Shotgun Metagenomic analysis of cutaneous microbiome in patients with atopic dermatitis

Abstract

Atopic dermatitis (AD) is a chronic complex inflammatory skin disorder. AD characterized by multiple contributing factors, such as impairment in skin barrier integrity, participation of either innate or adaptive immunity arms, in addition to the pivotal roles of cutaneous microbiome. The analysis of cutaneous microbiota was performed using shotgun metagenomic sequencing on an Illumina HiSeq platform in parallel with 16s rRNA genes using MiSeq sequencing. Two samples for each sequencing technique were collected from one child and one adult subjects with AD. Metagenomic data from 16srRNA was in accordance with those from shotgun sequencing. Taxonomic profile of samples at genus level showed overrepresentation of Streptococcus in child and Staphylococcus in adults. Species level analysis of reads revealed monoclonality of Staphylococcus aureus community in comparison to heterogeneity of Staphylococcus epidermidis. 16S rRNA gene based analysis was unable to provide comprehensive description of bacterial communities, while shotgun metagenomic analyses described the composition of microbiota with high resolution at different taxonomic levels especially subspecies and single nucleotide variants levels. Finally, further studies using shotgun metagenomic approaches will be required for characterization of microbiome in healthy and diseased subjects.

Changes in the Diversity of Human Skin Microbiota to Cosmetic Serum Containing Prebiotics: Results from a Randomized Controlled Trial

“…Furthermore, in this study, Bacillus and TEWL were significantly positively correlated in the ND group. Bacillus is a genus belonging to Firmicutes and is found on normal skin [40]. Further, increased colonization of Enterobacteriaceae is observed in adult and infant populations with AD [41,42].…”

Changes in The Diversity of Human Skin Microbiota to Cosmetic Serum Containing Prebiotics: Results From A Randomized Controlled Trial

“…Furthermore, in this study, Bacillus and TEWL were signi cantly positively correlated in the ND group. Bacillus is a genus belonging to Firmicutes and is found on normal skin [35]. Further, increased colonization of Enterobacteriaceae is observed in adult and infant populations with AD [36,37].…”

Multi-omics analysis of human gut microbiota in colorectal cancer patients

“…Gut microbiota dysbiosis as well as increased intestinal permeability are highly linked to colon inflammation, which could be the key factor for initiation and/or progression of CRC (Dzutsev et al, 2014).The association of the microbiota with cancer has recently been discussed, highlighting that different cancer types present distinct microbial signatures. Surprisingly, bacteria is found to be present inside the tumor cells in addition to immune cells of cancer patients (Nejman et al, 2020) .In Egypt, several studies showed that there is a relationship between the bacterial communities presents in the body and the impact of these communities on the development of the disease condition, whether positive or negative effect (Salah et al, 2019;Ali, M. S, 2019;Ramadan et al, 2019A;Ramadan et al, 2019B;Ramadan et al, 2021;Elsherbiny et al, 2022).…”