skip to Main Content

Every year the Center for the Study of Human Health hosts a booth at the Atlanta Science Festival. The topic and booth is conceived and built by a team of undergraduate students under the guidance of Human Health professor Dr. Amanda Freeman. This year’s booth focuses on the microbiome. This post gives an overview of the microbiome but make sure to come by our booth at the festival tomorrow to learn more and do some fun, hands-on activities (Piedmont Park, 11am – 4pm, Booth E-617: Your 100 Trillion Best Friends)

Trillions of microbes, including fungi, bacteria, and viruses, inhabit the human body and are referred to collectively as the human microbiota. While we often consider bacteria to be pathogenic, or disease causing, we have a mutually beneficial, symbiotic relationship with many of these microbes. The human microbiota composition is unique to every person and the microbial communities differ depending upon the area of the body. Our microbiome plays a key role in our health, in part through regulation of immune responses. The composition of our microbiome can be influenced through diet, environmental exposures, and antibiotics.

The first three years of life play an important role in determining the composition of the human microbiota.[1] An infant’s microbiome is largely influenced by birth mode. The gut microbiome of infants born vaginally closely resembles the microbial composition of the birth canal and fecal flora. Meanwhile, infants born via Cesarean section (C-section) have an increased proportion of microbes which typically reside on the skin.[2] The composition of breast milk, including antibodies, influences the diversity of gut microbes and helps shape a personalized microbial community. The transition to solid foods is another prominent influence on the gut microbiome.[3] Not only does the food we eat supply our bodies with nutrients and energy, but the microbes in our gut, which we need to stay healthy, are only able to thrive when supplied with nutrients from our diet. Environmental exposures influence the microbiota composition and individuals who live in urban areas tend to have less diverse microbiota than those living in more rural areas.[4] Going outside to increase your exposure to a wide variety of environmental microbes is important since the more diverse your microbiome is – the better!

The environment actually plays a bigger role in ruling the arrangement of the gut microbiome than the genetics of the individual. Only about two to eight percent of the human microbiome is actually heritable.[5] On the other hand, the microbiome-environment interactions are crucial, for they determine changes in the microbiome function that could later impact an individual’s health. For instance, decreases in the microbiome’s diversity associated with C-section births has been linked to increased risks of asthma,[6] Celiac disease,[7] and obesity.[8]

Diet plays one of the most significant roles in determining the composition of your gut microbiome. Compared to a typical Western diet, studies have shown that a diet low in fat and animal protein and high in starch, fiber, and plant-based carbohydrates increases beneficial gut bacteria that are found in those who have a healthy body weight.[9] These are also the same bacteria that are found in the gut when people with obesity lose weight.[10] These gut bacteria cause the decrease of fat production, inflammation, sugar levels, and can even decrease hunger and increase immune function. Breastfed infants living in different locations were found to have a similar microbiome composition,[9] which indicates that diet has a greater impact on the microbiome than does environment. Studies have also shown that twins do not have similar microbiomes, so diet is also more influential than genetics.[11] All of this data exemplifies that you are largely in control of your own microbiome through your diet! Foods that promote a healthy, diverse microbiome include high-fiber, low-sugar fruits, vegetables, and some fermented products.[12]

While antibiotics can be used to save your life, their constant or unnecessary use also disrupts the balance of your microbiome. Antibiotics are unable to differentiate between the good and bad bacteria living in our bodies, wiping out some of the good ones that protect us from future infections and cultivating some resistant bad bacteria. Diminishing the diversity of our gut microbiota has been linked to many chronic diseases, such as childhood diabetes, allergies, and cancer,[13, 14] Trace amounts of antibiotics that we are exposed to through non-organic foods and antibacterial soap slowly add up, contributing to the growth of antibiotic-resistant bacteria. After the introduction of albeit life-saving antibiotics, such as penicillin, the prevalence of bacterial infections has resurfaced over the years as a threat to our health in that resistance has been seen to nearly all antibiotics that have been developed.[14] The Centers for Disease Control and Prevention (CDC) has expressed concern about the increasingly common use of antibiotics and have stressed the importance of discretion in its distribution.[15] Ultimately, using antibiotics only when needed can help us avoid the unnecessary disruption of our microbiome, decreasing our risk for infections.

