Gut and salivary microbiota during FOS supplementation, Japan
66 fecal and salivary samples from healthy Japanese adults, studied before, during, and after fructooligosaccharide (prebiotic fibre) supplementation, using 16S rRNA amplicon sequencing and fecal shotgun metagenomics in an intervention design. machine-written summary
66 samples · 66 runs · JP · Adult · 2024 · 7.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 462 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 66 sample values (health condition) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
Prebiotic / dietary fibre supplement design single_arm_before_after · population healthy_control · Fructooligosaccharide (FOS) supplementation, before/during/after
“before, during, and after fructooligosaccharide supplementation” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
11 of 11 people sampled more than once (66 samples; median 6, up to 6 per person) · follow-up median 2 mo (max 2 mo) · median interval between samples 14 d (time from collection dates). Schedule stated by the source: “Fecal/saliva samples per subject at weeks 0,1,3,5,7,9 before/during/after FOS supplementation (per sample_title tokens)” (time origin: intervention_start).
Each row is one person (11 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 55 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 | 66 | 100% | ||||
| country | 66 | 100% | 66 | |||
| health_condition | 66 | 100% | 66 | |||
| subject_id | 66 | 100% | 66 | |||
| collection_date | 66 | 100% | 66 | |||
| detailed_location | 66 | 100% | ||||
| latitude | 66 | 100% | 66 | |||
| location_region | 66 | 100% | 66 | |||
| longitude | 66 | 100% | 66 | |||
| timepoint_label | 66 | 100% | 66 |
Archive description
Feces and salivary samples were collected from 11 healthy Japanese adults. The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and multiplexed amplicon pyrosequencing was carried out using Roche 454 GS FLX Titanium or 454 GS JUNIOR sequencing system. Whole metagenomic shotgun sequencing was performed for fecal samples using Illumina NovaSeq 6000 S4 flow cell (2 Ã 150bp).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “11 healthy Japanese adults”
- body site study.description · “shotgun sequencing was performed for fecal samples”
- life stage study.description · “11 healthy Japanese adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00524100 | collection_date | 2014-11-05 | R1 | 0.90 | biosample.attribute:collection_date | 2014-11-05 |
| SAMD00524100 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00524100 | health_condition | healthy_control | R4 | 0.50 | study.description | 11 healthy Japanese adults |
| SAMD00524100 | latitude | 35.4800 | R1 | 0.90 | biosample.attribute:lat_lon | 35.48 N 139.68 E |
| SAMD00524100 | location_region | Kanagawa | R1 | 0.60 | biosample.attribute:lat_lon | 35.48 N 139.68 E |
| SAMD00524100 | longitude | 139.6800 | R1 | 0.90 | biosample.attribute:lat_lon | 35.48 N 139.68 E |
| SAMD00524100 | subject_id | F001 | R1 | 0.70 | sample.name_rule:title | JAXA-F001-0W |
| SAMD00524100 | timepoint_label | week 0 | R1 | 0.70 | sample.name_rule:title | JAXA-F001-0W |
Sequencing
66 runs over 66 samples · mean 7.96 Gbp per run (median 7.27 Gbp, total 525.30 Gbp; 66 runs with a base count) · layout PAIRED 66 · platform ILLUMINA 66 · models Illumina NovaSeq 6000 (66) · 83% of runs with a Sandpiper profile · first public 2024-01-05
Authors (0)
No author record.
Downloads
PRJDB14273.csv.gz (2.7 KB) · parquet (72.8 KB) — all 66 samples, every field with route and confidence · PRJDB14273_determinations.csv.gz (4.2 KB) — 528 evidence rows