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Gut Microbiota Profiling of Lebanese Patients with Ulcerative Colitis and Healthy Controls: A Pilot Study

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Dataset overview

Participants 22
Samples 22
Reuse readiness 7.9/10 evidence-backed score

Gut microbiota profiling in Lebanese ulcerative colitis patients and healthy controls from a pilot study.

Yassine F, Abbas H, Kurdi A, Mansour R, Mourad FH, Matar G, Bilen M. · Scientific reports · 2025

Abstract

Ulcerative colitis (UC) is a chronic inflammatory disease of the colon, associated with gut microbiota dysbiosis. While global studies have explored this link, region-specific microbial profiles remain underreported. This pilot study aimed to characterize and compare, for the first time, the gut microbiota of Lebanese UC patients and healthy controls using 16 S rRNA gene sequencing (V3-V4 region). Fecal samples from 11 UC patients and 11 healthy individuals were analyzed. Alpha and beta diversity metrics were computed, and gut microbial composition was assessed across taxonomic levels. Statistical comparisons used Mann-Whitney and Fisher's exact tests. UC patients showed significantly reduced microbial diversity based on Faith's Phylogenetic Diversity and Shannon index (p < 0.05), though evenness was unaffected. Beta diversity also revealed significant group-level dissimilarities (p < 0.05). At the phylum level, Bacteroidota was elevated in UC, while Bacillota and Actinomycetota were reduced. Genera such as Ruminococcus, Bacteroides, and Coprococcus were depleted in UC. Faecalibacterium, commonly reduced in UC, showed no significant difference. This first analysis of gut microbiota in Lebanese UC patients reveals a distinct microbial signature that partially diverges from global trends, supporting the need for region-specific microbiome studies and personalized microbiota-targeted therapies.

doi:10.1038/s41598-025-31435-x ↗ PMID 41398357 ↗ PMC12804816 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina MiSeq
Age group
adult
Disease groups
Non-IBD controls, Ulcerative colitis
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

  • Feature/OTU tables are advertised
  • Taxonomic tables are advertised
  • Participant-to-sample mapping is available
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: raw reads are advertised
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.paired_end True
Raw paired-end reads were first processed

Section Bioinformatic analysis, offset —
assay.platform Illumina MiSeq
sequenced on the MiSeq® platform (Illumina, San Diego, CA, USA)

Section 16 S rRNA V3–V4 gene sequencing and bioinformatics analysis, offset —
assay.primers_reported True
The primers included Illumina adapter overhang sequences: forward...and reverse...

Section 16 S rRNA V3–V4 gene sequencing and bioinformatics analysis, offset —
assay.read_depth_reported 10000
samples were rarefied to an even sequencing depth of 10,000 reads per sample

Section Bioinformatic analysis, offset —
assay.sequencing_type amplicon_16s
using 16S rRNA gene sequencing (V3–V4 region)

Section ena_study.study.description, offset —
assay.target_region V3–V4
We used amplicon sequencing of the 16 S rRNA V3–V4 region on fecal samples

Section 16 S rRNA V3–V4 gene sequencing and bioinformatics analysis, offset —

Cohort

FieldValueEvidence
cohort.age_group adult
participants were eligible for inclusion if they were between 18 and 65 years of age

Section Exclusion and inclusion criteria, offset —
cohort.disease_activity_metadata_available True
The PRO2 score...was used to assess patient-reported disease activity... The endoscopic Mayo score...reflects mucosal appearance

Section Characteristics of the studied groups, offset —
cohort.non_ibd_controls 11
A total of 22 stool samples were collected, including 11 patients diagnosed with UC at AUBMC and 11 from healthy individuals.

Section Study cohort and sample collection, offset —
cohort.study_design cross_sectional
Overall design: Cross-sectional, observational, case-control pilot study using 16S rRNA gene sequencing.

Section ena_study.study.description, offset —
cohort.total_participants 22
Fecal samples from 11 UC patients and 11 healthy individuals were analyzed.

Section ena_study.study.description, offset —
cohort.treatment_exposure_documented True
Immunosuppressants included biologic and systemic agents used for ulcerative colitis management

Section Clinical and lifestyle data collection, offset —
cohort.treatment_response_metadata_available False inferred
Clinical scores for stool frequency, rectal bleeding, and Mayo endoscopic activity were recorded only for UC patients

Section Characteristics of the studied groups, offset —
cohort.ulcerative_colitis_participants 11
A total of 22 stool samples were collected, including 11 patients diagnosed with UC at AUBMC and 11 from healthy individuals.

Section Study cohort and sample collection, offset —

Data_Assets

FieldValueEvidence
data_assets.feature_or_otu_table True
The resulting output consisted of a feature table of amplicon sequence variants (ASVs)

Section Bioinformatic analysis, offset —
data_assets.open_access True from source
"isOpenAccess": "Y"

Section publication metadata, offset —
data_assets.pipeline_or_tool_versions True
Trimmed reads were then imported into QIIME2 (version 2025.4)

Section Bioinformatic analysis, offset —
data_assets.representative_sequences True
The resulting output consisted of a feature table of amplicon sequence variants (ASVs) and their representative sequences.

Section Bioinformatic analysis, offset —
data_assets.taxonomic_table True
Classification was performed...resulting in taxonomic labels spanning from phylum to species

Section Bioinformatic analysis, offset —

Specimens

FieldValueEvidence
specimens.body_site feces
descriptorName: Feces

Section MeSH metadata, offset —
specimens.inflamed_status_available True
The endoscopic Mayo score...reflects mucosal appearance

Section Characteristics of the studied groups, offset —
specimens.longitudinal_sampling False inferred
Overall design: Cross-sectional, observational, case-control pilot study

Section ena_study.study.description, offset —
specimens.number_of_samples 22
A total of 22 stool samples were collected

Section Study cohort and sample collection, offset —
specimens.participant_to_sample_mapping_available True
Approximately 200 mg of stool was collected per participant

Section Study cohort and sample collection, offset —
specimens.sample_type stool
A total of 22 stool samples were collected

Section Study cohort and sample collection, offset —