Gut microbiome in liver transplant patients, longitudinal
185 stool samples from liver transplant patients (adults, elderly, and some children), analyzed longitudinally to link gut microbial composition and metabolites, including E. faecium domination and tyramine, to mortality risk. machine-written summary
185 samples · 185 runs · US · Adult · 2026 · 2.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,405 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
longitudinal
51 of 134 people sampled more than once (102 samples; median 2, up to 2 per person) · follow-up median 12 d (max 22 d) · median interval between samples 12 d (time from collection dates). Schedule stated by the source: “pre-transplant, early post-transplant, and late post-transplant stool samples” (time origin: transplant).
Each row is one person (36 shown of 51); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 185 | 100% | ||||
| country | 185 | 100% | 185 | |||
| health_condition | 185 | 100% | 185 | |||
| subject_id | 185 | 100% | 185 | |||
| age_at_collection_days | 185 | 100% | 185 | |||
| collection_date | 185 | 100% | 185 | |||
| detailed_location | 185 | 100% | ||||
| health_condition_detail | 185 | 100% | 185 | |||
| latitude | 185 | 100% | 185 | |||
| location_locality | 185 | 100% | 185 | |||
| location_region | 185 | 100% | 185 | |||
| location_site | 185 | 100% | 185 | |||
| longitude | 185 | 100% | 185 | |||
| sex | 185 | 100% | 185 | |||
| timepoint_label | 185 | 100% | 185 |
Archive description
Liver Transplant (LT) is the definitive therapy for end stage liver disease but carries risk for mortality, which has been linked to reduced gut microbial diversity. However, diversity is a broad measure leaving specific features linked to mortality unknown. To investigate this, we performed metagenomic sequencing and LC-GC/MS analysis on the stool of LT patients. We found that their microbiomes had low diversity, typified by reduced commensal anaerobes, higher enteric pathogens, and reduced microbial metabolites, which was more pronounced late in hospitalization. We found that intact microbial generation of secondary bile acids was associated with survival. We found two non-overlapping taxonomic compositional clusters: one dominated by E. feacium and the other containing an array of commensal anaerobes. The E. feacium cluster had fewer health promoting metabolites and was enriched in tyramine. E. feacium dominated patients had a 4-fold higher risk of mortality. We also found that stool tyramine/tyrosine ratio can reliably identify E. feacium domination in both LT patients and a broad array of hospitalized patients. Here we discover that E. feacium domination and associated metabolic shifts are specific links to mortality and that stool tyramine could be useful to identify this state of dysbiosis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host study.description · “performed metagenomic sequencing and LC-GC/MS analysis on the stool of LT patients”
- body site study.description · “stool of LT patients”
- life stage sample.attr.host_age · “26.8 (n=142/185)”
- life stage sample.attr.host_age · “66.6 (n=33/185)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN60900895 | age_at_collection_days | 20697.9 | R1 | 0.85 | sample.attr.host_age | 56.7 |
| SAMN60900895 | collection_date | 2020-10-29 | R1 | 0.90 | biosample.attribute:collection_date | 2020-10-29 |
| SAMN60900895 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: University of Chicago, Chicago, Illinois |
| SAMN60900895 | health_condition | liver_disease | R1 | 0.70 | sample.name_rule:title | pre-transplant stool sample from Liver Transplant patient UC-022 |
| SAMN60900895 | health_condition_detail | pre-transplant | R1 | 0.70 | sample.name_rule:title | pre-transplant stool sample from Liver Transplant patient UC-022 |
| SAMN60900895 | latitude | 41.7919 | R1 | 0.90 | biosample.attribute:lat_lon | 41.79188074 N 87.60334891 W |
| SAMN60900895 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: University of Chicago, Chicago, Illinois |
| SAMN60900895 | location_region | Illinois | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: University of Chicago, Chicago, Illinois |
| SAMN60900895 | location_site | University of Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: University of Chicago, Chicago, Illinois |
| SAMN60900895 | longitude | -87.6033 | R1 | 0.90 | biosample.attribute:lat_lon | 41.79188074 N 87.60334891 W |
| SAMN60900895 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN60900895 | subject_id | UC-022 | R1 | 0.85 | sample.attr.host_subject_id | UC-022 |
| SAMN60900895 | timepoint_label | pre-transplant | R1 | 0.70 | sample.name_rule:title | pre-transplant stool sample from Liver Transplant patient UC-022 |
Sequencing
185 runs over 185 samples · mean 2.39 Gbp per run (median 2.18 Gbp, total 442.39 Gbp; 185 runs with a base count) · layout PAIRED 185 · platform ILLUMINA 185 · models NextSeq 2000 (185) · 0% of runs with a Sandpiper profile · first public 2026-06-17 – 2026-06-19
Authors (0)
No author record.
Downloads
PRJNA1398904.csv.gz (7.9 KB) · parquet (81.4 KB) — all 185 samples, every field with route and confidence · PRJNA1398904_determinations.csv.gz (21.2 KB) — 2,405 evidence rows