Commensal microbiome dysbiosis in keloid disease

Wound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that related to commensal microbiota and skin fibrosis remain mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterize microbial composition and divergence between the pathological and normal skin tissue. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease., 16S rDNA sequencing data
The data files here are raw 16S rDNA sequencing accompanied by R scripts that were used to analyze these data.
The source of the data was: (1) a swab test from the surface of normal and keloid skin; (2) the tissues of keloid patients from deeper parts of the skin.
Surface microbiota samples were collected from the pathological location or the normal lateral location of patients using a swab (Catch-all Sample Collection Swab, Epicenter) moistened in Yeast Cell Lysis Buffer (from MasterPure Yeast DNA Purification Kit; Epicenter). Samples were snap-frozen on dry ice, and DNA was isolated from specimens using the PureLink Genomic DNA Mini Kit (Invitrogen).
 Amplification of the 16S-V3+V4 region was performed according to the manufacturer’s specifications. Sequencing of 16S rRNA amplicons was conducted by Apexbio Co., Shanghai, China using the Illumina Novaseq platform. The data were analyzed with the attached R scripts.
Bulk RNA-Seq
For RNA sequencing, human dermal ..., , # Commensal microbiome dysbiosis in keloid disease

[https://doi.org/10.5061/dryad.d51c5b0bt](https://doi.org/10.5061/dryad.d51c5b0bt)

These datasets contain original fastq.gz readouts from 16S rDNA sequencing experiments and scripts used to analyze these data. The experiments were performed on patients with keloids, a fibrotic skin disease. We did two similar experiments with the same way of analysis:

* Swab test: we used sterile cotton swabs to acquire bacteria from the surface of undamaged skin covering keloid and adjacent normal skin. Therefore, we have 12 keloid and 12 normal swabs paired together.
* Tissue test: the keloid tissue with a margin of normal tissue was acquired from samples after surgery (5 patients).

Additionally, we provide the files from bulk RNA sequencing of human dermal fibroblasts treated with IL-8 and TGF-beta here.

## Description of the data and file structure

### 16S rDNA data

#### File naming convention

All the data, additional files, and R scripts ar...