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The surprising amount of bacteria in the human body and what you need to know about it

December 24, 2020 5 min read

The surprising amount of bacteria in the human body and what you need to know about it - Layer Origin Nutrition

What is the “gut microbiome”?

OK, here’s something that sounds kind of gross but is true: our bodies are FULL of trillions of bacteria, viruses and fungi. Yikes! 

In fact, there are more bacterial cells in our bodies than human cells. There are roughly 40 trillion bacterial cells in your body and only 30 trillion human cells.1  But even though some bacteria are associated with disease, others are actually extremely important (and beneficial) for your health.

Pink and green graphic showing comparison between Human and Bacterial cells

The gut microbiome refers to all of the microbes in the intestines, which act as another organ that’s crucial for your health. There are up to 1,000 species of bacteria in the human gut microbiome, and each of them plays a different role in your body. They influence your digestion, immune system, mood, cognitive function, metabolic rate, and even the way you age.2

Kind of strange how we never heard much about the microbiome in the 90s huh?Well, you're hearing about it now, and it's not too late to pay attention!

Why you should CARE about your gut microbiome

Digestion and nutrient production:Many foods we eat simply cannot be digested without the bacteria in our gut. Gut bacteria produce enzymes that help us digest sugars and other polysaccharides. A group of bacteria that first begin to grow inside babies’ intestines are called Bifidobacteria. They digest the healthy sugars in breast milk that are important for infant growth. Other bacteria specifically digest fiber, producing short-chain fatty acids, which are important for gut health. Fiber may help prevent weight gain, diabetes, heart disease and the risk of cancer. There are many ways to get sufficient fiber into your diet. Simply eating one avocado each day can give you a lot of fiber. Fruits and vegetables are great sources of fiber. If you struggle to eat enough whole foods like fruit and vegetables, you can choose to augment your fiber intake with a carefully selected supplement. Gut bacteria are also responsible for providing us with B vitamins and Vitamin K, which are both essential for body health.3,4

Graphic showing fiber's role in the Lumen

Immune system regulation: There’s a lot of interaction between the immune system and the bacteria in your gut. Gut bacteria mediates the relationship between the immune system and other organisms. By communicating with immune cells, the gut microbiome can also control how your body responds to infection.5

Green and yellow graphic of human body with text "The Immune System"

Control of the brain and mental health: It's kind of hard to wrap you head around, but there is a very strong connection between the gut and the brain. They are connected via the vagus nerve, enteric nervous system, and the gut-brain axis. The gut microbiome may affect the central nervous system, which controls brain function. So this means that your gut bacteria can actually affect your response to stress, anxiety, and even your memory. Research has shown that gut bacteria influences serotonin and dopamine production. Seratonin not only makes you feel happy, but aids in digestion as well. In fact, 90% of your body’s seratonin can be found in your gut.6-7

Blue and Yellow graphic representing the "gut brain axis"

Factors Influencing Microbial Colonization: Everyone’s microbiota is as unique as their own fingerprints. The composition of each person’s microbiome depends on diet, stress level, environment, age, and other factors. Infant gut colonization begins prenatally and continues during the first two to three years of life. It is essential for the gastrointestinal, metabolic, neural, and immune development of the infant. Genetic and environmental factors, including mode of delivery, antibiotic use, and diet, modulate the colonization process.8-9 

Human milk oligosaccharides (HMOs), the food for good bacteria in the gut

Diet is increasingly recognized as a key environmental factor that can shape the gut microbiome. What we give to babies can affect the composition of their gut bacteria through the availability of different foods (substrates) for bacterial fermentation. The beneficial biological effect of diet on the microbiome is attributed to its prebiotic components. 

