In vitro fecal fermentation of sorghum arabinoxylans, USA
8 samples from an in vitro sequential batch fecal fermentation (West Lafayette, Indiana, USA) using healthy-donor fecal inocula, comparing two sorghum arabinoxylan fibers (RSAX vs WSAX) to study gut microbial community assembly and metabolism. machine-written summary
8 samples · 8 runs · US · Age unknown · 2022 · 32.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 72 sample values (collection date, country, intervention, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 32 sample values (antibiotic exposure, health condition, health condition detail, location site) · PMC13358863 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
Prebiotic / dietary fibre supplement · In vitro fecal fermentation with sorghum arabinoxylan fibers (RSAX/WSAX)
“in vitro sequential batch fecal fermentation with four fecal inocula” — abstract:37321733 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
4 of 4 people sampled more than once (8 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 7 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 | 8 | 100% | ||||
| country | 8 | 100% | 8 | |||
| health_condition | 8 | 100% | 8 | |||
| subject_id | 8 | 100% | 8 | |||
| antibiotic_exposure | 8 | 100% | 8 | |||
| collection_date | 8 | 100% | 8 | |||
| detailed_location | 8 | 100% | ||||
| health_condition_detail | 8 | 100% | 8 | |||
| intervention | 8 | 100% | 8 | |||
| latitude | 8 | 100% | 8 | |||
| location_locality | 8 | 100% | 8 | |||
| location_region | 8 | 100% | 8 | |||
| location_site | 8 | 100% | 8 | |||
| longitude | 8 | 100% | 8 | |||
| timepoint_label | 8 | 100% | 8 |
- Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota. 2023 PMID 37321733 PMC13358863 own_data
Archive description
Dietary fibers are well known to regulate gut microbiome composition and metabolic function however, to what extent the impact of complex polysaccharide structures can shape the community assembly is still unclear. This study investigated subtle chemical structure differences in two sorghum arabinoxylans and how such difference modulates the human gut microbiome, emphasizing on community assembly, microbial division of labor, and organismal metabolic responses across individuals microbiome structures.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host study.title · “Human gut microbial consortia”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30154934 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | had not received any antibiotic treatment within three months |
| SAMN30154934 | collection_date | 2020-01 | R1 | 0.90 | biosample.attribute:collection_date | 2020-01 |
| SAMN30154934 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Indiana, West Lafayette |
| SAMN30154934 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Human fecal samples were collected fresh from three healthy donors |
| SAMN30154934 | health_condition_detail | healthy stool donors for fecal fermentation | R3 | 0.60 | paper.fulltext.methods | Human fecal samples were collected fresh from three healthy donors |
| SAMN30154934 | intervention | prebiotic_or_fibre | R1 | 0.70 | sample.name_rule:attr_source_material_id | donor1-day7-meta-w |
| SAMN30154934 | latitude | 40.4200 | R1 | 0.90 | biosample.attribute:lat_lon | 40.42 N 86.92 W |
| SAMN30154934 | location_locality | West Lafayette | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Indiana, West Lafayette |
| SAMN30154934 | location_region | Indiana | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Indiana, West Lafayette |
| SAMN30154934 | location_site | Purdue University | R3 | 0.70 | paper.fulltext.methods | Institutional Review Board of Purdue University |
| SAMN30154934 | longitude | -86.9200 | R1 | 0.90 | biosample.attribute:lat_lon | 40.42 N 86.92 W |
| SAMN30154934 | subject_id | donor1 | R1 | 0.70 | sample.name_rule:attr_source_material_id | donor1-day7-meta-w |
| SAMN30154934 | timepoint_label | day7 | R1 | 0.70 | sample.name_rule:attr_source_material_id | donor1-day7-meta-w |
Sequencing
8 runs over 8 samples · mean 35.47 Gbp per run (median 32.08 Gbp, total 283.75 Gbp; 8 runs with a base count) · layout PAIRED 8 · platform ILLUMINA 8 · models Illumina NovaSeq 6000 (8) · 88% of runs with a Sandpiper profile · first public 2022-08-11 – 2022-08-14
Authors (6)
Yao T first · Deemer DG · Chen MH · Reuhs BL · Hamaker BR · Lindemann SR last
Downloads
PRJNA866162.csv.gz (1.2 KB) · parquet (71.3 KB) — all 8 samples, every field with route and confidence · PRJNA866162_determinations.csv.gz (1.7 KB) — 104 evidence rows