Microbiome in liver transplant recipients, Chicago, long.
240 fecal samples from adult liver transplant candidates/recipients in Chicago, USA, studying microbiome diversity and metabolites (SCFAs, bile acids) linked to postoperative infection risk, in a longitudinal design. machine-written summary
240 samples · 240 runs · US · Adult · 2023 · 2.78 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,486 sample values (collection date, country, health condition, health condition detail, location locality, subject id, timepoint) |
| ✓ Abstract / description | 194 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · 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 |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population liver_disease · Liver transplant recipients, peri-transplant fecal sampling
“peri-transplant fecal microbiome compositions including relative” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
41 of 163 people sampled more than once (118 samples; median 2, up to 7 per person) · follow-up median 14 d (max 49 d) · median interval between samples 6 d (time from collection dates). Schedule stated by the source: “Peri-transplant serial fecal sampling with up to 7 numbered samples per subject (sample_number 01-07); exact day offsets not given in provided text” (time origin: transplant).
Each row is one person (36 shown of 41); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 210 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 240 | 100% | ||||
| country | 240 | 100% | 240 | |||
| health_condition | 240 | 100% | 143 | 97 | ||
| subject_id | 240 | 100% | 240 | |||
| collection_date | 240 | 100% | 240 | |||
| detailed_location | 240 | 100% | ||||
| health_condition_detail | 240 | 100% | 143 | 97 | ||
| location_locality | 240 | 100% | 240 | |||
| timepoint_label | 240 | 100% | 240 |
- Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome. 2026 PMID 41511994 PMC12788677 unsure
Archive description
Liver transplantation is associated with postoperative infections caused by antibiotic-resistant bacterial pathogens that reside in the intestine. An intact intestinal microbiome suppresses expansion of enteric pathogens, however patients with severe liver disease often have reduced microbiome diversity and increased density of antibiotic-resistant Enterococcus and Enterobacterales species. Experimental models have demonstrated that metabolites produced by the intestinal microbiome, including short chain fatty acids (SCFAs), secondary bile acids and indole compounds, enhance host epithelial and immune defenses against enteric pathogens. Microbiome derived metabolites likely contribute to resistance against infectious diseases in LT patients, however, this remains uninvestigated.</p><p>We prospectively enrolled 107 liver transplant candidates and determined peri-transplant fecal microbiome compositions including relative and absolute fecal metabolite concentrations.</p><p>Fecal microbiomes in LT recipients ranged from highly diverse to complete loss of diversity resulting in expansion of Enterococcus and/or Enterobacterales species that were associated with postoperative infection. Gas chromatographic (GC) and liquid chromatographic (LC) Mass spectrometric analyses revealed decreased concentrations of SCFAs, secondary bile acids, and indole compounds in fecal samples with low microbiome diversity and associated expansion of Enterococcus and Enterobacterales populations.</p><p>Fecal metabolite abundances accurately predicted LT patients with reduced microbial diversity and those who developed postoperative infection.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult 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 · “Fecal metabolite profiling identifies”
- body site study.description · “reside in the intestine . An intact”
- body site study.title · “metabolite profiling identifies liver transplant recipients at”
- body site study.description · “Liver transplantation is associated”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38225799 | collection_date | 2020-10-08 | R1 | 0.90 | biosample.attribute:collection_date | 2020-10-08 |
| SAMN38225799 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Chicago |
| SAMN38225799 | health_condition | liver_disease | R1 | 0.70 | sample.name_rule:subject | lt-059 |
| SAMN38225942 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | liver transplant candidates and determined peri-transplant |
| SAMN38225799 | health_condition_detail | lt | R1 | 0.70 | sample.name_rule:subject | lt-059 |
| SAMN38225942 | health_condition_detail | Liver transplant recipients; peri-transplant microbiome assessment | R4 | 0.50 | study.description | liver transplant candidates and determined peri-transplant |
| SAMN38225799 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Chicago |
| SAMN38225799 | subject_id | lt-059 | R1 | 0.85 | sample.attr.subject | lt-059 |
| SAMN38225799 | timepoint_label | 02 | R1 | 0.85 | biosample.attribute:sample_number | sample_number: 02 |
Sequencing
240 runs over 240 samples · mean 2.89 Gbp per run (median 2.78 Gbp, total 694.63 Gbp; 240 runs with a base count) · layout PAIRED 240 · platform ILLUMINA 240 · models NextSeq 500 (240) · 88% of runs with a Sandpiper profile · first public 2023-11-14
Authors (14)
Mullowney MW first · Moran A · Hernandez A · McMillin M · Rose AR · Moran D · Little J · Nguyen AB · Patel BK · Lehmann CJ · Odenwald MA · Pamer EG · Yeo KJ · Sidebottom AM last
Downloads
PRJNA1039781.csv.gz (8.0 KB) · parquet (80.7 KB) — all 240 samples, every field with route and confidence · PRJNA1039781_determinations.csv.gz (13.3 KB) — 1,680 evidence rows