SKIN MICROBIOME
skin microbiome. A limitation of amplicon sequencing is the lack of information on the interactions between microorganisms. On top of that, the resolution of typing the bacteria is often limited to the genus level. Species level is difficult and strain level is almost impossible. In other words, the music-ignorant person is
not able to identify a violin from the symphony but rather identifies it as a string instrument. Amplicon sequencing looks at the complete symphony; all the instruments are (partially) identified but it is not possible to listen to the music.
Metagenomics In vivo metagenomics is a revolutionary technique that considers the entire genome to find out who is there. This technique therefore also includes fungi, viruses, and other microorganisms. Because the complete genome is used, the resolution is much better than amplicon sequencing. Not only will the violin be identified, but
it is even possible to find out that the violin is a Stradivarius. Metagenomics even gives information about the interactions between microorganisms. The test also shows what microorganisms can potentially do. So, metagenomics can identify the complete symphony and it will highlight the individual sound of each instrument. Metagenomics is a relatively new test to
analyze microbial communities. The DNA can be directly acquired from the skin microbiome without cultivating bacteria. Smaller, fragmentized chunks of DNA are sequenced, meaning that the exact order of A, G, C, and T is determined because these letters form the alphabet of the DNA.
The output is an enormous list of DNA
strands. Imagine combining thousands of jigsaw puzzles and each piece of DNA represents a piece of a puzzle. The next step is to complete all these thousands of jigsaw puzzles. Luckily, those DNA puzzles are not solved by hand, but by a clever algorithm that tries to reassemble all the genomes back together. When the genome is complete, the
algorithm can identify to which microorganism the genome belongs. Imagine looking at a finished puzzle and the picture reveals an S. epidermidis or a C. acnes. This process is repeated for all the genomic
puzzles that are scattered throughout the data. As previously mentioned, metagenomics can determine what microorganisms are capable of. The algorithm can search for genes encrypted in the genome and annotate them to a function. This is a great way to learn about the potential of the skin microbiome. Although metagenomics is a revolutionary
technique to analyze a whole microbial community at once, it is not perfect. First, the genomes, or metaphorically, the
puzzles are often not complete. Many pieces are missing, which makes it more difficult to conclude to which species the DNA belongs. Second, algorithms make mistakes and
can misplace pieces of DNA. Chances are that a puzzle piece of the S. epidermidis is mixed with the C. acnes puzzle pieces. This creates a
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Figure 1: The collection of different molecular tests to choose from when analyzing the skin microbiome Amplicon
so-called chimera, after the Greek mythological creature. Third, the technique does not require any
prior knowledge. It is unknown whether there are only ten species or ten thousand species present. In other words, the number of puzzles that must be completed is unknown. Finally, the technique to identify a species
relies on databases. The database identifies the selected picture and assigns a piece of DNA to a species. However, chances are that the database is
outdated, or there is a completely new species found. When building a puzzle, it is easy to work from a reference image. It is much harder when there is no reference. Although metagenomics faces quite some
challenges, there is a whole branch of science dedicated to solving them. Bioinformatics designs algorithms to tackle all these problems. Today, easy-to-understand software exists to make metagenomics as accessible as possible. There are sequence devices on the market that are as big as a mobile phone. The costs of these tests have been
significantly reduced and with little training, people can easily analyze the output. So, metagenomics is part of the cosmetics analytical toolbox and is a great way to identify the microbial orchestra.
Metatranscriptomics The next step is to start listening to the symphony and this is achieved by metatranscriptomics. Instead of analyzing the DNA, the RNA is analyzed. RNA describes the function: “What is the skin microbiome doing?” RNA is the messenger that tells the cell which proteins should be manufactured. By analyzing all the RNA, it creates a snapshot of the cell’s gene expression. Metatranscriptomics completes the symphony. All the instruments are identified and for the first time, the music is audible. Metatranscriptomics is still in its infancy as
there are not many experienced commercial laboratories to analyze the skin microbiome by metatranscriptomics. The technique is more sensitive than metagenomics. RNA is a fragile molecule; the skin produces enzymes to break down the RNA and it is also difficult to have enough material. Although it is a powerful technique to map the function of the skin microbiome, it loses the power to precisely identify the microorganisms within the community because a small string of RNA is less identifiable than analyzing the whole genome. On the other hand, a big advantage of metatranscriptomics is that it allows us to distinguish between living and dead microorganisms. Metagenomics, which focuses on DNA,
April 2025 PERSONAL CARE Metabolomics
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Metagenomics
Microbiome Metatranscriptomics
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