IBD-associated Klebsiella phage therapy, case-control
536 adult samples from a case-control study examining phage therapy targeting IBD-associated Klebsiella pneumoniae strains in the gut microbiota. machine-written summary
537 samples · 537 runs · FR, IL, US · Adult · 2022 · 24.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11510655 |
| ✓ Supplementary tables | 671 sample values (country, health condition, health condition detail) |
| – 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
Bacteriophage therapy design single_arm_before_after · Oral five-phage combination targeting IBD-associated Klebsiella pneumoniae in healthy volunteers
“Kp-targeting phages in an artificial human gut and in healthy volunteers” — bioproject.description (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 455 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 | 537 | 100% | ||||
| country | 223 | 42% | 223 | |||
| health_condition | 224 | 42% | 224 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 224 | 42% | 224 |
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655 unsure
Archive description
Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflam- matory bowel diseases (IBDs), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n = 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, tar- geting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.
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 · “of human IBD-associated gut microbiota commensals for”
- body site study.description · “Human gut commensals are increasingly”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “and in healthy volunteers demonstrates gastric acid-dependent”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110452918 | country | FR | R2 | 0.85 | paper.supp.microorganisms-12-02086-s001.zip/SuppTables_241010.xlsx[S1|Sample Metadata!Country] | Country: France |
| SAMEA110452918 | health_condition | crohns_disease | R2 | 0.85 | paper.supp.microorganisms-12-02086-s001.zip/SuppTables_241010.xlsx[S1|Sample Metadata!Category] | Category: IBD-CD |
| SAMEA110452918 | health_condition_detail | IBD-CD | R2 | 0.85 | paper.supp.microorganisms-12-02086-s001.zip/SuppTables_241010.xlsx[S1|Sample Metadata!Category] | Category: IBD-CD |
Sequencing
537 runs over 537 samples · mean 32.38 Gbp per run (median 24.13 Gbp, total 17,387.47 Gbp; 537 runs with a base count) · layout PAIRED 537 · platform ILLUMINA 537 · models Illumina NovaSeq 6000 (537) · 85% of runs with a Sandpiper profile · first public 2022-08-21
Help complete this project
3 of the 4 core fields are below 50% coverage: country, health_condition, subject_id. Share metadata
Downloads
PRJEB50555.csv.gz (13.5 KB) · parquet (89.5 KB) — all 537 samples, every field with route and confidence · PRJEB50555_determinations.csv.gz (3.1 KB) — 671 evidence rows