Sulfoquinovose degradation in human gut microbiota, Vienna
3 fecal samples from healthy adults in Vienna, Austria, used in microcosm experiments amended with sulfoquinovose and controls (e.g., glucose, taurine) to study microbial sulfoquinovose and H2S metabolism. machine-written summary
3 samples · 3 runs · AT · Adult · 2020 · 6.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 36 sample values (age, collection date, country, diet, diet detail, latitude, lifestyle, lifestyle detail) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 6 sample values (health condition, health condition detail) · PMC8397734 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
Genera, mean relative abundance over 3 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 | 3 | 100% | ||||
| country | 3 | 100% | 3 | |||
| health_condition | 3 | 100% | 3 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 3 | 100% | 3 | |||
| collection_date | 3 | 100% | 3 | |||
| detailed_location | 3 | 100% | ||||
| diet | 3 | 100% | 3 | |||
| diet_detail | 3 | 100% | 3 | |||
| health_condition_detail | 3 | 100% | 3 | |||
| latitude | 3 | 100% | 3 | |||
| lifestyle | 3 | 100% | 3 | |||
| lifestyle_detail | 3 | 100% | 3 | |||
| location_locality | 3 | 100% | 3 | |||
| location_region | 3 | 100% | 3 | |||
| longitude | 3 | 100% | 3 | |||
| timepoint_label | 3 | 100% | 3 |
- Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. 2021 PMID 33790426 PMC8397734 own_data
- Metatranscriptomic analysis indicates prebiotic effect of isomalto/malto-polysaccharides on human colonic microbiota in-vitro. 2024 PMID 39143192 PMC11324910 unsure
Archive description
Exploration of sulfoquinovose degradation by the human gut microbiota. Homogenized human feces from 8 vegetarians was used to construct microcosms, which were amended with sulfoquinovose and controls (e.g. glucose, taurine, no amendment, etc.). Microcosms were subsampled and extracted nucleic acids were screened using amplicon sequencing (16S rRNA gene, dsrB), metagenomics, and metatranscriptomics.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Homogenized human feces from 8 vegetarians”
- life stage sample.attr.host_age · “26-55 years (n=3/3)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14930173 | age_at_collection_days | 14793.0 | R1 | 0.85 | biosample.attribute:host_age | host_age: 26-55 years |
| SAMN14930173 | collection_date | 2016-11-01 | R1 | 0.90 | biosample.attribute:collection_date | 2016-11-01 |
| SAMN14930173 | country | AT | R1 | 0.90 | sample.attr.geo_loc_name | Austria: Vienna |
| SAMN14930173 | diet | vegetarian | R1 | 0.90 | biosample.attribute:host_diet | Vegetarian |
| SAMN14930173 | diet_detail | Vegetarian | R1 | 0.90 | biosample.attribute:host_diet | Vegetarian |
| SAMN14930173 | health_condition | healthy_control | R3 | 0.60 | paper.fulltext.results | fecal slurries mixed from eight vegetarians |
| SAMN14930173 | health_condition_detail | vegetarian fecal donors used to construct microcosms | R3 | 0.60 | paper.fulltext.results | fecal slurries mixed from eight vegetarians |
| SAMN14930173 | latitude | 48.2084 | R1 | 0.90 | biosample.attribute:lat_lon | 48.2084 N 16.3735 E |
| SAMN14930173 | lifestyle | vegetarian_or_vegan | R1 | 0.85 | biosample.attribute:special_diet | vegetarian |
| SAMN14930173 | lifestyle_detail | vegetarian | R1 | 0.85 | biosample.attribute:special_diet | vegetarian |
| SAMN14930173 | location_locality | Vienna | R1 | 0.85 | biosample.attribute:geo_loc_name | Austria: Vienna |
| SAMN14930173 | location_region | Vienna | R1 | 0.85 | biosample.attribute:geo_loc_name | Austria: Vienna |
| SAMN14930173 | longitude | 16.3735 | R1 | 0.90 | biosample.attribute:lat_lon | 48.2084 N 16.3735 E |
| SAMN14930173 | timepoint_label | T28h | R1 | 0.70 | sample.name_rule:library_names | SQ_HumanFecalMicrocosmT28h_metagenome |
Sequencing
3 runs over 3 samples · mean 19.55 Gbp per run (median 6.39 Gbp, total 58.64 Gbp; 3 runs with a base count) · layout PAIRED 3 · platform ILLUMINA 3 · models Illumina HiSeq 3000 (3) · 100% of runs with a Sandpiper profile · first public 2020-05-30
Authors (20)
Hanson BT first · Dimitri Kits K · Löffler J · Burrichter AG · Fiedler A · Denger K · Frommeyer B · Herbold CW · Rattei T · Karcher N · Segata N · Schleheck D · Loy A last · Borewicz K first · Hornung B · Gu F · van der Zaal PH · Schols HA · Schaap PJ · Smidt H last
Downloads
PRJNA593787.csv.gz (1.0 KB) · parquet (71.3 KB) — all 3 samples, every field with route and confidence · PRJNA593787_determinations.csv.gz (1.2 KB) — 42 evidence rows