Take a Q-tip. Swipe it across the space between your eyebrows. That Q-tip now holds tens of thousands of bacteria. Before you scrub your face with an SOS pad, know that this is completely normal. Swabbing a 1 cm2 patch of skin on the human body typically collects about 10,000 bacterial cells (Grice et al., 2008). Not only is finding your skin covered in bacteria normal, it is a vital part of having healthy skin.
Just as the microbes that live in your digestive tract help with food digestion (Valdes et al., 2018), the microscopic organisms living on your skin help your body’s largest organ to be an effective barrier to the outside world. They not only help to prevent skin infections (Nakatsuji et al., 2017; Zheng et al., 2022) but also help your skin repair itself after injury (Uberoi et al., 2021; Xu et al., 2024).
To be fair, bacteria aren’t the only type of microbes on your skin. Viruses and fungi also live there. This complex community of microbial lifeforms is called the skin microbiome. The members that make up your skin microbiome tend to differ across different parts of your body (Grice et al., 2009; Oh et al., 2014). Just like you see different types of animals in a desert compared to a rainforest, you can expect to find different microbes on a dry elbow compared to a sweaty brow. Skin microbiomes also vary across people. So much so that an analysis of what microbes are on your skin and their relative abundance could be used to identify you out of a group of other people (Oh et al., 2014; Yilmaz et al., 2024). We’ve learned a great deal about what factors can influence the skin microbiome. But most of what we know is based on research that includes only a few populations of people who live in mostly western countries (e.g., United States) with modern building infrastructure and industrialization. We know that the microbial communities that occupy human skin can be influenced by a person’s environment and their behaviors (Grice et al., 2008; Moitinho‐Silva et al., 2021). Where you live, the clothes you wear, the cosmetics you use, your age, and the medicines you take can all affect your skin microbiome (Skowron et al., 2021). These factors change the landscape of your skin, what resources may or may not be available, and, by extension, what kind of microbes thrive there. So if you could compare the skin microbiomes of a group of people living in the U.S. to a group of people living in the Amazon rainforest, would they differ? It’s reasonable to think so. Not only do the environments differ, the cultural practices and human behaviors are also likely to vary. This is where any good research study starts: a question and a reasonable expectation. The next step is to test it.
What does a healthy skin microbiome look like outside of an industrialized environment?
The Yanomani are a group of around 36,000 people that live near the Brazil-Venezuala border in the Amazon rainforest. Their homes are communal, providing shelter for multiple families, and built from natural materials (e.g., wood, vines) with no artificial flooring. They live off of the land, hunting, foraging, and growing their own food (The Yanomani Foundation). This way of life is very different from what is predominantly represented by participants in skin microbiome research (e.g., Western cultures in industrialized settings). The Yanomani have played a critical role in expanding human microbiome research, contributing to multiple research studies since 2015 (The Yanomani Foundation). We’re going to focus on the latest of these studies where a research team focused on the Yanomani skin microbiome (Durack et al. 2025). These were their questions: What microbes make up the Yanomami skin microbiome? How do these microbes differ from the ones we see in more industrialized cultures? Can the characteristics of the Yanomami skin microbiome be acquired over time?
Investigating the Yanomani Skin Microbiome
To answer these questions, researchers undertook two expeditions to visit the Yanomami and collect samples from their skin microbiomes. Seventeen Yanomami, ranging in age from 1 to 70 years old, participated. The armpit, back, chest, face, scalp, forearm, crease behind the ears, and the space between the toes were sampled from each individual. These samples were sent back to a lab in the U.S. where they underwent DNA and RNA extraction. Both DNA and RNA sequences can be compared to databases with known sequences from microbes that have been previously identified. We can use DNA sequences to tell us what microbes are present (e.g., Staphylococcus or Enterococcus) and what they might be able to do (e.g., resist antibiotics, digest lipids). RNA sequences take this a bit further and tell us what these microbes are currently doing. Imagine sneaking into someone’s house and snooping through their kitchen. From a functional standpoint, the recipe book you find on the counter is like DNA; it tells you what they could potentially cook. But the chocolate chips, flour, and eggs you see on the counter are like RNA; they tell you that the person here is actively making chocolate chip cookies. The difference between functional potential and actual expression is an important distinction in microbiome research. The researchers in this study investigated both of these things: what microbes are there and what they are currently doing.
The Yanomani Skin Microbiome is Distinct in Membership and Function
In order to compare the Yanomani samples to those taken from people in a more industrialized setting, the researchers turned to a valuable resource called the Human Microbiome Project (HMP). The Human Microbiome Project was a study funded by the National Institutes of Health in 2007 with the mission of characterizing the human microbiome (The HMP Consortium, 2012). The publicly available dataset describes the microbial composition of the skin, gut, oral, and vaginal microbiomes of 300 Americans. Data from fifteen of those HMP skin samples were used for comparison against those collected from the Yanomani.
The microbial communities observed on Yanomani skin were distinct from those observed on Americans. The Yanomani samples were significantly more diverse with 80% more types of microbes, a metric called community richness, compared to the HMP samples. The researchers also found that some types of bacteria, like Brachybacterium and Brevibacterium, were unique to the Yanomani. Keep in mind this is only the microbes that could be identified. The researchers also generated 115 brand new bacterial genomes from the Yanomani data. These genomes represent microbes that haven’t been previously identified and aren’t in any available databases.
