	2015/2020
SAMN31287181	collection_date	2015/2020	R4	0.40	ena.study_description	transplantation at Duke University between 2015 and 2020
SAMN31287181	country	US	R1	0.90	sample.attr.geo_loc_name	USA: North Carolina, Durham
SAMN31287181	health_condition	transplant_or_immunocompromised	R1	0.70	sample.name_rule:alias	05ST004
SAMN31287181	health_condition_detail	ST	R1	0.70	sample.name_rule:alias	05ST004
SAMN31287181	latitude	36.0100	R1	0.90	biosample.attribute:lat_lon	36.01 N 78.94 W
SAMN31287181	location_locality	Durham	R1	0.85	biosample.attribute:geo_loc_name	USA: North Carolina, Durham
SAMN31287181	location_region	North Carolina	R1	0.85	biosample.attribute:geo_loc_name	USA: North Carolina, Durham
SAMN31287181	location_site	Duke University	R4	0.40	ena.study_description	hematopoietic cell transplantation at Duke University between 2015
SAMN31287181	longitude	-78.9400	R1	0.90	biosample.attribute:lat_lon	36.01 N 78.94 W
SAMN31287181	subject_id	05	R1	0.70	sample.name_rule:alias	05ST004

Sequencing

1,009 runs over 1,009 samples · mean 5.45 Gbp per run (median 3.00 Gbp, total 5,500.74 Gbp; 1,009 runs with a base count) · layout PAIRED 1,009 · platform ILLUMINA 1,009 · models NextSeq 500 (518), Illumina NovaSeq 6000 (491) · 84% of runs with a Sandpiper profile · first public 2023-04-09 – 2025-03-03

Authors (24)

Jiang D first · Soo N · Tan CY · Dankwa S · Wang HY · Theriot BS · Xue K · Hill D · Ardeshir A · Bain JR · Heston SM · Hurst JH · Siddiqui NY · Van Rompay KKA · Cervantes-Barragan L · Smith JP · Song R · Roper J · Kelly MS · Hudgens MG · De Paris K · Permar SR · Goswami R · Surana NK last

Downloads

PRJNA890666.csv.gz (22.7 KB) · parquet (101.3 KB) — all 1,009 samples, every field with route and confidence · PRJNA890666_determinations.csv.gz (67.6 KB) — 10,090 evidence rows

Samples (1,009 · every field this project has values for · hover a cell for its source)

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