ABSTRACTPercutaneous osseointegrated (OI) prostheses (POPs) are used to skeletally attach artificial limbs in amputees. While any permanent percutaneous interface is at risk of becoming infected by the resident microbiota colonizing the stoma, most of these patients remain infection‐free. Avoidance of infection likely depends upon a mechanically and/or biologically stable skin‐to‐implant interface. The ultimate question remains, “why do some stomata become infected while others do not?” The answer might be found in the dynamic bacterial communities of the patient and within the stomal site itself. This study is an appendix to the first Food and Drug Administration approved prospective early feasibility study of OI prosthetic docking, in which, 10 transfemoral amputees were implanted with a unique POP device. In this analytical, longitudinal cohort study, each patient's skin and stomal microbiota were analyzed from the initial surgery to 1 year following the second‐stage surgery. During each follow‐up visit, three swab samples—stomal, device thigh skin and contralateral thigh skin—were obtained. DNA was extracted, and bacterial 16S ribosomal RNA (rRNA) genes were amplified and sequenced to profile microbial communities. The stomal microbiota were distinct from the microbiota on the adjacent thigh skin and the skin of the contralateral thigh, with a significantly increased abundance of Staphylococcus aureus within the stoma. Early on stomal microbiota were characterized by high diversity and high relative abundance of obligate anaerobes. Over time, the stomal microbiota shifted and stabilized in communities of lower diversity dominated by Streptococcus, Corynebacterium, and/or Staphylococcus spp. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:2645–2654, 2019

Dataset S1. Results from differential expression analysis. Rows contain the 15,448 features analyzed. Columns contain Ensembl feature id, mean expression of GF samples, mean expression of SPF samples, the NOISeq differential expression statistic theta, the probability of differential expression (equal to 1-FDR-corrected p value when using NOISeqBio, DEGs defined as those with prob. > 0.9), the log2 fold change in expression (upregulated in GF > 0, downregulated in GF

Background: The skin harbors complex communities of resident microorganisms, yet little is known of their physiological roles and the molecular mechanisms that mediate cutaneous host-microbe interactions. Here, we profiled skin transcriptomes of mice reared in the presence and absence of microbiota to elucidate the range of pathways and functions modulated in the skin by the microbiota. Results: A total of 2820 genes were differentially regulated in response to microbial colonization and were enriched in gene ontology (GO) terms related to the host-immune response and epidermal differentiation. Innate immune response genes and genes involved in cytokine activity were generally upregulated in response to microbiota and included genes encoding toll-like receptors, antimicrobial peptides, the complement cascade, and genes involved in IL-1 family cytokine signaling and homing of T cells. Our results also reveal a role for the microbiota in modulating epidermal differentiation and development, with differential expression of genes in the epidermal differentiation complex (EDC). Genes with correlated co-expression patterns were enriched in binding sites for the transcription factors Klf4, AP-1, and SP-1, all implicated as regulators of epidermal differentiation. Finally, we identified transcriptional signatures of microbial regulation common to both the skin and the gastrointestinal tract. Conclusions: With this foundational approach, we establish a critical resource for understanding the genome-wide implications of microbially mediated gene expression in the skin and emphasize prospective ways in which the microbiome contributes to skin health and disease.

Sample summary statistics. Rows contain the 16 samples analyzed; with columns containing associated sequencing statistics and metadata. (XLSX 56Â kb)

Background/ObjectivesAcne, a common pediatric disease, tends to be more comedonal in preadolescents, whereas older individuals are more likely to have inflammatory lesions in addition to comedones. Thus the microbiome of preadolescents may be different. In this pilot study we aimed to characterize the preadolescent acne microbiome, compare the microbiome in preadolescents with and without acne, and investigate changes in the microbiome after topical treatment with benzoyl peroxide or a retinoid in a small cohort of preadolescents. MethodsParticipants were 7-10 years of age with (intervention group) or without (control group) acne and were recruited during routine outpatient dermatology visits. Baseline questionnaires, physical examination, and pore strip application were performed for all participants. Intervention group participants were randomized to receive topical therapy with benzoyl peroxide 5% gel or cream or tretinoin 0.025% cream. Participants with acne were followed up 8-10 weeks later and pore strip application was repeated. ResultsPreadolescents with acne were colonized with a greater diversity of cutaneous bacteria than controls and the most commonly identified bacterium was Streptococcus. The number of bacterial species and phylogenetic diversity decreased after treatment with benzoyl peroxide and tretinoin. ConclusionThe predominant bacteria in microbiome studies of adult acne is Propionibacterium, whereas in this pediatric population we saw a lot of Streptococcus bacteria. After treatment, the microbiomes of intervention group participants more closely resembled those of control group participants.

It is unclear how the skin maintains homeostasis with the colonizing microbiota, and how the host distinguishes commensal or symbiotic microbes from pathogens. We hypothesize that the cutaneous defense response, and in particular innate immune pathways, are differentially regulated in a microbiota-specific manner. We colonized germ free (GF) mice with microbial isolates and/or consortia and used RNA sequencing to identify differentially expressed genes and pathways in the skin. When comparing skin from GF mice to conventionally raised C57BL/6J mice (CONV), 1,017 genes were differentially expressed, and Gene Ontology terms that were significantly enriched included innate immunity genes involved in the complement pathway (i.e. C3) and genes encoding chemokines (i.e. Ccl5) and pattern recognition receptors (i.e. Tlr genes) were up regulated in CONV skin (FDR corrected p-value < 0.05). Keratinocytes provide the first cellular contact with microbiota and are a source of innate immune mediators; thus to determine the cellular contributions to gene expression we interrogated gene expression in CD45- epidermal cells. We are also establishing pathogen- (i.e. Staphylococcus aureus) and commensal- (i.e. S. epidermidis) specific signatures of gene expression which suggest that different microbial consortia elicit distinct host responses. These studies provide novel insights into the regulation of host gene expression and defense responses by the skin microbiota.