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Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial

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Dataset overview

Participants 8
Samples None
Reuse readiness 7.6/10 evidence-backed score

Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn's Disease: a first in human trial.

Guarino-Vignon P, Louis E, Pham HP, Orianne G, Tkacz E, Brot L, Mazzetti E, Sedda D, et al. · Nature communications · 2026

Abstract

A marked decrease in Faecalibacterium prausnitzii is a hallmark of Crohn's disease (CD)-associated dysbiosis and predicts disease relapse. Here, we present the development and first-in-human evaluation of F. prausnitzii strain EXL01 for CD treatment. The EXL01-strain demonstrates anti-inflammatory effects in four models of colitis in rodents. A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD, following corticosteroids-induced clinical response or remission. The primary endpoint was safety, and secondary endpoints included clinical, endoscopic, histological, molecular, and microbiome assessments. Exploratory endpoints included mucosa transcriptome and cytokine levels. EXL01 is well-tolerated with no treatment-related adverse events. Six participants completed the study; two discontinued treatment due to disease flare. While gut microbiota composition remains largely stable, transcriptomic analyses reveal distinct changes in ileal gene expression following EXL01 treatment, notably modulation of immune-related genes and upregulation of energy metabolism pathways. Compared to participants who remained in remission, those who flared show higher baseline systemic inflammation markers and innate immunity gene expression. These findings demonstrate that oral administration of EXL01 is feasible and well tolerated and establishes proof-of-concept for F. prausnitzii as a first-in-class live biotherapeutic for CD. ClinicalTrials.gov registration: NCT05542355.

doi:10.1038/s41467-026-72375-y ↗ PMID 42049742 ↗ PMC13332046 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina NovaSeq X Plus
Age group
adult
Disease groups
Crohn's disease
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Feature/OTU tables are advertised
  • Taxonomic tables are advertised
  • Participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.platform Illumina NovaSeq X Plus
the library pools were sequenced using the Novaseq X Plus platform (Illumina)

Section Library preparation and sequencing, offset —
assay.sequencing_type shotgun_metagenomics
Overall gut microbiota composition and diversity remained stable both for stool (assessed by shotgun metagenomics)

Section EXL01 Detection and microbiota changes, offset —

Cohort

FieldValueEvidence
cohort.age_group adult
eight adult participants with mild to moderate CD

Section study.description, offset —
cohort.crohns_disease_participants 8
conducted in eight adult participants with mild to moderate CD

Section study.description, offset —
cohort.disease_activity_metadata_available True
CDAI 180-350 ... achieved corticosteroid (CS)-induced clinical response (CDAI decrease ≥70) or remission (CDAI <150)

Section study.description, offset —
cohort.study_design longitudinal
Disease activity, QoL assessments, and collection of feces, serum, and blood were performed throughout the study

Section Trial design, offset —
cohort.total_participants 8
A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD

Section study.description, offset —
cohort.treatment_exposure_documented True
oral EXL01 was conducted ... following corticosteroid-induced clinical response or remission

Section study.description, offset —
cohort.treatment_response_metadata_available True
Six participants completed the study two discontinued treatment due to disease flare.

Section study.description, offset —

Data_Assets

FieldValueEvidence
data_assets.feature_or_otu_table True
The resulting ASV count table, and taxonomic assignments were transformed into taxa-level specific count tables

Section 16S: Data preprocessing and DADA2 taxonomic profiling, offset —
data_assets.open_access True
"isOpenAccess": "Y"

Section publication metadata, offset —
data_assets.pipeline_or_tool_versions True
Trim Galore (v0.6.10) ... Bowtie2 (v 2.5.3) ... MetaPhlAn4.1.0 ... HUMAnN3 v.3.9

Section Data preprocessing, profiling and analysis, offset —
data_assets.qc_or_negative_controls_reported True
Negative controls were required to show no signal

Section ddPCR to detect EXL01, offset —
data_assets.raw_reads True
the low-quality shotgun metagenomic reads ... were removed

Section Data preprocessing, profiling and analysis, offset —
data_assets.taxonomic_table True
The resulting ASV count table, and taxonomic assignments were transformed into taxa-level specific count tables

Section 16S: Data preprocessing and DADA2 taxonomic profiling, offset —

Specimens

FieldValueEvidence
specimens.body_site gastrointestinal tract: ileum, colon, rectum; stool
Participants underwent an endoscopy, with video capture and biopsy collection, at Screening, end of Induction and at the end of Maintenance treatment.

Section Human study design and study endpoints, offset —
specimens.inflamed_status_available True
participants with clinically active disease at baseline

Section Human study design and study endpoints, offset —
specimens.longitudinal_sampling True
The 63 stool samples ... were processed

Section Fecal samples, offset —
specimens.sample_type mixed
Symbols represent sample types: stool, blood, endoscopic biopsies (ileum, colon, rectum)

Section Trial design, offset —