Research Techniques: Shedding light on the Skin Microbiome

A great deal of research has gone into understanding the skin microbiome and its impact on skin health in recent years, and there is much more yet to be discovered. In this blog, we will explore the current research techniques used for studying and analyzing the complex ecosystem, including the strengths and limitations of each technique.

The human body is home to trillions of microorganisms, including bacteria, viruses, and fungi, which are known collectively as the microbiome. The diverse and intricate ecosystem of these microorganisms that reside on the surface of our skin is referred to as the skin microbiome. The composition of this skin microbiome varies across different parts of our bodies, such as our faces, hands, armpits, and feet, reflecting the unique environment at each area 1.

Across the body, the skin microbiome plays a crucial role in maintaining skin health and overall wellbeing. It acts as a protective barrier against pathogens, helps regulate the skin’s pH, and modulates the immune system. Additionally, a balanced skin microbiome contributes to maintaining good skin hydration, elasticity, and preventing skin disorders such as acne, eczema, and psoriasis 2.

Microbial Culturing

The first powerful practical tool in the study of the skin microbiome is microbial culturing. This research technique offers unique insights into the microorganisms that inhabit our skin. Individual microorganisms from the skin microbiome are isolated and grown in pure cultures under laboratory conditions, so that researchers can investigate their specific characteristics, behavior, and function 3.

StrengthsDetailed characterization: By studying individual, isolated microorganisms, researchers can gain valuable and deep insights into their behaviors and traits, including morphology, physiology, metabolism, and growth requirements.
Functional studies: Using the pure cultures, researchers can investigate the metabolic activities and interactions of individual microorganisms, such as what compounds they produce, what chemical reactions they regulate, and what relationships they could have with you or other microorganisms.
LimitationsBias in culture selection: Microbial culturing will innately favor the study of microorganisms that are able to grow well in the laboratory. Therefore, there is a risk of excluding much of the diverse and complex skin microbiome, leading to an incomplete understanding of the microbial community.
Underestimation of diversity: Microorganisms that are difficult to culture or require specific growth conditions may be missed or underestimated, which could limit our understanding of the true diversity of the skin microbiome.
Functional limitations: Because microbial culturing can only be used to study individual microorganisms, the complex functional interactions between those microorganisms may not be captured. Many interactions and metabolic pathways can only be studied in the context of the whole microbial population.
Time and resource intensive: Culturing microorganisms from skin samples can be time consuming and resource intensive. Skilled laboratory personnel and specialized media and equipment are required, and, even with these, isolating and cultivating microorganisms can take several weeks.

As you can see from these strengths and limitations, although microbial culturing is a powerful tool for understanding specific microorganisms within the skin microbiome, to achieve a more comprehensive understanding of the whole microbial community, this technique should be used in combination with other methods. These will be discussed below.

DNA sequencing

As they have done for many areas of research, DNA sequencing techniques have revolutionized the study of the skin microbiome 4. Two commonly used methods are 16S rRNA gene sequencing and shotgun metagenomic sequencing.

16S rRNA Gene Sequencing

16S rRNA sequencing is a culture-free research technique used to identify the bacterial diversity within complex microbiomes. By sequencing a conserved region of the bacterial genome (the 16S rRNA gene sequences), researchers can identify and classify many bacteria present in one sample.

The variation in the 16S rRNA gene sequences from bacteria of different genus or species is used to create genetic fingerprints, which allow numerous bacteria to be detected at once. This can provide valuable information about the diversity and relative abundance of different bacteria present in the skin microbiome 2.

StrengthsCost-effective and informative: The technique is cost-effective and provides valuable insights into the bacterial diversity and community structure of the skin microbiome. Samples from different individuals or body sites can be straightforwardly analyzed and compared.
Taxonomic resolution: Bacteria can be identified and classified at the genus- and (in some cases) species-level. This helps to build a picture of the specific bacterial groups present and their potential implications for skin health.
LimitationsLack of species-level resolution: 16S rRNA gene sequencing can be limited to providing only genus-level resolution. The technique targets a specific region of the bacterial genome, which may not be capable of accurately differentiating closely related species.
Non-bacterial microorganisms: The method is primarily focused on bacterial diversity, so the presence of non-bacterial microorganisms, such as viruses and fungi, may be overlooked.

Shotgun Metagenomic Sequencing

Shotgun metagenomic sequencing is a powerful approach that provides a comprehensive profile of all the microorganisms present in the sample. Unlike 16S rRNA gene sequencing, all the genetic material in the sample is sequenced, including bacterial, viral, and fungal DNA. The research technique therefore enables researchers to discover novel microorganisms as they investigate the function of the skin microbiome 2.

StrengthsUnveil complete microbial diversity: Metagenomic shotgun sequencing allows for the detection and analysis of all the microorganisms present in the skin microbiome, providing a more comprehensive overview.
Functional insights: This technique can provide insights into the function of the skin microbiome by identifying genes and pathways involved in various metabolic processes, virulence, and interactions with the host.
LimitationsComputationally- and cost-intensive: Metagenomic shotgun sequencing generates vast amounts of data, which requires substantial computational resources for analysis and interpretation. This can be prohibitively expensive.
Challenges in data analysis: Analyzing metagenomic data can be complex and demanding. Sophisticated bioinformatics tools and expertise are required to interpret the genetic information obtained.

Overall, therefore, DNA sequencing techniques are well suited to building a deeper understanding of the composition, diversity, and function of the complete skin microbiome.


Metabolomics is a field of study in which researchers analyze small molecule ‘metabolites’, which in this instance are produced by the microorganisms making up the skin microbiome. The findings can be used to gain insights into the functions and interactions of those microorganisms.

