Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E

Ramadan, Mohamed; Solyman, Samar; Yones, Mamdouh; Abdallah, Yaser; Halaby, Hamada; Hanora, Amro

doi:10.1089/omi.2019.0011

Cited by 21 publications

(17 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Communities were dominated by Cornebacterium and Staphylococcus species [31], and interpersonal variation far exceeded any impacts of variation associated with methodology. Closer inspection of the Staphylococcus communities revealed that AD patients and healthy controls differed significantly in composition across different metabarcoding approaches, echoing previous findings with more precise methodologies (such as culturing of bacteria [32] and shotgun metagenomics [5]), suggesting credible OTU/ASV assignments at the genus level [8]. However, crucially in this work, we highlight that metabarcoding provided inadequate taxonomic identification to investigate within-Staphylococcus community dynamics, as so few OTUs and ASVs were assigned to a species using automated approaches.…”

Section: Discussionsupporting

confidence: 75%

“…It is comparatively inexpensive and computationally less demanding than shotgun sequencing, but has been shown to lack the resolution to separate highly related species [6]. These previous metabarcoding studies were analysed using operational taxonomic unit (OTU) clustering approaches until fairly recently [8]. However, more recent methods such as DADA2 [9] and deblur [10] have emerged as complementary to, or an alternative approach to, OTU clustering, and have been shown to effectively reduce inflated bacterial richness to better represent mock bacterial communities, while also being better at aligning molecular datasets of larger organisms to morphological observations [11,12].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

Barnes

Rasmussen

Asplund

et al. 2020

Journal of Medical Microbiology

View full text Add to dashboard Cite

Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients’ skin has been shown to have an increased abundance of Staphylococcus aureus . More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus , but further studies are required to determine the effects of Staphylococcus community variation in AD. Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics. Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy). Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness. Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.

show abstract

Section: Discussionsupporting

confidence: 75%

Section: Introductionmentioning

confidence: 99%

Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

Barnes

Rasmussen

Asplund

et al. 2020

Journal of Medical Microbiology

View full text Add to dashboard Cite

show abstract

“…These new observations attest to the promise of microbiome science and metagenomic analysis in AD specifically, and clinical dermatology broadly. [ 193 ] Madagascar None Skin swabs Skin 16S rRNA, V3–V4 regions, Illumina MiSeq USA The Duke Global Health Institute and the Bass Connections Program at Duke University Cross-sectional 20 Cattle ownership had, at best, weak effects on the human skin microbiome. [ 194 ] Madagascar None Skin swabs Skin 16S rRNA, V3–V4 regions, Illumina MiSeq USA Duke University Cohort 20 We found that antibacterial soap impacts the structure of microbial communities and that these changes persist for at least two weeks.…”

Section: Resultsmentioning

confidence: 99%

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

et al. 2021

View full text Add to dashboard Cite

Background The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. Methodology We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. Results We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). Conclusions There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa.

show abstract

“…Of note, the AD group of subjects included some participants of adolescent age, while the control group of subjects were all adults (over age 18). The skin microbiota shifts as people move from childhood to adulthood due to changing levels of sebum production, lipid content, pH, and hair growth, and so there are different microbial signatures associated with AD at different ages [ 54 ]. Therefore, this study may be less applicable to children.…”

Section: Discussionmentioning

confidence: 99%

Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis

et al. 2021

View full text Add to dashboard Cite

Introduction Atopic dermatitis is a common skin disease characterized by altered cutaneous immunity in which patients often exhibit lower skin microbiota diversity compared to healthy skin and are prone to colonization by Staphylococcus aureus. Apple cider vinegar has been shown to have antibacterial effects; however, its effects on the skin microbiome have not previously been well-described. Objectives We aimed to examine the effects of topical dilute apple cider vinegar soaks on Staphylococcus aureus abundance, skin bacterial microbiome composition, and skin bacterial microbiome diversity in atopic dermatitis participants compared to healthy skin. Methods Eleven subjects with atopic dermatitis and 11 healthy controls were enrolled in this randomized, non-blinded, single-institution, split-arm pilot study. Subjects soaked one forearm in dilute apple cider vinegar (0.5% acetic acid) and the other forearm in tap water for 10 minutes daily. Skin bacteria samples were collected from subjects’ volar forearms before and after 14 days of treatment. 16S sequencing was used to analyze Staphylococcus aureus abundance and skin bacterial microbiome composition, and alpha diversity of microbiota were determined using Shannon diversity index. Results There was no difference in skin bacterial microbiome in atopic dermatitis subjects after 2 weeks of daily water or apple cider vinegar treatments (p = 0.056 and p = 0.22, respectively), or in mean abundance of S. aureus on apple cider vinegar-treated forearms (p = 0.60). At 2 weeks, the skin bacterial microbiomes of healthy control subjects were not significantly different from the skin bacterial microbiome of atopic dermatitis subjects (p = 0.14, 0.21, 0.12, and 0.05). Conclusions Our results suggest that daily soaks in 0.5% apple cider vinegar are not an effective method of altering the skin bacterial microbiome in atopic dermatitis. Further studies are needed to explore the effects of different concentrations of apple cider vinegar on skin microflora and disease severity. Trial number UVA IRB-HSR #19906.

show abstract

Skin Microbiome Differences in Atopic Dermatitis and Healthy Controls in Egyptian Children and Adults, and Association with Serum Immunoglobulin E

Cited by 21 publications

References 68 publications

Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

Apple cider vinegar soaks do not alter the skin bacterial microbiome in atopic dermatitis

Contact Info

Product

Resources

About