Kidney disease patients, live biotherapeutic trial, Knoxville TN
207 stool samples from participants with kidney disease (hyperoxaluria) in Knoxville, Tennessee, in an intervention trial of a live biotherapeutic (engineered Phocaeicola vulgatus) combined with a porphyran prebiotic/fibre. machine-written summary
207 samples · 207 runs · US · Age unknown · 2025 · 16.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,656 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 414 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC13308544 |
| ○ 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
Defined bacterial consortium / live biotherapeutic product Prebiotic / dietary fibre supplement design single_arm_before_after · population kidney_disease · NOV-001: recombinant live biotherapeutic NB1000S plus polysaccharide NB2000P
“NB1000S, a recombinant live biotherapeutic, and NB2000P” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
16 of 29 people sampled more than once (194 samples; median 12, up to 15 per person) · follow-up median 54 d (max 2 mo) · median interval between samples 3 d (time from collection dates). Schedule stated by the source: “Stool samples at Screening, D1, D2, D3, D4, D10, D14, D17, D21, D24, D28, D35 per subject (single-arm before-after trial)”; stated follow-up 35 d.
Each row is one person (16 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 183 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 | 207 | 100% | 207 | |||
| health_condition | 207 | 100% | 207 | |||
| subject_id | 207 | 100% | 207 | |||
| collection_date | 207 | 100% | 207 | |||
| detailed_location | 207 | 100% | ||||
| health_condition_detail | 207 | 100% | 207 | |||
| latitude | 207 | 100% | 207 | |||
| location_locality | 207 | 100% | 207 | |||
| location_region | 207 | 100% | 207 | |||
| longitude | 207 | 100% | 207 | |||
| timepoint_label | 207 | 100% | 207 |
- Controlled colonization of the human gut with a genetically engineered microbial therapeutic. 2025 PMID 40674481 PMC13308544 own_data
Archive description
This BioProject encompasses the metagenomic analysis associated with the Novome Biotechnologies study NOV-001-CL01 (ClinicalTrials.gov ID NCT04909723), which evaluates the safety, tolerability, pharmacodynamics, and early efficacy of NOV-001. NOV-001 is an investigational combination product composed of NB1000S, a recombinant live biotherapeutic, and NB2000P, a botanically derived polysaccharide. As part of the study, longitudinal stool samples were collected from participants and analyzed using metagenomic sequencing to assess changes in microbiome composition and function over the course of treatment. Metagenomic sequencing was performed using Illumina NovaSeq, and the resulting data includes raw sequencing reads and associated metadata. This dataset enables evaluation of microbiome shifts in response to NB1000S and NB2000P administration.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “stool samples were collected from participants”
- body site study.description · “longitudinal stool samples were collected”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46867614 | collection_date | 2021-06-08 | R1 | 0.90 | biosample.attribute:collection_date | 2021-06-08 |
| SAMN46867614 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Tennessee Knoxville |
| SAMN46867614 | health_condition | kidney_disease | R4 | 0.50 | study.description | evaluates the safety, tolerability, pharmacodynamics |
| SAMN46867614 | health_condition_detail | Phase 1/2a clinical trial of biotherapeutic intervention | R4 | 0.50 | study.description | evaluates the safety, tolerability, pharmacodynamics |
| SAMN46867614 | latitude | 35.9400 | R1 | 0.90 | biosample.attribute:lat_lon | 35.94 N 83.94 W |
| SAMN46867614 | location_locality | Knoxville | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Tennessee Knoxville |
| SAMN46867614 | location_region | Tennessee | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Tennessee Knoxville |
| SAMN46867614 | longitude | -83.9400 | R1 | 0.90 | biosample.attribute:lat_lon | 35.94 N 83.94 W |
| SAMN46867614 | subject_id | 102-103 | R1 | 0.70 | sample.name_rule:alias | 102-103Screening-V1 |
| SAMN46867614 | timepoint_label | Screening | R1 | 0.70 | sample.name_rule:alias | 102-103Screening-V1 |
Sequencing
207 runs over 207 samples · mean 17.07 Gbp per run (median 16.53 Gbp, total 3,533.44 Gbp; 207 runs with a base count) · layout PAIRED 207 · platform ILLUMINA 207 · models Illumina NovaSeq 6000 (207) · 88% of runs with a Sandpiper profile · first public 2025-05-15 – 2025-05-28
Authors (24)
Whitaker WR first · Russ ZN · Stanley Shepherd E · Popov LM · Louie A · Lam K · Zong DM · Gill CCC · Gehrig JL · Rishi HS · Tan JA · Buness A · Godoy J · Banta D · Jaidka S · Wilson K · Flood J · Bukshpun P · Yocum R · Cook DN · Warsi T · McLean L · Sonnenburg JL · DeLoache WC last
Downloads
PRJNA1224809.csv.gz (7.0 KB) · parquet (78.5 KB) — all 207 samples, every field with route and confidence · PRJNA1224809_determinations.csv.gz (16.6 KB) — 2,070 evidence rows