Gut microbiome in small bowel transplant recipients, UK
Longitudinal study of 40 ileal and colonic bowel effluent samples from adult small bowel transplant recipients in the United Kingdom, examining gut microbiome composition in relation to post-transplant bacterial infection. machine-written summary
40 samples · 40 runs · GB · Age unknown · 2023 · 0.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 280 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 40 sample values (health condition detail) |
| ✓ Full text | 120 sample values (health condition, location locality, location site) · PMC10936650 |
| ○ 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 transplant_or_immunocompromised · Small bowel transplantation, serial sampling before/after
“aspiration of ileal and colonic bowel effluents at transplantation” — abstract:38439546 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
5 of 5 people sampled more than once (40 samples; median 7, up to 12 per person). Schedule stated by the source: “Fecal/ileal/colonic effluent collected at transplant (day 0) and at follow-up endoscopies until death or up to 3 months post-transplant” (time origin: transplant); stated follow-up 3 mo.
Genera, mean relative abundance over 10 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 | 40 | 100% | ||||
| country | 40 | 100% | 40 | |||
| health_condition | 40 | 100% | 40 | |||
| subject_id | 40 | 100% | 40 | |||
| collection_date | 40 | 100% | 40 | |||
| detailed_location | 40 | 100% | ||||
| health_condition_detail | 40 | 100% | 40 | |||
| latitude | 40 | 100% | 40 | |||
| location_locality | 40 | 100% | 40 | |||
| location_region | 40 | 100% | 40 | |||
| location_site | 40 | 100% | 40 | |||
| longitude | 40 | 100% | 40 | |||
| timepoint_label | 40 | 100% | 40 |
- A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation. 2024 PMID 38439546 PMC10936650 own_data
Archive description
What is already known on this topic</p><p>Two-thirds of Small Bowel Transplantation recipients develop bacteremia post-transplantation. One-third die of sepsis, commonly with bacteria of gut origin, thought to translocate through the implanted organ. To improve patient outcomes, clinicians must predict and treat infection in a more timely manner.</p><p>What this study adds</p><p>Our metagenomic study showed that 4/5 patients had clinically significant infections thought to be of intestinal origin. In all cases, enteric pathogens had demonstrably colonized the gut between 1-10 days prior to invasive clinical infection.</p><p>How this study might affect research, practice, or policy</p><p>Fecal sampling in SBT patients could be a useful surveillance tool for impeding sepsis with specific gut bacteria. It would allow clinicians to predict organisms likely to cause infection and facilitate personalized antimicrobial prescribing.
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 run.scientific_name · “human gut metagenome”
- body site study.title · “gut microbiome composition”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36943301 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMN36943301 | country | GB | R1 | 0.90 | sample.attr.geo_loc_name | United Kingdom |
| SAMN36943301 | health_condition | transplant_or_immunocompromised | R3 | 0.70 | paper.fulltext.methods | five adult participants undergoing Small Bowel Transplantation |
| SAMN36943301 | health_condition_detail | Small bowel transplantation recipients | R4 | 0.50 | study.description | Small Bowel Transplantation recipients |
| SAMN36943301 | latitude | 52.1951 | R1 | 0.90 | biosample.attribute:lat_lon | 52.1951 N 0.1313 E |
| SAMN36943301 | location_locality | Cambridge | R3 | 0.70 | paper.fulltext.methods | Cambridge University Hospital NHS Foundation Trust, UK |
| SAMN36943301 | location_region | England | R1 | 0.60 | biosample.attribute:lat_lon | 52.1951 N 0.1313 E |
| SAMN36943301 | location_site | Cambridge University Hospital NHS Foundation Trust | R3 | 0.70 | paper.fulltext.methods | Cambridge University Hospital NHS Foundation Trust, UK |
| SAMN36943301 | longitude | 0.1313 | R1 | 0.90 | biosample.attribute:lat_lon | 52.1951 N 0.1313 E |
| SAMN36943301 | subject_id | 1 | R1 | 0.85 | biosample.attribute:description | description: 1 |
| SAMN36943301 | timepoint_label | 2 | R1 | 0.85 | sample.attr.timepoint | 2 |
Sequencing
40 runs over 40 samples · mean 1.06 Gbp per run (median 0.33 Gbp, total 42.55 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina NovaSeq 6000 (40) · 25% of runs with a Sandpiper profile · first public 2023-11-26
Authors (22)
Madhav A first · Bousfield R · Pereira-Dias J · Cormie C · Forrest S · Keane J · Kermack L · Higginson E · Dougan G · Spiers H · Massey D · Sharkey L · Rutter C · Woodward J · Russell N · Amin I · Butler A · Atkinson K · Dymond T · Bartholdson Scott J · Baker S · Gkrania-Klotsas E last
Downloads
PRJNA1004534.csv.gz (2.0 KB) · parquet (72.2 KB) — all 40 samples, every field with route and confidence · PRJNA1004534_determinations.csv.gz (3.2 KB) — 440 evidence rows