Gut metagenomics of resistant starch intervention in adults
97 fecal samples from healthy adults, part of a crossover intervention study comparing high- and low-dose type 2 resistant starch (RS2) supplementation, analyzed via pathway-based metagenomics. machine-written summary
97 samples · 97 runs · Adult · 2018 · 1.21 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 97 sample values (subject id) |
| ✓ Abstract / description | 97 sample values (health condition) |
| – Full text | no open-access full text linked · PMC6238065 |
| – 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 crossover · population healthy_control · Resistant starch type 2 (RS2), 48g vs 3g/2500kcal daily, 2 weeks, crossover
“high and low doses of type-2 RS” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
24 of 24 people sampled more than once (97 samples; median 4, up to 5 per person).
Genera, mean relative abundance over 88 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 | 97 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 97 | 100% | 97 | |||
| subject_id | 97 | 100% | 97 |
- Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota. 2018 PMID 30266729 PMC6238065 own_data
Archive description
Several studies monitoring alterations of the community structure upon resistant starch (RS) interventions are available, although comprehensive function-based analyses are lacking. Recently, a multiomics approach based on 16S rRNA gene-sequencing, metaproteomics and metabolomics on fecal samples from individuals subjected to high and low doses of type-2 RS (RS2 48 g and 3 g/2500 kcal, respectively, daily for 2 weeks) in a cross-over intervention experiment was performed. In the present study, we did pathway-based metagenomic analyses on samples from a subset of individuals (n=12) from that study to get additional, detailed insights into the functional structure at high resolution during RS2 intervention. A mechanistic framework based on obtained results is proposed where primary degradation was governed by Firmicutes, primarily via the keystone degrader Ruminococcus bromii providing fermentation substrates and increased acetate concentrations for growth of various major butyrate-producers exhibiting the enzyme butyryl-CoA:acetate CoA-transferase. H2-scavenging sulfite reducers and acetogens concurrently increased. Augmented fermentation products lowered the pH, further favoring Firmicutes including butyrate producers at the expense of pH-sensitive gram-negative bacteria, in particular Bacteroides. Individual responses of gut microbiota were noted where seven of the 12 participants displayed all features of the outlined pattern, whereas four individuals showed mixed behavior and one subject was unresponsive. Intervention order did not affect the outcome emphasizing a constant substrate supply for maintaining specific functional communities.
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 · “degradation by human gut microbiota”
- body site study.description · “and metabolomics on fecal samples from individuals”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA1100185 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | individuals subjected to high and low doses of type 2 RS |
| SAMEA1100185 | subject_id | 101 | R1 | 0.70 | sample.name_rule:title | 101_001 |
Sequencing
97 runs over 97 samples · mean 1.07 Gbp per run (median 1.21 Gbp, total 103.65 Gbp; 97 runs with a base count) · layout PAIRED 97 · platform ILLUMINA 97 · models Illumina HiSeq 2000 (97) · 91% of runs with a Sandpiper profile · first public 2018-04-11
Authors (6)
Vital M first · Howe A · Bergeron N · Krauss RM · Jansson JK · Tiedje JM last
Downloads
PRJEB25954.csv.gz (2.0 KB) · parquet (71.1 KB) — all 97 samples, every field with route and confidence · PRJEB25954_determinations.csv.gz (2.0 KB) — 194 evidence rows