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PRJEB50260 ERP134822

HBOT adjunct therapy in hospitalized UC patients, San Diego

Hyperbaric Oxygen Therapy for Ulcerative Colitis

84 samples from hospitalized ulcerative colitis patients (adults and elderly) in San Diego, CA, USA, studying hyperbaric oxygen therapy as an adjunct intervention to standard treatment. machine-written summary

84 samples · 84 runs · US · Adult · 2022 · 52.7 Mbp / sample

Sources
✓Sequence archive 1,013✓Abstract / description 44○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 archive1,013 sample values (age, collection date, country, health condition, health condition detail, intervention, intervention detail, latitude)
✓ Abstract / description44 sample values (health condition, health condition detail)
○ Full textread; no usable statement or table · PMC9117812
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

Other administered intervention (see intervention_detail) design single_arm_before_after · population ulcerative_colitis · Hyperbaric oxygen therapy as adjunct to steroids for UC flares

“hyperbaric oxygen therapy (HBOT) as an adjunct” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult82
elderly2
Condition
ulcerative_colitis84
Sex
female29
male29
Country
US84
Body site
primary62
unknown22
Collected 2017–2020
2017: 34 samples2018: 3 samples2019: 24 samples2020: 22 samples20172020
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 40 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 5 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 12 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 11 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 12 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 4 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 0.05 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

22 of 49 people sampled more than once (57 samples; median 2, up to 4 per person) · follow-up median 9 d (max 12 mo) · median interval between samples 5 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Stool collected at baseline (day0/day1) and follow-up days 3, 5, and 10 during hospitalization for UC flare.”; stated follow-up 10 d.

DHMC-001DHMC-001: day 0DHMC-001: day 9DHMC-006DHMC-006: day 0DHMC-006: day 9DHMC-007DHMC-007: day 0DHMC-007: day 9DHMC-008DHMC-008: day 0DHMC-008: day 9DHMC-009DHMC-009: day 0DHMC-009: day 9DHMC-010DHMC-010: day 0DHMC-010: day 9DHMC-011DHMC-011: day 0DHMC-011: day 9DHMC-012DHMC-012: day 0DHMC-012: day 9DHMC-013DHMC-013: day 0DHMC-013: day 9DHMC-014DHMC-014: day 0DHMC-014: day 2DHMC-014: day 4DHMC-014: day 10DHMC-015DHMC-015: day 0DHMC-015: day 2DHMC-016DHMC-016: day 0DHMC-016: day 2DHMC-016: day 4DHMC-017DHMC-017: day 0DHMC-017: day 2DHMC-017: day 4DHMC-017: day 9DHMC-019DHMC-019: day 0DHMC-019: day 2DHMC-019: day 4DHMC-019: day 9DHMC-020DHMC-020: day 0DHMC-020: day 3DHMC-020: day 5DHMC-020: day 10DHMC-021DHMC-021: day 0DHMC-021: day 12DHMC-021: day 14Mayo1Mayo1: day 0Mayo1: day 9Mayo3Mayo3: day 0Mayo3: day 9Mayo6Mayo6: day 0Mayo6: day 2Mayo6: day 379Mayo7Mayo7: day 0Mayo7: day 2Mayo7: day 4Mayo7: day 8UPMC2UPMC2: day 0UPMC2: day 9UTSW1UTSW1: day 0UTSW1: day 3690 d3 mo6 mo9 mo12 mo

Each row is one person (22 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Prevotella 18.4%Bacteroides 11.5%Phocaeicola 10.4%Ruthenibacterium 8.0%Faecalibacterium 6.1%Eisenbergiella 5.4%Dialister 4.5%Caccovicinus 2.3%Roseburia 2.2%Alistipes 1.9%Mediterraneibacter 1.8%Collinsella 1.8%not assigned to a genus 5.2%other genera 20.5%

