AT-HOME, SELF-SAMPLING OF THE SKIN MICROBIOME: DEVELOPMENT OF AN UNSUPERVISED SAMPLING APPROACH
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Large-scale skin microbiome studies are often restricted due to the need for participants to visit a research centre to have their skin swabbed by a trained individual. If samples taken by participants at home returned high quality data, similar to that generated from samples taken by trained experts under controlled conditions, it would provide the potential for studies to have larger cohorts, include participants from multiple locations, and facilitate longitudinal sample collection. Here, we describe the development of a novel unsupervised skin microbiome sample collection method and compare data quality with supervised, in lab sample collection. We enrolled 57 participants to collect skin swabs of their axilla, forearm, cheek and scalp. Initially samples were collected in our research centre under strict supervision by a trained expert. Participants then collected swabs from the same body sites 24 hours later, unsupervised, at home, which they returned to the research centre within 3 – 5 days. All samples then underwent bacterial DNA extraction and 16S rRNA gene sequencing. Yield of extracted bacterial DNA was different depending on body site, with the dry swabs from the forearm producing the lowest amount. There were no significant differences in alpha and beta-diversities between supervised and unsupervised sampling methods, regardless of body site. Taxonomic analysis of bacterial genera identified also did not differ for axilla, cheek or scalp. Our data suggest that self-sampling skin microbiome methods can produce data that is comparable to samples collected under supervision of a trained expert in lab settings. These findings should encourage scalability of future research and allow for greater representative population diversity in genomic and microbiome research.
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Please address the comments raised by the reviewers, particularly they ask for clarification on some parts of the methodology (statistics and controls) and rationale for picking sampling sites.
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Comments to Author
Generally, this paper while addressing a subject of limited novelty, does contain important information to aid with study design, presenting important information on the differences between study led sample collection and self collection for meta analysis of the skin microbiome across multiple body sites. The introduction is well researched and presents major key works. The methodologies are likely reproducible and the results are presented in an understandable format. A couple of minor points for the authors to consider: Line 51/52: The author refers to the skin microbiome as the bacteria, fungi and viruses found on the human epidermidis. While this is what is being studied within this report, the skin microbiome includes species that may reside deeper within the skin layers. Line 125: It is stated …
Comments to Author
Generally, this paper while addressing a subject of limited novelty, does contain important information to aid with study design, presenting important information on the differences between study led sample collection and self collection for meta analysis of the skin microbiome across multiple body sites. The introduction is well researched and presents major key works. The methodologies are likely reproducible and the results are presented in an understandable format. A couple of minor points for the authors to consider: Line 51/52: The author refers to the skin microbiome as the bacteria, fungi and viruses found on the human epidermidis. While this is what is being studied within this report, the skin microbiome includes species that may reside deeper within the skin layers. Line 125: It is stated the age range of the volunteers. It would have been helpful to show a scatter of the age distribution of volunteers, especially females as changes are known to occur post menopause and this population appears to be primarily consist of older volunteers. It is also unclear if an environmental control swab is included in these samples. Section starting line 136 Skin microbiome sampling: it is made clear elsewhere that the swabs used were dry, but it is not clear in this section that only dry swabs were used. Sections starting line 163/171: While the methodology for the PCR and qPCR's are referenced, it would be helpful for the primer sequences and thermocycling conditions to be reported. Line 275: A comment is made about environmental contamination, but no environmental control appears to have been taken. It would be useful to have a comment about the potential use of environmental controls. Figure 2: It was unclear if any statistical testing had been performed on the data especially figure 2a. I would suggest that the authors make this more explicit.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
The authors present a very interesting manuscript that provides a protocol that can be exploited to sample the microbiome at home. Overall, this manuscript will prove a valuable tool for skin microbiome researchers in the design/planning of studies but requires some additional context in places. Specific comments provided below: Line 101 - 102: How did you select sites for sampling. Was this to identify difference across sebaceous, moist and dry site, or perhaps photexposed/unexposed. Perhaps justification of sampling sites is warranted. Line 106 - 107: Why did you select 16s sequencing, when perhaps other methods such as nanopore/metagenomics might provide better species resolution and kingdom wide assessment? Line 125 - 127: Why this age range, any justification? Or simply just those that signed up?
Comments to Author
The authors present a very interesting manuscript that provides a protocol that can be exploited to sample the microbiome at home. Overall, this manuscript will prove a valuable tool for skin microbiome researchers in the design/planning of studies but requires some additional context in places. Specific comments provided below: Line 101 - 102: How did you select sites for sampling. Was this to identify difference across sebaceous, moist and dry site, or perhaps photexposed/unexposed. Perhaps justification of sampling sites is warranted. Line 106 - 107: Why did you select 16s sequencing, when perhaps other methods such as nanopore/metagenomics might provide better species resolution and kingdom wide assessment? Line 125 - 127: Why this age range, any justification? Or simply just those that signed up? Perhaps a brief discussion of methods of sampling, rather than just in the supplementary information? Line 292 - 293: Could you hypothesis on how you might improve microbial sampling based upon the literature. For example, there are swabs emerged in gel that might be beneficial for your applications. Figure 4: Nomenclature, Propionibacterium and Cutibacterium are the same genus? Can you pool data in figures from these? Do you have an ethical approval number for sampling?
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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