Foundry120 atlas

← IBD microbiome

16S V3-V4 -based microbial profiling of matched healthy and inflamed ileal mucosa from patients affected by Crohn’s disease (set 2)

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Dataset overview

Participants 28
Samples None
Reuse readiness 8.3/10 evidence-backed score

Crohn's disease recurrence updates: first surgery <i>vs</i>. surgical relapse patients display different profiles of ileal microbiota and systemic microbial-associated inflammatory factors.

Russo E, Cinci L, Di Gloria L, Baldi S, D'Ambrosio M, Nannini G, Bigagli E, Curini L, et al. · Frontiers in immunology · 2022

Abstract

<h4>Background and aims</h4>Crohn's disease (CD) pathogenesis is still unclear. Remodeling in mucosal microbiota and systemic immunoregulation may represent an important component in tissue injury. Here, we aim to characterize the ileal microbiota in both pathological and healthy settings and to evaluate the correlated systemic microbial-associated inflammatory markers comparing first-time surgery and relapse clinical conditions.<h4>Methods</h4>We enrolled 28 CD patients at surgery; we collected inflamed and non-inflamed mucosa tissues and blood samples from each patient. Bacterial wall adherence was observed histologically, while its composition was assessed through amplicon sequencing of the 16S rRNA gene. In addition, we evaluated the systemic microRNA (miRNA) using quantitative real-time PCR amplification and free fatty acids (FFAs) using gas chromatography-mass spectroscopy.<h4>Results</h4>The total number of mucosal adherent microbiota was enriched in healthy compared to inflamed mucosa. In contrast, the phylum <i>Tenericutes</i>, the family <i>Ruminococcaceae</i>, and the genera <i>Mesoplasma</i> and <i>Mycoplasma</i> were significantly enriched in the pathological setting. Significant microbiota differences were observed between the relapse and first surgery patients regarding the families <i>Bacillaceae 2</i> and <i>Brucellaceae</i> and the genera <i>Escherichia/Shigella</i>, <i>Finegoldia</i>, <i>Antrobacter</i>, <i>Gemmatimonas</i>, <i>Moraxella</i>, <i>Anoxibacillus</i>, and <i>Proteus</i>. At the systemic level, we observed a significant downregulation of circulating miR-155 and miR-223, as well as 2-methyl butyric, isobutyric, and hexanoic (caproic) acids in recurrence compared to the first surgery patients. In addition, the level of hexanoic acid seems to act as a predictor of recurrence risk in CD patients (OR 18; 95% confidence interval 1.24-261.81; <i>p</i> = 0.006).<h4>Conclusions</h4>We describe a dissimilarity of ileal microbiota composition comparing CD and healthy settings, as well as systemic microbial-associated inflammatory factors between first surgery and surgical relapse. We suggest that patterns of microbiota, associated with healthy ileal tissue, could be involved in triggering CD recurrence. Our findings may provide insight into the dynamics of the gut microbiota-immunity axis in CD surgical recurrence, paving the way for new diagnostics and therapeutics aimed not only at reducing inflammation but also at maintaining a general state of eubiosis in healthy tissue.

doi:10.3389/fimmu.2022.886468 ↗ PMID 35967326 ↗ PMC9374303 ↗

Study facts

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

Data availability

  • Analysis code

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Feature/OTU tables are advertised
  • Taxonomic tables are advertised
  • Analysis code is available
  • Participant-to-sample mapping is available
  • 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.paired_end True
sequenced in paired–end (2 × 300 cycles)

Section Materials and methods — Characterization of paraffin–embedded tissue microbiota, offset —
assay.platform Illumina MiSeq
sequenced in paired–end (2 × 300 cycles) on the Illumina MiSeq platform

Section Materials and methods — Characterization of paraffin–embedded tissue microbiota, offset —
assay.read_length 300
paired–end (2 × 300 cycles)

Section Materials and methods — Characterization of paraffin–embedded tissue microbiota, offset —
assay.sequencing_type amplicon_16s
16S rDNA amplicons (V3-V4 region)

Section study.description, offset —
assay.target_region V3-V4
amplicons of the variable V3–V4 region of the bacterial 16S rRNA gene were sequenced

Section Characterization of paraffin–embedded tissue microbiota, offset 10800

Cohort

FieldValueEvidence
cohort.age_group adult
We enrolled 28 adult patients

Section Materials and methods > Patients, offset 10220
cohort.crohns_disease_participants 28
We enrolled 28 adult patients ... affected by ileal CD

Section Materials and methods — Patients, offset 7000
cohort.disease_activity_metadata_available True
we divided the patients into two groups (a: first surgery and b: relapse)

Section Results > Differences between first surgery vs. surgical relapse, offset 17000
cohort.study_design cross_sectional inferred
We enrolled 28 adult patients ... at ... between 2018 and 2019

Section Materials and methods > Patients, offset 12000
cohort.total_participants 28
We enrolled 28 adult patients (16 men and 12 women, mean age 46.82 years, age range 19–72 years) affected by ileal CD

Section Materials and methods — Patients, offset 7000
cohort.treatment_exposure_documented True
Patients have not been treated with antibiotics, aminosalicylates or immunosuppressants, biological therapy, and steroids for at least 3 weeks before the ICR.

Section Materials and methods > Patients, offset 11180

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
the analysis scripts ... are available at GitHub

Section Data availability statement, offset —
data_assets.feature_or_otu_table True
raw reads, OTU tables, and taxonomic assignments

Section Data availability statement, offset —
data_assets.open_access True from source
license: cc by

Section Publication metadata, offset —
data_assets.pipeline_or_tool_versions True
raw sequences were processed following the software pipeline MICCA

Section Characterization of paraffin–embedded tissue microbiota, offset —
data_assets.qc_or_negative_controls_reported True
sterile swabs that also underwent sequencing as controls

Section Materials and methods > Characterization of paraffin–embedded tissue microbiota, offset 15100
data_assets.raw_reads True
The microbial–related data (raw reads, OTU tables, and taxonomic assignments) are freely available

Section Data availability statement, offset —
data_assets.taxonomic_table True
raw reads, OTU tables, and taxonomic assignments

Section Data availability statement, offset —

Specimens

FieldValueEvidence
specimens.body_site ileum
paraffin-embedded ileal tissue specimens

Section study.description, offset —
specimens.inflamed_status_available True
significant differences between CD and healthy tissues

Section Results — Dysbiotic variation of the ileal microbiota, offset —
specimens.participant_to_sample_mapping_available True
The lines connect the samples from the same patient.

Section Results — Dysbiotic variation of the ileal microbiota, offset —
specimens.sample_type mucosal_biopsy
Samples of affected ... and apparently normal mucosa, harvested at surgery, were fixed in Carnoy’s solution and embedded in paraffin.

Section Materials and methods > Characterization of paraffin-embedded tissue microbiota, offset 7000