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PRJNA854889 SRP384524

SCD vs Mediterranean diet RCT in adults with Crohn's disease

A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults With Crohn's Disease

339 gut metagenome samples from adults with Crohn's disease in the USA, from a randomized trial comparing the Specific Carbohydrate Diet to a Mediterranean diet over 12 weeks. machine-written summary

339 samples · 339 runs · US · Adult · 2024 · 1.92 Gbp / sample

Sources
✓Sequence archive 4,041○Abstract / description✓Full text 366–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 archive4,041 sample values (collection date, country, diet, diet detail, health condition, intervention, intervention detail, latitude)
○ Abstract / descriptionread; no usable statement
✓ Full text366 sample values (health condition, health condition detail) · PMC8396394
– Supplementary tablesno supplementary tables available (or none open access)
– 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

Controlled / prescribed diet or feeding regimen design randomized_controlled_trial · population crohns_disease · Specific Carbohydrate Diet vs Mediterranean Diet, 12 weeks

“randomly assigned 1:1 to consume the MD or SCD for 12 weeks” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult339
Condition
crohns_disease339
Country
US339
Body site
primary339
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 20 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 1 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 2 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: 299 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 6 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 1.92 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

116 of 127 people sampled more than once (302 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 42 d (time from timepoint labels).

1023725010237250: day 010237250: day 4210237250: day 841023875710238757: day 010238757: day 4210238757: day 841024025310240253: day 010240253: day 4210240253: day 841125015111250151: day 011250151: day 4211250151: day 841125045511250455: day 011250455: day 4211250455: day 841125060311250603: day 011250603: day 4211250603: day 841125090311250903: day 011250903: day 4211250903: day 841329515513295155: day 013295155: day 4213295155: day 841329545813295458: day 013295458: day 4213295458: day 841329590313295903: day 013295903: day 4213295903: day 841329635013296350: day 013296350: day 4213296350: day 841329680413296804: day 013296804: day 4213296804: day 841735590117355901: day 017355901: day 4217355901: day 841938530219385302: day 019385302: day 4219385302: day 841938620419386204: day 019386204: day 4219386204: day 841938785119387851: day 019387851: day 4219387851: day 841938815519388155: day 019388155: day 4219388155: day 841938860519388605: day 019388605: day 4219388605: day 841938875619388756: day 019388756: day 4219388756: day 841938920519389205: day 019389205: day 4219389205: day 841938950519389505: day 019389505: day 4219389505: day 842040360220403602: day 020403602: day 4220403602: day 842141515221415152: day 021415152: day 4221415152: day 842141590821415908: day 021415908: day 4221415908: day 842141635421416354: day 021416354: day 4221416354: day 842141665021416650: day 021416650: day 4221416650: day 842141695521416955: day 021416955: day 4221416955: day 842243015422430154: day 022430154: day 4222430154: day 842243135622431356: day 022431356: day 4222431356: day 842243150622431506: day 022431506: day 4222431506: day 842243195822431958: day 022431958: day 4222431958: day 842446090624460906: day 024460906: day 4224460906: day 842852150028521500: day 028521500: day 4228521500: day 842953695529536955: day 029536955: day 4229536955: day 843156605831566058: day 031566058: day 4231566058: day 843258105432581054: day 032581054: day 4232581054: day 840 d21 d42 d2 mo3 mo

Each row is one person (36 shown of 116); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 19.6%Phocaeicola 15.0%Alistipes 4.7%Faecalibacterium 3.5%Roseburia 3.4%Enterocloster 3.2%Escherichia 3.2%Parabacteroides 2.9%Prevotella 2.7%Vibrio 2.1%Lachnospira 2.1%Blautia_A 2.0%not assigned to a genus 7.1%other genera 28.4%

Genera, mean relative abundance over 279 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category339 100%
country339 100%339
health_condition339 100%31227
subject_id313 92%313
collection_date339 100%339
detailed_location339 100%
health_condition_detail339 100%339
latitude339 100%339
location_region339 100%339
longitude339 100%339
diet313 92%313
diet_detail313 92%313
intervention313 92%313
intervention_detail313 92%313
timepoint_label313 92%313
medication156 46%156
Papers (1)
  • A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults With Crohn's Disease. 2021 PMID 34052278 PMC8396394 own_data
Details
Archive description

