Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.

Intestinal parasitosis was found in 23.64% of patients across the study cohort.

• Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis based on classic parasitological analysis of faecal samples.
• The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009).
• Faecal samples were collected from all patients for classic parasitological analysis alongside metagenomic sequencing.

The most abundant microorganism species found in the faeces of all evaluated patients was Escherichia coli.

• This finding was consistent across the psoriasis (n = 24), hidradenitis suppurativa (n = 10), pemphigus foliaceus (n = 11), and healthy control (n = 10) groups.
• Gut microbiome analysis was conducted using shotgun next-generation sequencing.
• Four bioinformatics tools (Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2) were used to evaluate concordance and differential abundance.

Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family compared to other groups.

• The psoriasis group included 24 omnivorous nonsmokers and nondrinkers.
• The differential abundance finding was identified using concordance analysis across Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools.
• This finding represents a disease-specific bacterial abundance pattern distinguishing psoriasis from hidradenitis suppurativa, pemphigus foliaceus, and healthy controls.

Pemphigus foliaceus patients presented a greater abundance of Firmicutes bacteria compared to other groups.

• The pemphigus foliaceus group included 11 omnivorous nonsmokers and nondrinkers.
• Greater Firmicutes abundance represented a disease-specific finding for PF distinct from psoriasis and hidradenitis suppurativa profiles.
• Differential abundance was evaluated using four concordant bioinformatics tools.

Pemphigus foliaceus patients showed increased E. coli virulence and antibiotic resistance functional markers.

• Increased virulence and antibiotic resistance functional markers were specifically identified in PF patients.
• Immunosuppression, particularly systemic corticosteroid therapy, significantly influenced increased virulence of functional markers in PF patients.
• The PF group (n = 11) was receiving systemic corticosteroid therapy, which was associated with both parasitosis and altered functional marker profiles.

The study included omnivorous nonsmokers and nondrinkers across all patient groups to control for dietary and lifestyle confounders.

• Patient groups included psoriasis (n = 24), hidradenitis suppurativa (n = 10), pemphigus foliaceus (n = 11), and healthy controls (n = 10).
• All participants were characterized as omnivorous nonsmokers and nondrinkers, standardizing dietary and substance use variables.
• Shotgun next-generation sequencing was used for species-level metagenomic analysis, providing higher resolution than 16S rRNA approaches.