Skin Microbiome Testing: Practical Guidance from Sample Collection to DNA Extraction
1. Why the skin microbiome matters
The skin is the body’s largest organ and one of its most exposed biological interfaces. It is also a microbial habitat. Bacteria, fungi, viruses and other microorganisms live across its surface and within specific skin structures, where they interact with the barrier, immune system, sweat, sebum and local environmental conditions. These communities are not random; they are shaped by the physiology of each skin site, including whether the area is sebaceous, moist or dry [1].
Skin microbiome is increasingly relevant in dermatology research, cosmetic science, wound research and microbiome-based product development. Altered microbial communities have been reported in conditions such as atopic dermatitis, psoriasis and acne [2], and microorganisms can also influence chronic wound environments [3]. The association is not always simple or causal, but it is biologically meaningful enough to justify careful investigation.
Skin microbiome testing usually aims to answer a practical question: which microorganisms are present, in what relative abundance, and how does that profile change across sites, time points, interventions or disease states? The quality of the answer depends less on sequencing alone than on the full workflow before sequencing begins.
2. Skin is a difficult sample type
Skin is a low-biomass sample source. Compared with stool or oral samples, the microbial load is low, while the risk of environmental or reagent-derived contamination is higher. Differences in swab handling, storage, lysis and extraction can therefore have a visible effect on the final microbiome profile.
Host DNA is another challenge, particularly for shotgun metagenomics. Human DNA can dominate the total DNA pool and reduce the proportion of useful microbial reads. For this reason, 16S rRNA gene sequencing is often used in skin microbiome studies, as it targets bacterial marker genes rather than sequencing all DNA present in the sample. This can make it a practical option for bacterial community profiling when microbial biomass is low.
Site-specific variation also matters. A cheek, axilla, forearm and scalp sample should not be treated as interchangeable. Sebaceous, moist and dry zones support different microbial communities, and factors such as cosmetics, washing, sweating, topical medication and recent environmental exposure can influence what is collected.
3. Skin sample collection: choosing the method carefully
Several collection methods are used in skin microbiome studies. Each has a place, but consistency within a study is more important than switching methods to chase higher yield.
Table 1: Comparison of common skin microbiome sampling methods.
|
Method |
Pratical advantages |
Main limitations |
|
Swabbing |
Non-invasive, scalable and suitable for repeated or decentralised sampling |
Mainly collects surface material; pressure and stroke number must be standardised |
|
Scraping |
Can increase collected material in some settings |
Less comfortable and more operator-dependent |
|
Tape stripping
|
Captures superficial layers and may be useful for viable bacteria studies |
Adhesive type, pressure and repeated strips can affect tolerability and yield |
|
Biopsy |
Accesses deeper skin structures |
Invasive and rarely suitable for large or longitudinal studies |
A recent pilot cohort study comparing flocked swabs with skin scrapings in healthy children found that both methods produced similar bacterial compositional profiles, but flocked swabs collected a higher total bacterial load and followed a simpler protocol. [4]
For practical studies, the key variables should be fixed before sampling begins: swab material, moistening buffer, sampled area, sampling duration, pressure, and body site marking. A defined sampling square, a fixed swabbing time and clear operator instructions can reduce avoidable variation.
4. Stabilisation: the step that protects the study design
Once a skin sample has been collected, the sample is no longer in its original environment. Without suitable preservation, storage time, temperature and freeze-thaw events can influence the material available for analysis. Immediate freezing at very low temperature has often been preferred in research settings, but this is not always practical for field studies, self-collection or multi-site sampling.
A stabilisation buffer system should aim to preserve the microbial DNA profile at the point of collection and allow realistic transport conditions. Room-temperature stability is particularly useful when samples are collected outside a laboratory or shipped from participants to a central processing site.
The practical recommendation is clear: do not treat stabilisation as an administrative detail. It is part of the analytical workflow.
5.DNA extraction from skin swabs
DNA extraction from skin samples is technically demanding because the starting material is limited and mixed. A robust protocol must lyse Gram-positive bacteria, Gram-negative bacteria and, where relevant, fungi, while limiting inhibitors that can interfere with PCR, library preparation or sequencing.
Extraction kit choice is not neutral. In a study comparing 12 commercial DNA extraction kits for skin microbiome analysis, successful 16S rRNA library preparation ranged from 39% to 100%, showing how strongly extraction methodology can influence sequencing success. [5]
Quality control should include DNA yield, purity ratios where sufficient DNA is available, inhibition checks for PCR-based workflows, and library preparation success. For long-read or metagenomic applications, fragment size and host DNA contribution become more important.
6. Downstream analysis: match the method to the question
The choice of downstream analysis should follow the study question. For many skin microbiome studies, 16S rRNA gene sequencing is a practical method for bacterial taxonomic profiling. The 16S ribosomal RNA gene contains conserved regions that allow broad bacterial amplification and variable regions that allows to differentiate bacterial groups. This makes it suitable for comparing bacterial community composition across body sites, participant groups, treatment conditions or time points.
Because 16S rRNA sequencing targets a bacterial marker gene, it also reduces the impact of human host DNA compared with shotgun metagenomic sequencing. This is particularly relevant for skin swabs, where microbial biomass is often low and host DNA can make up a large proportion of the total DNA recovered.
