Live biotherapeutic intervention trial, Sweden, 86 samples
86 gut metagenome samples from Sweden, from an intervention study testing a live biotherapeutic (F. prausnitzii/D. piger co-formulation) as a next-generation probiotic. machine-written summary
86 samples · 86 runs · SE · Age unknown · 2023 · 13.48 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 602 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 86 sample values (location locality) · PMC10412450 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Defined bacterial consortium / live biotherapeutic product design single_arm_before_after · population healthy_control · Oxygen-tolerant F. prausnitzii + D. piger synbiotic formulation (NCT03728868)
“demonstrate that the symbiotic product is tolerated by mice and humans” — abstract:37532933 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
43 of 43 people sampled more than once (86 samples; median 2, up to 2 per person). Schedule stated by the source: “stool sampled before and after eight weeks of administration (pre/post)” (time origin: intervention_start); stated follow-up 56 d.
Genera, mean relative abundance over 78 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 | 0 | 0% | ||||
| country | 86 | 100% | 86 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 86 | 100% | 86 | |||
| collection_date | 86 | 100% | 86 | |||
| detailed_location | 86 | 100% | ||||
| latitude | 86 | 100% | 86 | |||
| location_locality | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| longitude | 86 | 100% | 86 | |||
| timepoint_label | 86 | 100% | 86 |
- Synergy and oxygen adaptation for development of next-generation probiotics. 2023 PMID 37532933 PMC10412450 own_data
Archive description
In this study, we present the co-isolation of Faecalibacterium prausnitzii, a butyrate producer and Desulfovibrio piger, a sulfate-reducing bacterium, and investigate their mutualistic relationship, particularly in terms of growth promotion and butyrate production. To produce a next-generation probiotic formulation, we adapted F.prasunitzii to tolerate oxygen exposure, and we demonstrate that the symbiotic product is tolerated by mice and humans. Our study describes a new technology for the production of next-generation probiotics based on the adaptation of strictly anaerobic bacteria to tolerate oxygen exposures without reduction of potential beneficial properties.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.50. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “strictly anaerobic bacteria to tolerate oxygen”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA113537084 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA113537084 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA113537084 | latitude | 57.7089 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 57.70887 11.97456 |
| SAMEA113537084 | location_locality | Mölndal | R3 | 0.70 | paper.fulltext.methods | Sahlgenska University Hospital, Mölndal |
| SAMEA113537084 | location_region | Vaestra Goetaland | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 57.70887 11.97456 |
| SAMEA113537084 | longitude | 11.9746 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 57.70887 11.97456 |
| SAMEA113537084 | subject_id | 30 | R1 | 0.70 | sample.name_rule:alias | S30pre |
| SAMEA113537084 | timepoint_label | pre | R1 | 0.70 | sample.name_rule:alias | S30pre |
Sequencing
86 runs over 86 samples · mean 13.52 Gbp per run (median 13.48 Gbp, total 1,163.14 Gbp; 86 runs with a base count) · layout PAIRED 86 · platform ILLUMINA 86 · models Illumina NovaSeq 6000 (86) · 91% of runs with a Sandpiper profile · first public 2023-07-17
Authors (9)
Khan MT first · Dwibedi C · Sundh D · Pradhan M · Kraft JD · Caesar R · Tremaroli V · Lorentzon M · Bäckhed F last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB62463.csv.gz (3.1 KB) · parquet (73.3 KB) — all 86 samples, every field with route and confidence · PRJEB62463_determinations.csv.gz (5.4 KB) — 688 evidence rows