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PRJNA912122 SRP413645

Gut microbiome in liver disease patients, USA

Lactulose-mediated Bifidobacteria expansion promotes a beneficial fecal metabolite profile that is associated with exclusion of antibiotic-resistant pathogens and improved outcomes in advanced liver disease

Shotgun metagenomics with paired faecal metabolite measurements of 850 stool samples from about 260 hospitalised patients with acute or chronic liver disease in Chicago, USA, studying lactulose, Bifidobacteria and infection outcomes. machine-written summary

850 samples · 850 runs · US · Age unknown · 2022 · 2.51 Gbp / sample · cohort Fecal Butyrate and Deoxycholic Acid Concentrations

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Sources

✓Sequence archive 3,390✓Abstract / description 1,700○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	3,390 sample values (collection date, country, subject id, timepoint)
✓ Abstract / description	1,700 sample values (health condition, health condition detail)
○ Full text	read; no usable statement or table · PMC11055453, PMC11059310, PMC12197998, PMC12788677
○ 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

Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance

1 country

Age

unknown850

Condition

liver_disease850

Country

US850

Body site

primary850

Collected 2021–2022

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

160 of 263 people sampled more than once (742 samples; median 3, up to 22 per person) · follow-up median 18 d (max 11 mo) · median interval between samples 4 d (time from collection dates).

Each row is one person (36 shown of 160); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

No Sandpiper profile for this project's samples yet.

Field coverage

field	samples	coverage	R1	R4
age_category	0	0%
country	850	100%	850
health_condition	850	100%		850
subject_id	845	99%	845
collection_date	850	100%	850
health_condition_detail	850	100%		850
timepoint_label	845	99%	845

Papers (4)

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. 2024 PMID 38177297 PMC11055453 cites_accession
Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease. 2025 PMID 40574876 PMC12197998 cites_accession
Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome. 2026 PMID 41511994 PMC12788677 cites_accession
Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease. 2023 PMID 37845315 PMC11059310 own_data

Details

Archive description

The link between gut microbiome of chronic liver disease (CLD) and clinical outcomes of the patients is lacking in the field, and this study takes a chance in investigating the relationship metagenomically and metabolomical, along with animal experiments.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by curator_audit with confidence 0.55. Assay shotgun_dna.

host papers[0].abstract · “shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples”
host runs.scientific_name · “human gut metagenome (850)”
body site papers[0].abstract · “shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples”
body site runs.scientific_name · “human gut metagenome (850)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN32225265	collection_date	2021-04-07	R1	0.85	biosample.attribute:collection_date	collection_date: 2021-04-07
SAMN32225265	country	US	R1	0.90	sample.attr.geo_loc_name	USA: Chicago, IL
SAMN32225265	health_condition	liver_disease	R4	0.50	paper.abstract	patients with acute or chronic liver disease
SAMN32225265	health_condition_detail	acute or chronic liver disease	R4	0.50	paper.abstract	patients with acute or chronic liver disease
SAMN32225265	subject_id	LiverD-001	R1	0.70	sample.name_rule:library_name	library_name: LiverD-001.01
SAMN32225265	timepoint_label	01	R1	0.70	sample.name_rule:library_name	library_name: LiverD-001.01

Sequencing

850 runs over 850 samples · mean 2.50 Gbp per run (median 2.51 Gbp, total 2,123.08 Gbp; 850 runs with a base count) · layout PAIRED 850 · platform ILLUMINA 850 · models Illumina NovaSeq 6000 (533), NextSeq 500 (317) · 91% of runs with a Sandpiper profile · first public 2022-12-20 – 2022-12-22

Authors (0)

No author record.

Downloads

PRJNA912122.csv.gz (24.2 KB) · parquet (104.2 KB) — all 850 samples, every field with route and confidence · PRJNA912122_determinations.csv.gz (42.5 KB) — 5,090 evidence rows

Samples (850 · every field this project has values for · hover a cell for its source)

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