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PRJNA529487 SRP189794

Ketogenic diet and gut microbiome in obese adults, USA

Ketogenic diet and the gut microbiome

34 samples from obese adults across four US sites (NIDDK, CUMC, PBRC, TRI), studying gut microbiome shifts during baseline vs. ketogenic diet in a crossover intervention design. machine-written summary

34 samples · 34 runs · US · Adult · 2019 · 6.71 Gbp / sample

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Sources
✓Sequence archive 296○Abstract / description○Full text○Supplementary tables✓External resources 68–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive296 sample values (collection date, country, diet, diet detail, intervention, intervention detail, latitude, location region)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC12199706, PMC7293577, PMC8038126
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources68 sample values (health condition, health condition detail) · from BugSigDB
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention · arms resolved

no interventionwashoutdiet17 people
crossover: arm sequences observed per person

Controlled / prescribed diet or feeding regimen design crossover · population healthy_control · Ketogenic diet vs baseline diet, crossover

“baseline diet (BD) and ketogenic diet (KD) in crossover study” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
4 sampling locations · 1 country
Age
adult34
Condition
obesity34
Country
US34
Body site
primary34
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 3 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 23 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 8 samplesall 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 6.71 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

17 of 17 people sampled more than once (34 samples; median 2, up to 2 per person) · follow-up median 28 d (max 35 d) · median interval between samples 28 d (time from collection dates). Schedule stated by the source: “stool samples collected during baseline diet (BD) and ketogenic diet (KD) in a crossover study over an 8-week inpatient study” (time origin: intervention start); stated follow-up 56 d.

01-00301-003: day 001-003: day 2801-00401-004: day 001-004: day 2801-00501-005: day 001-005: day 2801-00601-006: day 001-006: day 2801-00801-008: day 001-008: day 2802-00102-001: day 002-001: day 3302-00402-004: day 002-004: day 2802-00502-005: day 002-005: day 2802-00902-009: day 002-009: day 2803-00203-002: day 003-002: day 2803-00803-008: day 003-008: day 2803-00903-009: day 003-009: day 2803-01003-010: day 003-010: day 2704-00604-006: day 004-006: day 2804-00704-007: day 004-007: day 3504-01104-011: day 004-011: day 2804-01204-012: day 004-012: day 270 d9 d18 d26 d35 d

Each row is one person (17 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Phocaeicola 16.3%Bacteroides 12.1%Alistipes 6.6%Faecalibacterium 4.8%Prevotella 4.6%Acetatifactor 3.4%Lachnospira 2.3%Blautia_A 2.3%Parabacteroides 1.9%Bifidobacterium 1.8%Vescimonas 1.6%Roseburia 1.6%not assigned to a genus 9.2%other genera 31.5%

Genera, mean relative abundance over 28 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category34 100%
country34 100%34
health_condition34 100%34
subject_id34 100%34
collection_date34 100%34
health_condition_detail34 100%34
intervention34 100%34
intervention_detail34 100%34
latitude34 100%34
longitude34 100%34
diet17 50%17
diet_detail17 50%17
detailed_location16 47%
location_region16 47%16
location_site8 24%8
Papers (3)
  • Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells. 2020 PMID 32437658 PMC7293577 own_data
  • Diet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome. 2021 PMID 33915727 PMC8038126 unsure
  • Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp. 2025 PMID 40569694 PMC12199706 unsure
Details
Archive description

Metagenomic shotgun and V4 16S rRNA amplicon sequencing of human gut communities during the baseline diet (BD) and ketogenic diet (KD) in crossover study.</p><p>V4 16S rRNA amplicon sequencing of mouse gut communities studying the impact of the ketogenic diet and ketogenesis on the gut microbiome and immune responses.

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.title · “diet and the gut microbiome”
  • body site study.description · “sequencing of human gut communities during the”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN11268238collection_date2014-03-16R10.90biosample.attribute:collection_date2014-03-16
SAMN11268238countryUSR10.90sample.attr.geo_loc_nameUSA: NIDDK
SAMN11268239dietlow_carbohydrate_or_ketogenicR10.85biosample.attribute:host_diethost_diet: KD
SAMN11268239diet_detailhost_diet: KDR10.85biosample.attribute:host_diethost_diet: KD
SAMN11268238health_conditionobesityR20.60external.bugsigdb sourceOverweight/Obese Men on Baseline Diet (BD)
SAMN11268238health_condition_detailResponse to ketogenic dietR20.60external.bugsigdb sourceCondition: Response to ketogenic diet
SAMN11268238interventionno_interventionR10.80biosample.attribute:host_diethost_diet: BD
SAMN11268238intervention_detailBaseline (habitual) diet before ketogenic dietR10.80biosample.attribute:host_diethost_diet: BD
SAMN11268238latitude39.0000R10.90biosample.attribute:lat_lon39.00 N 77.10 W
SAMN11268256location_regionFloridaR10.60biosample.attribute:lat_lon28.57 N 81.37 W
SAMN11268264location_siteCUMCR10.85biosample.attribute:geo_loc_nameUSA: CUMC
SAMN11268238longitude-77.1000R10.90biosample.attribute:lat_lon39.00 N 77.10 W
SAMN11268238subject_id01-003R10.85sample.attr.host_subject_id01-003
Sequencing

34 runs over 34 samples · mean 7.17 Gbp per run (median 6.71 Gbp, total 243.78 Gbp; 34 runs with a base count) · layout PAIRED 34 · platform ILLUMINA 34 · models Illumina NovaSeq 6000 (26), Illumina HiSeq 2500 (8) · 82% of runs with a Sandpiper profile · first public 2019-04-06

Authors (27)

Ang QY first · Alexander M · Newman JC · Tian Y · Cai J · Upadhyay V · Turnbaugh JA · Verdin E · Hall KD · Leibel RL · Ravussin E · Rosenbaum M · Patterson AD · Turnbaugh PJ last · Jia B first · Park D · Chun BH · Hahn Y · Jeon CO last · Kasmanas JC first · Magnúsdóttir S · Zhang J · Smalla K · Schloter M · Stadler PF · de Leon Ferreira de Carvalho ACP · Rocha U last

Downloads

PRJNA529487.csv.gz (2.2 KB) · parquet (72.8 KB) — all 34 samples, every field with route and confidence · PRJNA529487_determinations.csv.gz (3.6 KB) — 364 evidence rows

Samples (34 · every field this project has values for · hover a cell for its source)
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