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PRJNA928758 SRP419436

Gut microbiome in liver transplant recipients, Chicago

Microbiome in Liver Transplant Infections

143 gut microbiome samples from liver transplant/immunocompromised patients in Chicago, IL, USA, spanning infant to elderly age groups, studied in relation to surgery. machine-written summary

143 samples · 143 runs · US · Adult · 2023 · 2.18 Gbp / sample

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Sources

✓Sequence archive 1,284✓Abstract / description 286–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	1,284 sample values (age, collection date, country, latitude, location locality, location region, longitude, sex)
✓ Abstract / description	286 sample values (health condition, health condition detail)
– 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
– Human verified	not yet checked by a person · I checked this project — verify it

Interventions

intervention — arms not resolved

Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population transplant_or_immunocompromised · Gut microbiome sampled in liver transplant recipients

“gut microbiome of liver transplant recipients” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 sampling locations · 1 country

Age

adult102

elderly37

infant2

adolescent1

child1

Condition

transplant_or_immunocompromised143

Sex

male80

female63

Country

US143

Body site

primary143

Collected 2020–2022

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

25 of 106 people sampled more than once (59 samples; median 2, up to 4 per person) · follow-up median 13 d (max 37.9 y) · median interval between samples 9 d (time from collection dates).

Each row is one person (25 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Enterococcus_B 24.3%Bifidobacterium 8.6%Lacticaseibacillus 4.5%Streptococcus 4.2%Escherichia 3.6%Klebsiella 3.3%Bacteroides 3.3%Phocaeicola 2.9%Enterococcus 2.5%Blautia_A 1.9%Enterococcus_D 1.9%Lactococcus 1.7%not assigned to a genus 4.3%other genera 32.9%

Genera, mean relative abundance over 124 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	143	100%
country	143	100%	143
health_condition	143	100%		143
subject_id	140	98%	140
age_at_collection_days	143	100%	143
collection_date	143	100%	143
detailed_location	143	100%
health_condition_detail	143	100%		143
latitude	143	100%	143
location_locality	143	100%	143
location_region	143	100%	143
longitude	143	100%	143
sex	143	100%	143

Papers (1)

Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection. 2024 PMID 38103544 own_data

Details

Archive description

Human gut microbiome of liver transplant recipients

How this project entered the registry

Classified as human blood / tissue / internal fluids / gut / stool shotgun DNA metagenome of adult and elderly 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 · “Microbiome in Liver Transplant Infections”
body site study.description · “gut microbiome of liver transplant recipients”
body site study.description · “Human gut microbiome of liver”
body site external_curation.infant_catalog · “body_site_call gut”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
life stage sample.attr.host_age · “68 (n=35/143)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN32942414	age_at_collection_days	18262.5	R1	0.70	sample.attr.host_age	50
SAMN32942414	collection_date	2021-04-20	R1	0.90	biosample.attribute:collection_date	2021-04-20
SAMN32942414	country	US	R1	0.90	sample.attr.geo_loc_name	USA: Chicago, IL
SAMN32942414	health_condition	transplant_or_immunocompromised	R4	0.50	paper.abstract.abstract	107 patients undergoing liver transplantation (LT)
SAMN32942414	health_condition_detail	patients undergoing liver transplantation	R4	0.50	paper.abstract.abstract	107 patients undergoing liver transplantation (LT)
SAMN32942414	latitude	41.7900	R1	0.90	biosample.attribute:lat_lon	41.79 N 87.60 W
SAMN32942414	location_locality	Chicago	R1	0.85	biosample.attribute:geo_loc_name	USA: Chicago, IL
SAMN32942414	location_region	Illinois	R1	0.75	biosample.attribute:geo_loc_name	USA: Chicago, IL
SAMN32942414	longitude	-87.6000	R1	0.90	biosample.attribute:lat_lon	41.79 N 87.60 W
SAMN32942414	sex	male	R1	0.90	sample.attr.host_sex	male
SAMN32942414	subject_id	001	R1	0.70	sample.name_rule:alias	lt-001-01

Sequencing

143 runs over 143 samples · mean 2.31 Gbp per run (median 2.18 Gbp, total 330.46 Gbp; 143 runs with a base count) · layout PAIRED 143 · platform ILLUMINA 143 · models Illumina NovaSeq 6000 (143) · 87% of runs with a Sandpiper profile · first public 2023-02-01

Authors (0)

No author record.

Downloads

PRJNA928758.csv.gz (5.7 KB) · parquet (78.4 KB) — all 143 samples, every field with route and confidence · PRJNA928758_determinations.csv.gz (12.5 KB) — 1,570 evidence rows

Samples (143 · every field this project has values for · hover a cell for its source)

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