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PRJNA1007579 SRP458304

Gut microbiome time-series during 10-day complete fasting

FECAL Raw sequence reads

51 fecal samples from 13 adult volunteers undergoing a 10-day complete fasting intervention, tracked longitudinally to assess time-series changes in gut microbiome composition and diversity. machine-written summary

51 samples · 51 runs · CN · Adult · 2024 · 7.31 Gbp / sample

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Sources
✓Sequence archive 102○Abstract / description✓Full text 357○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 archive102 sample values (collection date, subject id)
○ Abstract / descriptionread; no usable statement
✓ Full text357 sample values (antibiotic exposure, country, health condition, health condition detail, location locality, location site, sex) · PMC11722564
○ 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

Controlled / prescribed diet or feeding regimen design single_arm_before_after · population healthy_control · 10-day complete fasting regimen in healthy male volunteers

“we performed a 10-day fasting experiment on 13 volunteers” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 country
Age
adult51
Condition
healthy_control51
Sex
male51
Country
CN51
Body site
primary51
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 %)all projects, 1–3 Gbp: 124,983 samples (22 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 51 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 7.31 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal

13 of 13 people sampled more than once (51 samples; median 4, up to 5 per person) · follow-up median 20 d (max 20 d) · median interval between samples 6 d (time from collection dates). Schedule stated by the source: “3-day baseline (BF), 10-day CF (fasting), 4-day calorie restriction (CR), 5-day full recovery (FR)” (time origin: intervention_start); stated follow-up 22 d.

replicate = biolreplicate = biological replicate 1: day 0replicate = biological replicate 1: day 6replicate = biological replicate 1: day 12replicate = biological replicate 1: day 16replicate = biological replicate 1: day 20replicate = biolreplicate = biological replicate 10: day 0replicate = biological replicate 10: day 16replicate = biological replicate 10: day 20replicate = biolreplicate = biological replicate 11: day 0replicate = biological replicate 11: day 16replicate = biological replicate 11: day 20replicate = biolreplicate = biological replicate 12: day 0replicate = biological replicate 12: day 16replicate = biological replicate 12: day 20replicate = biolreplicate = biological replicate 13: day 0replicate = biological replicate 13: day 20replicate = biolreplicate = biological replicate 2: day 0replicate = biological replicate 2: day 6replicate = biological replicate 2: day 12replicate = biological replicate 2: day 16replicate = biological replicate 2: day 20replicate = biolreplicate = biological replicate 3: day 0replicate = biological replicate 3: day 6replicate = biological replicate 3: day 12replicate = biological replicate 3: day 16replicate = biological replicate 3: day 20replicate = biolreplicate = biological replicate 4: day 0replicate = biological replicate 4: day 6replicate = biological replicate 4: day 12replicate = biological replicate 4: day 16replicate = biological replicate 4: day 20replicate = biolreplicate = biological replicate 5: day 0replicate = biological replicate 5: day 6replicate = biological replicate 5: day 12replicate = biological replicate 5: day 16replicate = biological replicate 5: day 20replicate = biolreplicate = biological replicate 6: day 0replicate = biological replicate 6: day 6replicate = biological replicate 6: day 12replicate = biological replicate 6: day 16replicate = biological replicate 6: day 20replicate = biolreplicate = biological replicate 7: day 0replicate = biological replicate 7: day 6replicate = biological replicate 7: day 16replicate = biological replicate 7: day 20replicate = biolreplicate = biological replicate 8: day 0replicate = biological replicate 8: day 16replicate = biological replicate 8: day 20replicate = biolreplicate = biological replicate 9: day 0replicate = biological replicate 9: day 16replicate = biological replicate 9: day 200 d5 d10 d15 d20 d

Each row is one person (13 shown); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 13.3%Phocaeicola 12.4%Megamonas 5.4%Roseburia 5.0%Faecalibacterium 4.6%Enterocloster 4.5%Escherichia 4.1%Prevotella 3.1%Alistipes 2.6%Vescimonas 2.4%Acetatifactor 2.1%Phascolarctobacterium 1.9%not assigned to a genus 3.9%other genera 34.6%

Genera, mean relative abundance over 47 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category51 100%
country51 100%51
health_condition51 100%51
subject_id51 100%51
antibiotic_exposure51 100%51
collection_date51 100%51
detailed_location51 100%
health_condition_detail51 100%51
location_locality51 100%51
location_site51 100%51
sex51 100%51
Papers (1)
  • Effects of Long-Term Fasting on Gut Microbiota, Serum Metabolome, and Their Association in Male Adults. 2024 PMID 39796469 PMC11722564 own_data
Details
Archive description

we performed a 10-day fasting experiment on 13 volunteers and tracked time-series fluctuations in the fecal microbiome using metagenomic sequencing.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.title · “FECAL Raw sequence reads”
  • body site study.description · “fecal microbiome using metagenomic sequencing”
  • life stage study.description · “10-day fasting experiment on 13 volunteers”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN37073027antibiotic_exposurenoR30.70paper.fulltext.methodsantibiotic use within 3 months
SAMN37073027collection_date2018-05-16R10.90biosample.attribute:collection_date2018-05-16
SAMN37073027countryCNR30.70paper.fulltext.methodscame from 8 different provinces in China
SAMN37073027health_conditionhealthy_controlR30.70paper.fulltext.methods10-day water-only CF under medical supervision
SAMN37073027health_condition_detail10-day water-only complete fasting (CF) experimentR30.70paper.fulltext.methods10-day water-only CF under medical supervision
SAMN37073027location_localityShenzhenR30.70paper.fulltext.methodsreviewed during a complete medical examination at Longgang Center Hospital, Shenzhen
SAMN37073027location_siteLonggang Center HospitalR30.70paper.fulltext.methodscomplete medical examination at Longgang Center Hospital, Shenzhen, China
SAMN37073027sexmaleR30.70paper.fulltext.methodsThirteen male adults were enrolled to participate
SAMN37073027subject_idreplicate = biological replicate 1R10.85biosample.attribute:replicatereplicate: replicate = biological replicate 1
Sequencing

51 runs over 51 samples · mean 7.27 Gbp per run (median 7.31 Gbp, total 370.79 Gbp; 51 runs with a base count) · layout PAIRED 51 · platform ILLUMINA 51 · models Illumina HiSeq 1500 (51) · 92% of runs with a Sandpiper profile · first public 2024-09-24

Authors (15)

Wu F first · Guo Y · Wang Y · Sui X · Wang H · Zhang H · Xin B · Yang C · Zhang C · Jiang S · Qu L · Feng Q · Dai Z · Shi C · Li Y last

Downloads

PRJNA1007579.csv.gz (2.3 KB) · parquet (72.3 KB) — all 51 samples, every field with route and confidence · PRJNA1007579_determinations.csv.gz (3.4 KB) — 459 evidence rows

Samples (51 · every field this project has values for · hover a cell for its source)
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