But some qualities of the Yanomani skin microbiome followed the same trends that we see in American samples. Both groups tended to lose microbial diversity as they aged and the microbes that live on the skin varied by body site (e.g., face vs. elbow). Some genera, like Staphylococcus, were common in both Yanomani and American samples at similar abundances. However, the Yanomani had more different types of Staph living on their skin and these strains tended to have fewer genes associated with the ability to make people sick. You may have heard of Staphylococcus as a common cause for skin infections. MRSA (multi-drug resistant Staphylococcus aureus) is a well known public health threat because of how difficult it is to treat. But some Staph species actually help to prevent infections, keeping other dangerous strains at bay (Maciag et al., 2023).
Another beneficial microbe that is abundant on Yanomani skin is Malassezia globosa, a fungi. The researchers found that this fungi often co-occurs with many other microbes, in other words, it plays well with others and may encourage microbial diversity. The fungi that is most abundant in the HMP samples is Malassezia restricta. While in the same genus, this fungus does not share M.globosa’s tendency to associate with a bunch of other microbes. Remember, microbial diversity is generally found to be a positive thing for human health. Infections tend to occur when one pathogenic microbe is able to take over, hog resources, and reduce the presence of other microbes.
Not only did the microbes that make up the skin microbiome differ between the Yanomani and HMP samples, they also differed in how active those microbes appeared to be in certain functions. The RNA analysis showed greater activity related to breaking down fats and fatty acids, modifying proteins, and reducing compounds known to cause damage to DNA from the Yanomani skin microbiome. These functions may help the skin to be a more effective and resilient barrier.
Can the characteristics of the Yanomami skin microbiome be acquired over time?
If you were lucky enough to visit the Yanomani and engage in their everyday lifestyle would your skin microbiome start to resemble theirs? Probably, yes! One of the American researchers traveling on this research expedition was sampled in the same way the Yanomani were, in the same 7 locations. But instead of just being sampled once, he was sampled prior to leaving the U.S., while travelling to the Yanomani, while he lived in the community (once a week for 3 weeks), and then once he returned to the States. His skin microbiome dramatically changed while staying with the Yanomani.
Over time, the diversity of his skin microbiome increased across all body sites and he gained additional bacterial taxa. In other words, there were more different microbes living on his skin. The researchers compared his samples against the Yanomani samples using a measurement called Bray-Curtis Similarity Index. The more similar two microbial communities are, the higher the value. If you were to compare a microbial community to itself you would get a value of 1 (the same); if you were to compare a sample from Old Faithful to a sample from your arm you’d likely get a value close to 0 (not similar). When this researcher started his journey the microbial community of his arm was not similar to the Yanomani (Bray-Curtis similarity ~0.2), by week 1 of his stay it was very similar (Bray-Curtis similarity ~0.7), and shortly after his return to the U.S. he was already losing that similarity (Bray-Curtis similarity ~0.4). This occurred across all body sites. The inverse was observed with a Yanomani woman who travelled back to the States with the researchers. Over time, her skin lost diversity and certain members unique to the Yanomani (e.g., Brachybacterium and Brevibacterium) disappeared from her skin microbiome. These observations suggest that the qualities of the Yanomani skin microbiome can indeed be gained…and lost.
What else can we discover?
These expeditions are an exciting starting point for researchers to work with other understudied populations. The microbiome research done with the Yanomani suggests that their microbiomes have beneficial potential due to increased diversity and functional activity. But it appears that the qualities of their microbiome are tied to their home and way of life. This is supported by the change in skin microbiome experienced by the American researcher and Yanomani participant who were sampled while traveling. But leaving one’s way of life is not always voluntary. Many Indigenous communities have experienced forced displacement and persecution of their way of life. The threat is not purely historical. An estimated 60% of Indigenous lands worldwide are currently threatened by growing industrialization, deforestation, and loss of land rights (Kennedy et al., 2023). These threats are also present for the Yanomani (The Yanomani Foundation). Is the loss of potentially beneficial skin microbial diversity another way in which Indigenous communities are harmed when they are forcibly displaced? The implications of further research could not only broaden our understanding of the human skin microbiome but also help to protect the sovereignty of these communities and their way of life.
If You’re Interested to Learn More
The Yanomani Foundation is an organization that partners with the Yanomani people. Its mission is to assist in their pursuit for autonomy, sovereignty, and ethical partnership with outside entities. On this website you can learn more about the Yanomani people, their history, and the research they’ve participated in.
The first microbiome study with Yanomani participation. In this study they looked at fecal, oral, as well as skin samples. They mainly focus on the question of “who’s there” when looking at these microbial communities but also look into whether or not some of the bacteria are resistant to antibiotics.
This TEDx talk by Dr. Brian Beck is a great introduction into human microbiome research. He gives an overview of what we know and don’t know about the microbes that live in and on humans. He discusses the impacts of exercise, diet, and probiotics on the human microbiome.
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