Sarah Araten ’20

The human microbiome, or the various microbes that live inside and on our bodies, is fragile yet resilient. Upon humans’ entrance into the world, they acquire their unique microbiome. These microbes take up residence all over the human body: in the stomach, the mouth, and on the human skin (21). There are many different factors that affect an individual’s microbiome, as well as the different parts of this individual’s microbiome; in fact, many of the common things that we do today are affecting our microbiomes in a big way.  In particular, the skin microbiome is affected by a wide range of common practices. This includes our interactions with different people, hand washing, using bandages, and using makeup products and ointments (19)(18)(20).


The four bacterial phyla commonly found on the skin are Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes, with the phyla Actinobacteria being the most abundant in the skin microbiome (18). The first step in determining which bacteria are in a specific region involves sampling from these regions, which is then followed by two separate methods. The first method involves culturing the bacteria from the samples (18) by letting them grow in the lab, and then analyzing the ones that grow to determine what types of bacteria are present (19). A downside to this method is that not all extracted microbes can be grown on the general medium that is used in the lab. Without these microbes, entire categories of microbes could become unculturable, if  a subset that could not grow was essential for the growth of others (19). A different method involves taking the DNA from the sample and using PCR to amplify the 16S rRNA gene (18)(19)(20). 16S rRNA is a gene on the bacterial DNA that will eventually give rise to the rRNA that will be in the small subunit of bacterial ribosomes (19). Since this sequence encodes the bacteria specific ribosomal subunit, no human DNA, or eukaryotic DNA, will be amplified by the PCR reaction, so only bacterial DNA will be analyzed (18). Once the 16S rRNA gene has been amplified, this region will be sequenced and then analyzed to figure out what species of microbes are present in the sample (19). This method is effective because although there are some shared genetic regions across all bacteria in the 16S rRNA gene, there are also unique regions for each species. In this way, DNA sequences can help to determine what bacterial species are present in a region of skin (19)(18)(20). This sequencing method informed scientists of the presence of  microbes on the skin that were different and more numerous than did the standard culture method. However, the method is not foolproof and does have some disadvantages (19). One such disadvantage is that since the DNA does not have to first be found in living cells, it is impossible to tell whether the DNA samples were solely of bacteria that had been living on the site at the time, or if the DNA was a mix, belonging to both living bacteria and ones that had been long dead but whose DNA samples remained and could still be detected (18)(20). Another disadvantage of this method is that PCR amplification step does not necessarily amplify each strand equally, so the proportions of different species per sample can be skewed (18). Despite these problems, sequencing techniques still enable the investigation of many microbiomes from different regions on the body. It is also important to note that along with the bacteria in the skin’s microbiome, other organisms such as fungi and mites also make the human skin their home (18)(19)(13), and although not yet officially members of the skin microbiome, viruses can also be found on the human skin(19)(13).

The skin microbiome is essential to humans, as the presence of bacteria on the skin helps to keep human pathogens from growing there and causing harm (5). The bacteria Staphylococcaceae epidermidis (S. epidermidis), a type of Firmicutes (18) is evidence of this, because its excretions make the skin environment inhospitable for microbes that are harmful to humans. The S. epidermidis bacteria also help strengthen the human immune system because with microbes in the vicinity, the immune system is able to recognize that these bacteria have some of the same characteristics as pathogens and thus can create immune responses that will be useful once a real pathogen appears (5)(18)(4). Although these microbes are beneficial in this sense, it is important to note that some of these microbes can at some point become pathogenic as well, depending on the condition of the skin or their entrance into the human body (19). In fact, the very species S. epidermidis that is useful for warding off other pathogenic bacteria can itself become pathogenic. In these cases, the S. epidermidis bacteria gets inside the human body and forms structures – especially in artificial components of the body – that help them thrive even in the presence of antibiotics. Although these bacteria normally live on the human skin without causing trouble, it is once they get into the body that their presence becomes problematic (18)(5)(13)(11). There are some interesting correlations between these types of infections and unintentional human actions. One such example is the usage of bandages to protect a wound. The rationale behind this habit is to apply a bandage to shield the wound from any outside bacteria that could then infect the wound and cause further complications. However, it turns out that covering up the wound with a bandage provides the perfect conditions in which bacteria on the skin can thrive and enter the wound, causing infections nonetheless (19).

