Your Body is an Ecosystem: Why Microbiomes Matter

Though invisible to the naked eye, rich worlds of microbes are contained in our bodies. Our gut, skin, mouth, and most of our body is home to unique communities of microbes including viruses, protists, bacteria, archaea, and fungi. These communities are also known as the microbiome. It is estimated [1] that approximately half of the cells in our body come from our microbiome! The colonization of microbes within our body begins at birth, when we are inundated by our mother’s skin and vaginal microbiomes [2]. Once breastfeeding begins, the microbes in breastmilk begin the first colonization of our guts [2]. This early maternal exchange of microbiomes determines what kind of microbes can establish within us in the future [2]. With approximately 30-50 trillion microbial cells in the human body, they play a major role in the healthy function of our bodies.

Research overwhelmingly suggests this is the case! In our gut, microbes help break down food our stomach enzymes cannot fully digest on our own, and even produce vitamins and store energy that we can absorb later [3]. In some non-human primates that eat a lot of leaves and tough vegetation, specialized gut bacteria ferment vegetative fibers, producing energy-rich short chain fatty acids for the animal host and sugars for the bacteria [4]. Healthy gut and skin microbiomes also help protect us from harmful bacteria by preventing them from colonizing [2]. Skin and gut microbes typically work with our immune system and alert it to these potential pathogens, and even help regulate inflammation in the linings of our intestines and in our skin [2]. Our microbiomes are obviously important to our health, so what happens when they are disrupted?

Figure 1. This graphic illustrates how microbiome composition changes within different regions of human skin. From Grice and Segre [5].

Imbalances in the microbiome can be caused by a lot of different factors. Illnesses and weak immune systems can allow for the growth of harmful bacteria. Sometimes, bacteria beneficial in smaller numbers within our microbiome can take over and become harmful when our immune system is not effectively regulating them [2]. These types of bacterial overgrowths can contribute to chronic health issues and diseases like digestive inflammation and eczema [2]. For example, recent research on irritable bowel syndrome has found that symptoms are correlated with higher ratios of bacteria in the group of bacteria known as Firmicutes [6]. Firmicutes is typically present in healthy gut microbiomes, but even a 20% increase in their abundance has a major effect on gut health [6]. Using systemic antibiotics to try and solve this bacterial overgrowth problem only makes things worse, by wiping out our gut microbiomes instead of carefully changing the abundance of harmful or overgrown bacteria [7]. Another example is a small mite known as Demodex: this mite typically lives around hair follicles and oily glands on the human face without any negative impact, but overgrowth of them is tied to skin inflammation disorders like rosacea [8]. Additionally, external stress can depress the immune system and have an effect on our microbial health—researchers exploring correlates with irritable bowel syndrome also found that individuals with symptoms reported higher levels of stress and early childhood trauma [6].

Figure 2. Demodex brevis, a type of mite found in the oily glands of adult human faces. An over-abundance of Demodex brevis is associated with the chronic inflammatory skin disease rosacea [8]. Image Source: Austin Whittall

So, now we know that microbiomes have important roles to play in our bodies, but can be disturbed when our immune systems are compromised or when we are facing a lot of external stress. This information is changing the way we think about human health issues and our use of systemic antibiotics, but it is also important to the field of animal welfare and conservation! Issues like human habitat disturbance and habitat destruction can affect the health of animals by changing their microbiomes [9]. The combination of environmental stress due to human habitat disturbance and disruption of their healthy microbiota can also make animals more susceptible to diseases and parasites, particularly ones carried by humans and domestic animals invading their habitat [9]. A recent experiment controlling for the establishment of microbiota in tadpoles found that reduced microbiome diversity early in life made the frogs more susceptible to parasites as adults [10]. Other research on non-human primates has found that habitat degradation reduces the range of food resources they have access to, which in turn reduces their gut microbiome diversity and affects their health [9].

Figure 3. A mantled howler monkey. Research has shown that these primates’ microbiota is affected by human disturbance and environmental stress [9]. Image Source: Dr. Ariel Rodriguez-Vargas

Understanding how microbiomes affect our health and the health of animals is a growing area of research. Learning more about them will further our knowledge of many common human diseases, as well as influence our conservation strategies for animals as we try to reduce their susceptibility to parasites and environmental stress. There is still much to be explored in the rich world of microbiomes, which is why this summer I will be collecting pilot data on how habitat type affects the microbiomes of two lemur species in Beza Mahafaly Reserve, Madagascar. I will also explore how species-specific host traits like diet, sociality, and behavior influence microbiomes, and how microbiomes in different body regions vary. Hopefully, my pilot study will lay groundwork for future research on non-human primate health in the wake of changing habitats, particularly in Madagascar.



[2] Chen, Y. E., & Tsao, H. (2013). The skin microbiome: current perspectives and future challenges. Journal of the American Academy of Dermatology, 69(1), 143-155.

[3] Krajmalnik-Brown, R., Ilhan, Z. E., Kang, D. W., & DiBaise, J. K. (2012). Effects of gut microbes on nutrient absorption and energy regulation. Nutrition in Clinical Practice, 27(2), 201-214.

[4] Amato, K. R., Leigh, S. R., Kent, A., Mackie, R. I., Yeoman, C. J., Stumpf, R. M., ... & Garber, P. A. (2015). The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microbial Ecology, 69(2), 434-443.

[5] Grice, E. A., Segre, J. A. (2011). The skin microbiome. Nature Reviews Microbiology 9(4), 244.

[6] Labus, J. S., Hollister, E. B., Jacobs, J., Kirbach, K., Oezguen, N., Gupta, A., ... & Savidge, T. (2017). Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome. Microbiome, 5(1), 49.

[7] Stern, E. K., & Brenner, D. M. (2018). Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. Clinical and Translational Gastroenterology, 9(2), e134.

[8] Grice, E. A. (2014, June). The skin microbiome: potential for novel diagnostic and therapeutic approaches to cutaneous disease. In Seminars in Cutaneous Medicine and Surgery (Vol. 33, No. 2, pp. 98-103). Frontline Medical Communications.

[9] Amato, K. R., Martinez-Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., ... & Williams, L. (2016). Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia, 180(3), 717-733.

[10] Knutie, S. A., Wilkinson, C. L., Kohl, K. D., & Rohr, J. R. (2017). Early-life disruption of amphibian microbiota decreases later-life resistance to parasites. Nature Communications, 8(1), 86.

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