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PRJEB102033 ERP183436

Gut microbiome in US hospitalized patients and healthy donors

Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance

1877 fecal samples from healthy donors and liver disease, liver transplant, heart transplant, and MICU patients in the USA, studying lanthipeptide/lantibiotic-producing bacteria; cross-sectional design. machine-written summary

1,877 samples · 1,877 runs · US · Age unknown · 2025 · 2.08 Gbp / sample

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 16,210✓Abstract / description 333○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	16,210 sample values (collection date, country, health condition, health condition detail, location locality, location region, location site, subject id)
✓ Abstract / description	333 sample values (health condition detail)
○ Full text	read; no usable statement or table · PMC12766783
○ 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

Other administered intervention (see intervention_detail) design observational_with_procedure · Mouse gavage with lantibiotic-producing Blautia pseudococcoides SCSK after antibiotic dysbiosis

“BpSCSK administration prevents intestinal recolonization by a wide range of commensal species” — abstract:41330369 (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 country

Age

unknown1,877

Condition

other_disease662

liver_disease571

transplant_or_immunocompromised311

Country

US1,877

Body site

primary1,877

Collected 2020–2021

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

399 of 628 people sampled more than once (1,648 samples; median 3, up to 20 per person) · follow-up median 13 d (max 16 mo) · median interval between samples 4 d (time from collection dates). Schedule stated by the source: “Human fecal samples collected repeatedly per patient across up to 32 distinct timepoint labels (subject_id coverage 628 distinct across 1877 samples); exact calendar offsets not given per patient.”.

Each row is one person (36 shown of 399); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Enterococcus_B 15.6%Bacteroides 6.3%Phocaeicola 4.5%Streptococcus 4.2%Bifidobacterium 4.1%Lacticaseibacillus 4.0%Blautia_A 3.4%Enterococcus 2.7%Klebsiella 2.7%Parabacteroides 2.3%Escherichia 2.2%Mediterraneibacter 2.1%not assigned to a genus 4.8%other genera 41.0%

Genera, mean relative abundance over 1,833 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	0	0%
country	1,877	100%	1,877
health_condition	1,544	82%	1,544
subject_id	1,877	100%	1,877
collection_date	1,877	100%	1,877
detailed_location	1,877	100%
health_condition_detail	1,877	100%	1,544	333
location_locality	1,877	100%	1,877
location_region	1,877	100%	1,877
location_site	1,877	100%	1,877
timepoint_label	1,860	99%	1,860

Papers (1)

Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance. 2025 PMID 41330369 PMC12766783 own_data

Details

Archive description

In this study, we investigate the presence of lanthipeptides in fecal samples that have undergone shallow-shotgun sequencing from healthy human donors as well as liver disease, liver transplant, heart transplant, and medical intensive care unit (MICU) patients. Using 16S rRNA gene sequencing of mouse fecal pellets, we demonstrate that the lantibiotic-producing bacterium Blautia pseudococcoides SCSK prevents intestinal recolonization of mice by a wide range of commensal species following antibiotic-induced dysbiosis and markedly reduces fecal concentrations of microbiota-derived metabolites. Blautia producta KH6, a closely related Blautia strain that lacks a known lantibiotic, does not have the same effect. Lantibiotic-mediated dysbiosis results in sustained loss of colonization resistance against Klebsiella pneumoniae and Clostridioides difficile infection.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.

host run.host_tax_id · “9606”
host study.description · “healthy human donors”
body site study.description · “fecal samples that have undergone shallow-shotgun sequencing”
body site run.scientific_name · “human gut metagenome”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMEA120478552	collection_date	2020-10-19	R1	0.90	biosample.attribute:collection_date	2020-10-19
SAMEA120478552	country	US	R1	0.90	sample.attr.geographic_location_country_and_or_sea	USA
SAMEA120478552	health_condition	other_disease	R1	0.70	sample.name_rule:alias	MICU-077.01
SAMEA120478552	health_condition_detail	MICU	R1	0.70	sample.name_rule:alias	MICU-077.01
SAMEA120478567	health_condition_detail	mixed_case_control: healthy donors vs liver disease, transplant, and MICU patients	R4	0.40	study.description	healthy human donors as well as liver disease, liver transplant, heart transplant,
SAMEA120478552	location_locality	Chicago	R1	0.85	biosample.attribute:geographic_location_region_and_locality	USA: University of Chicago, Chicago, Illinois
SAMEA120478552	location_region	Illinois	R1	0.85	biosample.attribute:geographic_location_region_and_locality	USA: University of Chicago, Chicago, Illinois
SAMEA120478552	location_site	University of Chicago	R1	0.85	biosample.attribute:geographic_location_region_and_locality	USA: University of Chicago, Chicago, Illinois
SAMEA120478552	subject_id	Patient_100	R1	0.85	sample.attr.host_subject_id	Patient_100
SAMEA120478552	timepoint_label	01	R1	0.70	sample.name_rule:alias	MICU-077.01

Sequencing

1,877 runs over 1,877 samples · mean 2.25 Gbp per run (median 2.08 Gbp, total 4,229.25 Gbp; 1,877 runs with a base count) · layout PAIRED 1,877 · platform ILLUMINA 1,877 · models Illumina NovaSeq 6000 (1,290), NextSeq 2000 (538), Illumina HiSeq 4000 (21), Illumina MiniSeq (15), NextSeq 500 (13) · 98% of runs with a Sandpiper profile · first public 2025-12-01

Authors (14)

Cole CG first · Zhang ZJ · Dommaraju SR · Dong Q · Pope RL · Son SS · McSpadden EJ · Woodson CK · Lin H · Dylla NP · Sidebottom AM · Sundararajan A · Mitchell DA · Pamer EG last

Downloads

PRJEB102033.csv.gz (55.0 KB) · parquet (146.5 KB) — all 1,877 samples, every field with route and confidence · PRJEB102033_determinations.csv.gz (131.0 KB) — 16,543 evidence rows

Samples (1,877 · every field this project has values for · hover a cell for its source)

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