Green striped graphic discussing diet and the microbiome

HMOs (found in breast milk) functionas the first prebiotics for infants. The nondigestible and structurally diverse oligosaccharides, known collectively as HMOs, form one of the major breastmilk components.HMOs areresistant to digestion in the intestine, which means the majority of HMOs reach the infant colon largely undigested and unabsorbed. That makes them available for probiotic bacteria to consume. The prebiotic bacteria are essentially the "food" for the probiotic bacteria. Therefore, a main function of HMOs is to promote a healthy gut microbiome. The survival advantage of breastfed infants over non-breastfed infants has been recognized since the late 1800s. One key observation was the stool bacterial composition of breastfed infants, which was reported to be different from that of the formula-fed infants. This observation leads to the later discovery of HMOs. Researchers found that HMOs helped to modulate the gut microbiome ecology, and establishment of an age-appropriate gut microbiota.10

Blue and pink graphic of acronym "HMOS"

How HMOs promote a healthy gut microbiome

HMOs shape the developing gut microbiome in several ways: they serve as prebiotics to promote the growth of beneficial bacteria and provide them with a growth advantage compared with potential pathogens. Studies have demonstrated that HMOs play a major role in promoting the growth of Bifidobacteria and Bacteroides .11 The gut microbiome of breastfed infants is typically dominated by Bifidobacterial species, particularly by Bifidobacterium Infantis. Serving as prebiotic agents, HMOs selectively enrich bifidogenic gut bacteria. This leads to a selective advantage to bifidobacterial species over other pathogens, providing further protection against infectious disease.

In additional, HMOs are also fermented to short-chain fatty acids (SCFAs), acetate, propionate, butyrate and lactate, which reduce the pH of the lumen and create an environment favoring the growth of beneficial bacteria. SCFAs can also be used by other bacteria and the host. 

Yellow graphic representing short chain fatty acids

Furthermore, sialylated and fucosylated HMOs mimic pathogen receptors and inhibit the binding of pathogens to cell surface receptors by acting as soluble decoy receptors, which reduces diarrhoeal disease.12

The development of the gut microbial community is vitally important to health and wellness. By promoting beneficial bacteria diversity, and preventing pathogen attachment, HMOs are thought to play a crucial role from the early stage of human life and beyond. 


  1. Sender, Ron, Shai Fuchs, and Ron Milo. "Revised estimates for the number of human and bacteria cells in the body." PLoS biology 14.8 (2016): e1002533.
  2. Integrative, H. M. P. "The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease." Cell host & microbe 16.3 (2014): 276.
  3. Turroni, Francesca, et al. "Diversity of bifidobacteria within the infant gut microbiota." PloS one 7.5 (2012): e36957.
  4. Marcobal, A., and J. L. Sonnenburg. "Human milk oligosaccharide consumption by intestinal microbiota." Clinical Microbiology and Infection 18 (2012): 12-15.
  5. Rooks, Michelle G., and Wendy S. Garrett. "Gut microbiota, metabolites and host immunity." Nature reviews immunology16.6 (2016): 341-352.
  6. Cryan, John F., and Timothy G. Dinan. "Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour." Nature reviews neuroscience 13.10 (2012): 701-712.
  7. Spohn, Stephanie N., and Gary M. Mawe. "Non-conventional features of peripheral serotonin signalling—the gut and beyond." Nature reviews Gastroenterology & hepatology 14.7 (2017): 412-420.
  8. Li, Min, Mei Wang, and Sharon M. Donovan. "Early development of the gut microbiome and immune-mediated childhood disorders." Seminars in reproductive medicine. Vol. 32. No. 01. Thieme Medical Publishers, 2014.
  9. Wang, Mei, et al. "Fecal microbiota composition of breast-fed infants is correlated with human milk oligosaccharides consumed." Journal of pediatric gastroenterology and nutrition60.6 (2015): 825.
  10. Berger, Bernard, et al. "Linking Human Milk Oligosaccharides, Infant Fecal Community Types, and Later Risk To Require Antibiotics." Mbio 11.2 (2020).
  11. Marcobal, Angela, et al. "Consumption of human milk oligosaccharides by gut-related microbes." Journal of agricultural and food chemistry 58.9 (2010): 5334-5340.
  12. Bode, Lars. "The functional biology of human milk oligosaccharides." Early human development 91.11 (2015): 619-622

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