Oral FMT for CPE gut colonization in adults, Haifa, Israel
33 gut metagenome samples from adult/elderly carriers of carbapenemase-producing Enterobacteriaceae in Haifa, Israel, studied in an intervention cohort receiving oral capsulized fecal microbiota transplantation to eradicate colonization. machine-written summary
33 samples · 33 runs · IL · Adult · 2020 · 4.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 312 sample values (age, collection date, country, intervention, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 27 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC10821315, PMC12180181 |
| ✓ Supplementary tables | 39 sample values (health condition, health condition detail) |
| – 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 resolved
Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · Oral capsulized FMT for 2 days to eradicate CPE carriage
“all consenting eligible CPE carriers received oral capsulized FMT” — abstract:32511695 (study level; per-sample arms are in the intervention column below)
longitudinal
13 of 14 people sampled more than once (26 samples; median 2, up to 2 per person) · follow-up median 14 d (max 14 d) · median interval between samples 14 d (time from collection dates).
Each row is one person (13 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 29 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 | 27 | 82% | ||||
| country | 33 | 100% | 33 | |||
| health_condition | 33 | 100% | 6 | 27 | ||
| subject_id | 27 | 82% | 27 | |||
| collection_date | 33 | 100% | 33 | |||
| detailed_location | 33 | 100% | ||||
| health_condition_detail | 33 | 100% | 33 | |||
| intervention | 33 | 100% | 33 | |||
| latitude | 33 | 100% | 33 | |||
| location_locality | 33 | 100% | 33 | |||
| location_region | 33 | 100% | 33 | |||
| longitude | 33 | 100% | 33 | |||
| age_at_collection_days | 27 | 82% | 27 | |||
| timepoint_label | 27 | 82% | 27 |
- Oral capsulized Fecal microbiota transplantation for eradication of carbapenemase-producing Enterobacteriaceae colonization with a metagenomic perspective. 2020 PMID 32511695 own_data
- Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. 2023 PMID 37910603 PMC10821315 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Archive description
Carbapenemase-producing Enterobacteriaceae (CPE) infections lead to considerable morbidity and mortality. We assessed the potential of fecal microbiota transplantation (FMT) to eradicate CPE carriage and to explain failure or success through microbiome analyses.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and elderly 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 · “Oral capsulized Fecal microbiota transplantation for”
- body site study.description · “the potential of fecal microbiota transplantation (FMT)”
- body site study.title · “Oral capsulized Fecal microbiota”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “65 (n=8/33)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14734815 | age_at_collection_days | 9898.3 | R1 | 0.70 | sample.attr.host_age | 27.1 |
| SAMN14734815 | collection_date | 2018-03-04 | R1 | 0.90 | biosample.attribute:collection_date | 2018-03-04 |
| SAMN14734815 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel: Haifa |
| SAMN14734842 | health_condition | healthy_control | R2 | 0.85 | paper.supp.40168_2025_2046_MOESM8_ESM.xlsx[S2!Condition] | healthy_donor |
| SAMN14734815 | health_condition | other_infection | R4 | 0.50 | paper.abstract | all consenting eligible CPE carriers |
| SAMN14734815 | health_condition_detail | MDRB_infections | R2 | 0.85 | paper.supp.40168_2025_2046_MOESM8_ESM.xlsx[S2!Condition] | MDRB_infections |
| SAMN14734815 | intervention | fmt | R1 | 0.70 | sample.name_rule:description | Non-responders |
| SAMN14734815 | latitude | 32.8330 | R1 | 0.90 | biosample.attribute:lat_lon | 32.833049 N 34.985710 E |
| SAMN14734815 | location_locality | Haifa | R1 | 0.85 | biosample.attribute:geo_loc_name | Israel: Haifa |
| SAMN14734815 | location_region | Haifa | R1 | 0.60 | biosample.attribute:lat_lon | 32.833049 N 34.985710 E |
| SAMN14734815 | longitude | 34.9857 | R1 | 0.90 | biosample.attribute:lat_lon | 32.833049 N 34.985710 E |
| SAMN14734815 | subject_id | case1 | R1 | 0.70 | sample.name_rule:library_name | case1_after |
| SAMN14734815 | timepoint_label | after_FMT | R1 | 0.70 | sample.name_rule:library_name | case1_after |
Sequencing
33 runs over 33 samples · mean 4.75 Gbp per run (median 4.31 Gbp, total 156.87 Gbp; 33 runs with a base count) · layout PAIRED 33 · platform ILLUMINA 33 · models Illumina NovaSeq 6000 (33) · 88% of runs with a Sandpiper profile · first public 2020-06-10
Authors (65)
Bar-Yoseph H first · Carasso S · Shklar S · Korytny A · Even Dar R · Daoud H · Nassar R · Maharshak N · Hussein K · Geffen Y · Chowers Y · Geva-Zatorsky N · Paul M last · Woodworth MH first · Conrad RE · Haldopoulos M · Pouch SM · Babiker A · Mehta AK · Sitchenko KL · Wang CH · Strudwick A · Ingersoll JM · Philippe C · Lohsen S · Kocaman K · Lindner BG · Hatt JK · Jones RM · Miller C · Neish AS · Friedman-Moraco R · Karadkhele G · Liu KH · Jones DP · Mehta CC · Ziegler TR · Weiss DS · Larsen CP · Konstantinidis KT · Kraft CS last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last
Downloads
PRJNA628604.csv.gz (2.1 KB) · parquet (72.5 KB) — all 33 samples, every field with route and confidence · PRJNA628604_determinations.csv.gz (4.0 KB) — 378 evidence rows