Metabolomics techniques involve the identification and quantification of the metabolites using analytical methods such as mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy 5.

StrengthsFunctional insights: Metabolomics enables us to understand the actual biochemical activities of microorganisms, rather than only the potential function based on their genetics. It therefore allows researchers to understand the specific metabolic pathways and interactions occurring within the skin microbiome.
Non-biased approach: Metabolomics allows us to study the skin microbiome without bias, as it provides a snapshot of the active metabolic processes, which does not rely on appropriate genetic markers or culturing conditions, etc.
Identify bioactive molecules: Metabolomics identifies bioactive molecules produced by microorganisms, such as antimicrobial compounds, signaling molecules, or metabolites, which may offer potential benefits for skin health.
LimitationsIdentify metabolites: Identifying and characterizing metabolites is challenging due to the complexity of the skin microbiome and subsequent diversity of metabolites. Extensive databases and expertise in metabolomics analysis are required.
Dynamic nature of metabolites: The profile of metabolites within the skin microbiome can vary depending on environmental conditions, host factors, and microbial interactions. Obtaining a comprehensive understanding of all these variants can therefore be challenging.

Imaging Techniques

Advanced imaging techniques play a crucial role in visualizing and locating specific microorganisms within the skin microbiome. Two commonly used imaging research techniques are confocal microscopy and fluorescence in situ hybridization (FISH) 6.

Confocal Microscopy

Confocal microscopy allows researchers to study the 3D structure and distribution of microorganisms within the skin. Laser scanning and fluorescence detection are used to obtain high resolution images of labelled microorganisms.

StrengthsVisualize microbial communities: Confocal microscopy can show the distribution and arrangement of microorganisms within the skin microbiome. Researchers can observe microbial aggregates, biofilms, and interactions with host cells.
Live imaging: Live imaging enables real-time imaging of dynamic microbial processes, such as growth, movement, and interactions within the skin.
LimitationsLimited depth penetration: Confocal microscopy cannot be used to observe microorganisms in deep skin layers as it has limited penetration depth into the skin tissue. It is best suited to studying surface-associated microorganisms.
Sample preparation: Preparing skin samples for confocal microscopy is technically challenging. Careful fixation, staining, and mounting procedures are required to preserve the integrity of the microbial structures and minimize artifacts.

Fluorescence In Situ Hybridization (FISH)

In FISH, fluorescently labelled DNA or RNA probes are used to target and visualize specific microorganisms within the skin microbiome. The fluorescent probes bind to genetic sequences in the selected microorganisms and allow them to be seen using a fluorescence microscope 7.

StrengthsIdentify specific microorganisms: FISH can be used to identify and localize specific microorganisms within the skin microbiome. It can differentiate between different species or strains.
Quantitative analysis: FISH can be combined with image analysis software to quantify the abundance and distribution of specific microorganisms.
LimitationsTargeted microorganisms: FISH is limited to the microorganisms targeted by the chosen probes. It may therefore fail to capture the full diversity of the skin microbiome if the probes are designed only for specific groups of microorganisms.
False positives and false negatives: Factors such as probe specificity, hybridization conditions, and potential cross-reactivity with closely related microorganisms can result in false positives or false negatives. Careful experimental optimization and validation are needed to ensure good quality results.

What next?

While each of these experimental research techniques have both strengths and limitations, in combination they can be used to great effect to unveil the remarkable world of microorganisms that reside on our skin and influence its health and function. Researchers are working tirelessly to overcome the challenges faced throughout the workflow and discover more about the fascinating world of the skin microbiome. We expect upcoming research to include:

  • Functional studies: Researchers are exploring the functional capabilities and interactions between microorganisms in the skin microbiome, including metabolic activities, bioactive compounds, and communication mechanisms, to better understand their impact on skin health.
  • Longitudinal studies: Long-term studies are underway, following individuals over time to research the stability and dynamics of the skin microbiome. By investigating how the skin microbiome changes with age, environment, lifestyle, and the development of any skin conditions, we can uncover the factors that affect it and impact our skin health.
  • Microbiome-host interaction studies: It is vital that we determine the complex interactions between the skin microbiome and the host immune system, skin barrier function, etc. If we can understand these interactions at a molecular level, we can hope to establish the mechanisms by which the skin microbiome influences skin health and disease.

As understanding of the skin microbiome improves thanks to this ongoing research, we can expect innovative skincare approaches to follow, which harness the potential of the skin microbiome to promote skin health and treat dermatological conditions.


  1. Gilbert, J. A. et al. Current understanding of the human microbiome. Nature Medicine 24, 392-400, doi:10.1038/nm.4517 (2018).
  2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nature Reviews Microbiology 16, 143-155, doi:10.1038/nrmicro.2017.157 (2018).
  3. Khayyira, A. S., Rosdina, A. E., Irianti, M. I. & Malik, A. Simultaneous profiling and cultivation of the skin microbiome of healthy young adult skin for the development of therapeutic agents. Heliyon 6, e03700, doi: (2020).
  4. Chen, Y., Knight, R. & Gallo, R. L. Evolving approaches to profiling the microbiome in skin disease. Front Immunol 14, doi:10.3389/fimmu.2023.1151527 (2023).
  5. Chen, H. et al. Skin Microbiome, Metabolome and Skin Phenome, from the Perspectives of Skin as an Ecosystem. Phenomics 2, 363-382, doi:10.1007/s43657-022-00073-y (2022).
  6. Acosta, E. M. et al. Bacterial DNA on the skin surface overrepresents the viable skin microbiome. eLife 12, RP87192, doi:10.7554/eLife.87192 (2023).
  7. Amann, R. I. et al. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and environmental microbiology 56, 1919-1925, doi:10.1128/aem.56.6.1919-1925.1990 (1990).

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