Shotgun metagenomic sequencing on the other hand can provide broader information, including higher-resolution taxonomic data and functional insights. However, it generally requires higher DNA quality and quantity and is more sensitive to host DNA background. ITS sequencing may be added when fungal community profiling is part of the study design.
For all low-biomass skin microbiome workflows, controls are essential. Swab blanks, extraction blanks and library blanks help identify background contamination introduced during collection, extraction or sequencing preparation. Consistent collection, stabilisation, extraction and library preparation also help reduce batch effects and support more reliable interpretation.
7. Best practice summary
|
Step |
Best practice |
Why it matters |
||
|
Sampling site |
Define the exact body site and record where the sample was taken. |
Skin microbiome profiles vary between dry, moist and sebaceous areas. |
||
|
Collection technique |
Use the same swab type, sampling area, swabbing time, pressure and number of strokes across comparable samples. |
Standardisation reduces avoidable technical variation. | ||
|
Pre-sampling conditions |
Ask participants to avoid washing, cosmetics, lotions and deodorants on the target area before sampling, according to the study protocol. |
Recent skin preparation can influence the microbial profile collected. |
||
|
Documentation |
Record recent washing, swimming, antibiotic exposure, topical product use and protocol deviations. |
Metadata helps interpret unexpected variation between samples. |
||
|
Stabilisation |
|
|
||
|
DNA extraction |
Use a protocol designed for low-biomass skin samples and efficient microbial lysis. |
Skin swabs often contain limited microbial material and mixed microbial cell types. |
||
|
Controls |
Include swab blanks, extraction blanks and library blanks. |
Controls help identify background contamination in low-biomass workflows. |
||
|
Quality control |
Assess DNA yield, purity and suitability before PCR, 16S rRNA sequencing, ITS sequencing or shotgun metagenomics. |
Early QC reduces the risk of failed downstream analysis. |
||
|
Workflow consistency |
Apply the same collection, stabilisation, extraction and analysis approach across comparable samples. |
Consistency supports clearer comparison across sites, groups or time points. |
8. What Invitek offers for skin microbiome research
At Invitek Diagnostics, we support skin microbiome workflows from sample collection to microbial DNA extraction.
The DermaSwab® DNA Collection Kit enables standardised collection and stabilisation of skin microbiome samples from dry, wet and sebaceous skin. Samples are transferred into a Skin DNA Stabilizer Tube, where microbial DNA can be stabilised for up to 6 months at room temperature.
The PSP® Spin Skin DNA Kit is designed for microbial DNA extraction from fresh or stabilised skin samples collected with DermaSwab®. Purified DNA is suitable for downstream applications such as 16S rRNA gene sequencing, ITS sequencing, and shotgun metagenomic sequencing.
Together, the DermaSwab DNA Collection Kit and the PSP® Spin Skin DNA Kit provide a practical workflow from skin swab collection to purified microbial DNA. By connecting collection, stabilisation and extraction, the workflow helps laboratories manage key variables before downstream microbiome analysis begins.
9. Summary
Skin microbiome testing can provide useful insight into microbial community composition, but reliable results depend on careful control of the full workflow. Standardised sampling, immediate stabilisation or freezing, suitable DNA extraction and appropriate downstream analysis all help reduce technical variation.
At Invitek Diagnostics, we support this workflow with solutions for skin sample collection, stabilisation and microbial DNA extraction, helping laboratories manage key variables before downstream microbiome analysis begins.
👉 Stay Ahead in Molecular Diagnostics
Subscribe to Invitek’s blog and get expert insights, research updates, and emerging technology trends - straight to your inbox.
References
(1) Grice EA, Segre JA. The skin microbiome. Nature reviews. Microbiology. 2011 Apr;9(4):244-253. DOI: 10.1038/nrmicro2537. PMID: 21407241; PMCID: PMC3535073.
(2) Orsmond A, Bereza-Malcolm L, Lynch T, March L, Xue M. Skin Barrier Dysregulation in Psoriasis. International Journal of Molecular Sciences. 2021 Oct;22(19):10841. DOI: 10.3390/ijms221910841. PMID: 34639182; PMCID: PMC8509518.
(3) Falanga V, Isseroff RR, Soulika AM, et al. Chronic wounds. Nature reviews. Disease Primers. 2022 Jul;8(1):50. DOI: 10.1038/s41572-022-00377-3. PMID: 35864102; PMCID: PMC10352385.
(4) Smith A, Ghori NU, Foster R, et al. Optimisation of the sampling method for skin microbiome studies in healthy children: a pilot cohort study. Frontiers in Microbiomes. 2024 ;3:1446394. DOI: 10.3389/frmbi.2024.1446394. PMID: 41853531; PMCID: PMC12993633.
(5) Bjerre RD, Hugerth LW, Boulund F, et al. Effects of sampling strategy and DNA extraction on human skin microbiome investigations. Scientific Reports. 2019 Nov;9(1):17287. DOI: 10.1038/s41598-019-53599-z. PMID: 31754146; PMCID: PMC6872721.