This study compared the effectiveness of the Specific Carbohydrate Diet (SCD) to the Mediterranean diet (MD) as treatment for Crohn's disease (CD) with mild to moderate symptoms. Adult patients with CD and with mild-to-moderate symptoms were randomly assigned 1:1 to consume the MD or SCD for 12 weeks. For the first 6 weeks, participants received prepared meals and snacks according to their assigned diet. After 6 weeks, participants were instructed to follow the diet independently. The primary outcome was symptomatic remission at week 6. Key secondary outcomes at week 6 included fecal calprotectin (FC) response (FC <250 g/g and reduction by >50% among those with baseline FC >250 g/g) and C-reactive protein (CRP) response (high-sensitivity CRP <5 mg/L and >50% reduction from baseline among those with high-sensitivity CRP >5 mg/L). The study randomized 194 patients, and 191 were included in the efficacy analyses. The percentage of participants who achieved symptomatic remission at week 6 was not superior with the SCD (SCD, 46.5% MD, 43.5% P = .77). FC response was achieved in 8 of 23 participants (34.8%) with the SCD and in 4 of 13 participants (30.8%) with the MD (P = .83). CRP response was achieved in 2 of 37 participants (5.4%) with the SCD and in 1 of 28 participants (3.6%) with the MD (P = .68). The SCD was not superior to the MD to achieve symptomatic remission, FC response, and CRP response. CRP response was uncommon. Given these results, the greater ease of following the MD and other health benefits associated with the MD, the MD may be preferred to the SCD for most patients with CD with mild to moderate symptoms. ClinicalTrials.gov Identifier: NCT03058679

How this project entered the registry

Classified as human gut / stool 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.description · “week 6 included fecal calprotectin (FC) response”
  • body site external_curation.infant_catalog · “body_site_call gut”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage study.title · “Mediterranean Diet in Adults With Crohn's Disease”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN29470759collection_date2017R10.90biosample.attribute:collection_date2017
SAMN29470759countryUSR10.90sample.attr.geo_loc_nameUSA
SAMN29470759diettherapeutic_or_study_dietR10.90biosample.attribute:dietSCD
SAMN29470759diet_detailSCDR10.90biosample.attribute:dietSCD
SAMN29470759health_conditioncrohns_diseaseR10.70biosample_attrIleum alone
SAMN29470916health_conditioncrohns_diseaseR30.70paper.abstractAdult patients with CD and with mild-moderate symptoms were randomly assigned 1:1
SAMN29470759health_condition_detailCrohn's disease (CD)R30.70paper.abstractAdult patients with CD and with mild-moderate symptoms were randomly assigned 1:1
SAMN29470759interventiondiet_interventionR10.80biosample.attribute:DietDiet: SCD
SAMN29470759intervention_detailSpecific Carbohydrate DietR10.80biosample.attribute:DietDiet: SCD
SAMN29470759latitude39.9473R10.90biosample.attribute:lat_lon39.9473 N 75.1958 W
SAMN29470759location_regionPennsylvaniaR10.60biosample.attribute:lat_lon39.9473 N 75.1958 W
SAMN29470759longitude-75.1958R10.90biosample.attribute:lat_lon39.9473 N 75.1958 W
SAMN29470762medicationimmunosuppressant_or_biologicR10.85biosample.attribute:biologic_at_baseline1
SAMN29470759subject_id10237250R10.85sample.attr.subjectid10237250
SAMN29470759timepoint_labelW0R10.85sample.attr.study_weekW0
Sequencing

339 runs over 339 samples · mean 1.84 Gbp per run (median 1.92 Gbp, total 622.81 Gbp; 339 runs with a base count) · layout PAIRED 339 · platform ILLUMINA 339 · models Illumina HiSeq 2500 (339) · 82% of runs with a Sandpiper profile · first public 2024-06-30

Authors (0)

No author record.

Downloads

PRJNA854889.csv.gz (10.7 KB) · parquet (85.2 KB) — all 339 samples, every field with route and confidence · PRJNA854889_determinations.csv.gz (29.6 KB) — 4,407 evidence rows

Samples (339 · every field this project has values for · hover a cell for its source)
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