Genera, mean relative abundance over 4 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category84 100%
country84 100%84
health_condition84 100%6222
subject_id84 100%84
detailed_location84 100%
health_condition_detail84 100%6222
latitude84 100%84
location_locality84 100%84
location_region84 100%84
longitude84 100%84
collection_date83 99%83
age_at_collection_days62 74%62
intervention62 74%62
intervention_detail62 74%62
sex58 69%58
timepoint_label58 69%58
Papers (2)
  • The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients. 2022 PMID 35378331 PMC9117812 own_data
  • Ulcerative Colitis Host-Microbiome Response to Hyperbaric Oxygen Therapy 2022 own_data
Details
Archive description

Hyperbaric oxygen therapy (HBOT) markedly increases tissue oxygen delivery. Case series suggest it may have a potential therapeutic benefit in ulcerative colitis (UC). We investigated the therapeutic potential of HBOT as an adjunct to steroids for UC flares requiring hospitalization. Ulcerative colitis (UC) is a chronic inflammatory bowel disease which significantly affects the lives of nearly 1 million Americans. It is estimated that 25% of patients will need hospitalization for acute moderate to severe flares. Although colectomy is curative, it can be associated with significant morbidity, mortality and a reduction in quality of life. The mainstay of medical therapy for these patients is high dose intravenous steroids but approximately one-third of patients will be refractory and require second line rescue therapy with either cyclosporine or Infliximab, both of which are associated with a lack of significant efficacy in maintaining remission over the long term. Furthermore, corticosteroids have considerable long-term consequences and these immune suppressive drugs are associated with life-threatening infections and lymphomas. In an attempt to address this gap, we investigated the potential application of hyperbaric oxygen therapy (HBOT) as an adjunct to standard medical treatment. In a small phase 2A pilot study of 18 hospitalized UC patients, we were able to demonstrate a statistically significant increase in response, remission, and trend towards significance for avoidance of colectomy. We are now preparing for a phase 2B study in anticipation of a phase 3 registration trial and a multi-PI R01

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 external_curation.infant_catalog · “body_site_call gut”
  • body site study.description · “(HBOT) markedly increases tissue oxygen delivery. Case”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA12363447age_at_collection_days10957.5R10.90sample.attr.host_age30
SAMEA12363447collection_date2017R10.85biosample.attribute:collection_timestamp2017
SAMEA12363447countryUSR10.90sample.attr.geo_loc_nameUSA:CA:San Diego
SAMEA12363447health_conditionulcerative_colitisR10.90biosample_attrulcerative colitis
SAMEA12363551health_conditionulcerative_colitisR40.50paper.abstractHBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients
SAMEA12363447health_condition_detailulcerative colitisR10.90sample.attr.diseaseulcerative colitis
SAMEA12363551health_condition_detailUC patientsR40.50paper.abstractHBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients
SAMEA12363447interventionplaceboR10.90biosample.attribute:treatment_grouptreatment_group: sham
SAMEA12363447intervention_detailsham HBOT placebo armR10.90biosample.attribute:treatment_grouptreatment_group: sham
SAMEA12363447latitude32.8420R10.90biosample.attribute:latitude+longitude32.842 -117.258
SAMEA12363447location_localitySan DiegoR10.85biosample.attribute:geo_loc_nameUSA:CA:San Diego
SAMEA12363447location_regionCaliforniaR10.75biosample.attribute:geo_loc_nameUSA:CA:San Diego
SAMEA12363447longitude-117.2580R10.90biosample.attribute:latitude+longitude32.842 -117.258
SAMEA12363447sexmaleR10.90sample.attr.sexmale
SAMEA12363447subject_idUPMC2R10.85sample.attr.host_subject_idUPMC2
SAMEA12363447timepoint_label1R10.85sample.attr.day1
Sequencing

84 runs over 84 samples · mean 0.54 Gbp per run (median 52.7 Mbp, total 45.63 Gbp; 84 runs with a base count) · layout PAIRED 84 · platform ILLUMINA 84 · models Illumina NovaSeq 6000 (84) · 5% of runs with a Sandpiper profile · first public 2022-01-19

Authors (0)

No author record.

Downloads

PRJEB50260.csv.gz (3.7 KB) · parquet (75.9 KB) — all 84 samples, every field with route and confidence · PRJEB50260_determinations.csv.gz (8.1 KB) — 1,057 evidence rows

Samples (84 · every field this project has values for · hover a cell for its source)
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