A common condition that is linked to the skin microbiome activity is acne, which stems from the growing population of Propionibacterium acnes (P. acnes)(17), a type of Actinobacteria (12) that live on the pilosebaeceous unit, regions on the face that contain both hair and glands which produce oil (17). During the teenage years, the number of P. Acnes goes up as a result of the growing unit. When these organisms are there, they hurt the unit, causing the unit to inflame, which may be what produces the acne inflammations (6)(18)(17)(13)(4).

What most people do not realize is that the common practice of using deodorant or antiperspirants alters the skin microbiome (16). An early study on the matter, conducted by Natsch in 2002, examined two different chemicals that caused odor in the axilla, or underarm. This study explained that the products of the human sweat glands in the underarms do not actually have any odors, but that these products are used by microbes in the armpit region to synthesize the molecules that give off an odor. These final products are 3-methyl-2-hexenoic acid and 3-hydroxy-3-methylhexanoic acid, and are produced by different microbes.  Scientists looked for these compounds by sifting through samples from human underarms and looking for the compounds that would begin to give off an odor over time, which was indicated by bacteria producing odor upon contacting these compounds. The researchers found that the sweat glands produce 3-methyl-2-hexenoic acid and 3-hydroxy-3-methylhexanoic acid with glutamines attached to each compound. Bacteria have an enzyme that recognizes a compound with a glutamine attached to it and subsequently cleaves the bond between the substance and the amino acid. This new product, lacking the glutamine, gives off an odor which causes the common body odor smell (8). In subsequent years, there have been a few more discoveries of compounds that can be broken down by the bacteria to create this odor, resulting in a total of four known products that are able to cause this odor once broken down by the bacteria (15)(9)(10)(14). Some people have a specific mutation that causes them to have a lower level of production of these principal compounds, and thus these individuals had less odor. Despite this, people with these mutations still had some bodily odor from their underarms, which may demonstrate that there are other components of this process that can cause bodily odors. One part of the experiment involved the participants reflecting on their deodorant or antiperspirant daily habits. The results showed that fewer people with the mutation ended up using deodorant or antiperspirants on a daily basis, likely because their bodily odor was not as defined as those who did not have the mutation on both strands (7). Studies have also been conducted to classify the types of microbes that live in the armpit region, and it has been found that the majority of them belong to the genera Staphyloccocus and Coryneaubacteria (3)(2). There are a number of ways that humans have attempted to limit the odor that are produced by these bacteria. One method is applying deodorant, which works by emitting different, more pleasant, odors in the region where the microbes are producing odorous compounds. Deodorant often also contains molecules that kill microbes in the region so that although the preliminary compounds are produced, the microbes that facilitate conversion to an odorous compound are lacking. Another method to combat body odor involves the use of antiperspirants. These work to eliminate sweat altogether by utilizing metal components that combine with biological compounds to clog sweat excretion sites (1).

A study conducted by Julie Urban of the North Carolina Museum of Natural Sciences analyzed the different effects that underarm products have on the armpit microbiome. In part of this study, samples were taken from the armpits of three different types of people: those who used antiperspirant, those who used deodorant, and those who used no product. The study lasted eight days. During the first day, participants went about their normal routine. For the next five days, participants abstained from using products, but still had samples taken from their armpits to analyze the change in their microbiome. During the last two days, all participants used an antiperspirant and their armpits were sampled as before. From these samples, the researchers grew the bacteria in the lab in cultures to see what types of bacteria were living in the armpit at each of these stages. They also performed 16S rRNA sequencing to identify any bacteria that had been there but that could not grow on the culture. The results showed that people who originally used deodorant or antiperspirants had more Staphylococcaceae bacteria than those who used no product, but had fewer Corynebacterium than did those who did use product (16). A previous study had shown that people who used deodorant and were sampled had more types of microbes in their armpit microbiome than did people who used deodorant (3). Once everyone stopped using their products, the amount of bacteria growing in the armpits of each participant increased, but those who had just stopped using antiperspirant did not have as large of an immediate increase in microbes as the others did. Overall, those who ceased using antiperspirant gradually experienced a large increase in the Staphylococcaceae bacteria and only a slight increase in the number of Corynebacterium, while those who stopped using deodorant got an increase in Corynebacterium and a decrease in Staphylococcaceae bacteria. Then, once everyone used an antiperspirant product, they all had a significant decrease in the number of microbes found in their armpits, something that could be seen that day (16). These results are interesting because they show the day by day effect that changes in underarm product use has on the armpit microbiome. These changes invoke a question as to whether there is any correlation between these microbiome changes and  health benefits or detriments. Hopefully, future research will seek to elucidate answers to this question.



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