While the microbiome differs greatly from person to person, the functions that the bacteria in the gut perform are fairly consistent and that is why the composition of the microbiome is really important. We need different kinds of bacteria to perform different functions, aiding in different metabolic pathways.[16] Several studies have also shown a relationship between an imbalanced microbiome composition (called dysbiosis) and the occurrence of diseases. For example, obesity is correlated with altered microbial composition, including a reduction in beneficial bacteria, and pathological bacteria dominate inflammatory bowel disease.[17, 18] A diverse microbiome is key in promoting health, through feedback and interaction between our immune system and our microbiome.[19]

The microbiome of a person changes overtime. When we are born, we have little to no microbes in or on our bodies. Our first microbes are given to us by our mothers, either vaginally or through skin touch.[20] We gain microbes from everyone and everything that we touch and everything we eat.[21] Our microbiome makeup changes overtime based on the needs of our body and as a child, our microbiome makeup is more variant. The body reaches a “baseline” state around 3 years old in which it tends to revert back to after illness, changes in diet, and antibiotics, though antibiotics may cause a change in microbiome that can be permanent.[22] In old age, microbiome becomes very distinct, many of some microbes and few of others.[1] Our microbiomes are similar to a fingerprint, different in every person. Those variations can be caused by age, diet, gender, environment, and more.[23] The microbiomes of people who live together tend to be more similar. Certain microbes on different parts of the body tend to be similar on different people; microbes on separate peoples’ forearms is more similar than one person’s microbes on their ear and forearm.[21]

The microbiome plays an essential role for our well being. Across the lifespan, microbiomes are constantly changing and many of these changes are due to diet, varying environments, and the use of antibiotics. Our booth will give you an insider (literally!) understanding the importance of a diverse microbiome and the consequences of an imbalance. From hands-on demonstrations of yeast’ favorite food to taking a selfie with your favorite bacteria, you won’t want to miss one second of the fun. Think you have the guts? Your microbiome thinks you do!

Booth E-617: Your 100 Trillion Best Friends
The Atlanta Science Festival Exploration EXPO
March 24, 2018
11am — 4pm

1. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7.

2. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971-5.

3. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4578-85.

4. Parajuli A, Gronroos M, Siter N, Puhakka R, Vari HK, Roslund MI, et al. Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors. Front Microbiol. 2018;9:84.

5. Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555(7695):210-5.

6. Kero J, Gissler M, Gronlund MM, Kero P, Koskinen P, Hemminki E, et al. Mode of delivery and asthma — is there a connection? Pediatr Res. 2002;52(1):6-11.

7. Decker E, Engelmann G, Findeisen A, Gerner P, Laass M, Ney D, et al. Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children. Pediatrics. 2010;125(6):e1433-40.

8. Mueller NT, Whyatt R, Hoepner L, Oberfield S, Dominguez-Bello MG, Widen EM, et al. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes (Lond). 2015;39(4):665-70.

9. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107(33):14691-6.

10. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444(7122):1022-3.

11. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480-4.

12. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med. 2011;3(106):106ra.

13. Petersen C, Round JL. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol. 2014;16(7):1024-33.

14. Ventola CL. The antibiotic resistance crisis: Part 1: causes and threats. Pharmacy and Therapeutics. 2015;40(4):277-83.

15. Centers for Disease Control and Prevention. About Antimicrobial Resistance 2018 [March 23, 2018]. Available from:

16. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-14.

17. Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A, Delaney ML, et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe. 2010;8(3):292-300.

18. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027-31.

19. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336(6086):1268-73.

20. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al. Topographical and temporal diversity of the human skin microbiome. Science. 2009;324(5931):1190-2.

21. Robinson CJ, Bohannan BJ, Young VB. From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev. 2010;74(3):453-76.

22. Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One. 2010;5(3):e9836.

23. Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 2011;9(4):279-90.