The microbes inside us

How our gut bacteria are integral to our Digestive health

by Dr. Sarah Nyrose BSc ND

Once viewed as being harmful, the bacterial residents of our digestive system are now being recognized as playing a key role in our health.

It’s hard to imagine that our bodies host trillions of microorganisms both inside and out. Our skin, our gut, our airways and every mucosal surface are lined with a rich composition of bacteria and other single-celled organisms, such as fungi. Together, along with their genetic material, these microorganisms make up what’s termed the human microbiome.

Our history with bacteria

Studies of the human microbiome started as early as the 1680’s, when Antonie van Leewenhoek analysed the difference between his oral and faecal bacteria. This was the beginning of our understanding of the diversity of microorganisms that inhabit the human body. Fast-forward to the late 1800’s, when Louis Pasteur was credited with the discovery of anaerobic bacteria, and by the early 20th century, numerous papers have been published highlighting the role of anaerobic bacteria in various types of infection1. This led to our fundamental understanding that microbes can cause infection and started the widespread effort to kill bacteria as a means to prevent and treat disease. While this discovery was monumental for modern medicine, it also cultivated a belief that “all bacteria are bad”. Only recently have we begun to understand the importance of our microbiome, and that our health, well-being and development depends on these microbes.

Where did our microbiome come from?

For every 1 human cell there is an average of 1.3 bacteria cells, meaning that an average 70 kg man has approximately 30 trillion human cells and 39 trillion bacteria cells.2 The human microbiome begins to develop in utero; bacteria are transferred from the mother to the fetus through the placenta and amniotic fluid.3 The second major exposure happens during vaginal delivery, where the baby is exposed to vaginal bacteria, which leads to gastric colonization in the first week of life. Infants born vaginally are shown to have higher amounts of bacteria than infants delivered by C-section;4 studies have suggested this may be a reason why babies born by C-section have a higher risk of conditions including asthma and type I diabetes. This critical period during birth and the first few months of life is vital for the development of our unique microbiome. The blueprint of our individual bacteria and fungi composition is established, directly impacting our initial gut health and immunity.

Our microbiome continues to change dynamically over the first two years, shaped by breast milk, the introduction of solid foods, the environment and other factors. By the age of three, the microbiome begins to stabilize and look more like that of an adult’s. Throughout our lives, numerous factors such as our diet, stress, drugs and our environment shape the microbes within us. Each individual has a unique and variable microbiome, although there are core microorganisms common to all individuals.5

What’s all the hype? Starting with digestion.

In recent years, the microbiome has come to the forefront of scientific research, with particular attention paid to the gut microbiota. The gut, or rather the large colon is home to more than 1,000 different species of bacteria, 90% of which belong to Firmicutes and Bacteroidetes.4

Our gut and the microbiota inside it have a special arrangement when it comes to digestion. Not all of the food we eat is digestible by our gut without the assistance of our bacterial residents. Picture our gut as a factory line: the bacteria as the labourers, working symbiotically with our gut cells to break food down, produce energy and synthesize vitamins. Bacteria break down undigested carbohydrates, producing short chain fatty acids (SCFA), which feed the cells lining our colon. These SCFA’s are markers of gut health, and have potential anti-cancer activity and a beneficial effect on blood-sugar regulation.6 Additionally, the bacteria contribute to the digestion of proteins by further breaking them down into shorter peptides, amino acids and derivatives.

Within the past 10 years, the connection between gut microbiota and multiple conditions such as inflammatory bowel disease (IBD) has captured the attention of the research community.

The microbiota’s role in digestion extends beyond the metabolism of carbohydrates and proteins. For over 40 years we’ve known that the gut microbiota is responsible for the synthesis of numerous vitamins, specifically: vitamin K, B vitamins including biotin, cobalamin, folate, nicotinic acid, pantothenic acid, pyridoxine, riboflavin and thiamine.6 It is estimated that 86% of the required daily intake of vitamin B6 is produced by the gut microbiota alone.6

The connection between gut microbiota and inflammatory bowel disease.

Within the past 10 years, the connection between gut microbiota and multiple conditions such as inflammatory bowel disease (IBD) has captured the attention of the research community.

At the core of this research is a focus on the gut bacteria’s influence on inflammation and immune function. As discussed earlier, through fermentation of carbohydrates, bacteria produce SCFA’s. These SCFA’s have been shown to enhance the action of our regulatory T-cell function in the gut lining, effectively promoting immune tolerance and reducing inflammation.7 In studies using germ-free mice, these mice were shown to have an impaired immune development, damaged gut lining, and treatment with oral antibiotics worsened the outcomes of viral infections. Thus, the microbiota influences immune function through suppressing pathogens, promoting immune tolerance, and by supporting gut lining repair.7

Dysbiosis, as defined as microbial imbalance, in patients with inflammatory bowel disease has been well documented. Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is characterized by chronic intestinal inflammation. Numerous studies, animal models and early therapeutic trials all highlight the important role of the gut microbiota and their metabolites in the development of IBD. The use of antibiotics early in life has been associated with an increased risk of Crohn’s disease, suggesting that an altered gut flora can facilitate the development of IBD.8

The challenge we face today is translating the information from multiple animal studies (where all variables are controlled) to the highly variable lives of humans. IBD is complex, our microbiome is complex, and understanding the direct role that bacteria play in the development and progression of such a condition requires further human studies.

Nevertheless, given what we know, our gut microbiota is indisputably important. Taking steps, as outlined in Top Six Ways to Support your Microbiome (stay tuned!), will help to promote a diverse and thriving gut microbiota, support your immune system and enhance your digestive health.

  1. Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition reviews, 70(suppl_1), S38-S44.
  2. Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS biology, 14(8), e1002533.
  3. Gritz, E. C., & Bhandari, V. (2015). The human neonatal gut microbiome: a brief review. Frontiers in pediatrics, 3, 17.
  4. Clapp, M., Aurora, N., Herrera, L., Bhatia, M., Wilen, E., & Wakefield, S. (2017). Gut microbiota’s effect on mental health: The gut-brain axis. Clinics and practice, 7(4).
  5. Tremaroli, V., & Bäckhed, F. (2012). Functional interactions between the gut microbiota and host metabolism. Nature, 489(7415), 242.
  6. Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I., & Tuohy, K. (2017). Gut microbiota functions: metabolism of nutrients and other food components. European journal of nutrition, 1-24.
  7. Ni, J., Wu, G. D., Albenberg, L., & Tomov, V. T. (2017). Gut microbiota and IBD: causation or correlation?. Nature Reviews Gastroenterology & Hepatology, 14(10), 573.
  8. Shaw, S. Y., Blanchard, J. F., & Bernstein, C. N. (2010). Association between the use of antibiotics in the first year of life and pediatric inflammatory bowel disease. The American journal of gastroenterology, 105(12), 2687.

More Stories

Food Insecurity

Food Insecurity

COVID-19 has illuminated many of the existing problems in our society, including food insecurity. We wanted to learn more about who is most affected, and discuss why these conversations are necessary, especially in the health and wellness world. 

Gardening with Ariel & Jess

Gardening with Ariel & Jess

Ariel and Jess Reyes Barton are the creators of Palenke Greens, which is a burlap sack gardening initiative aimed at assisting people of African descent facing food insecurity. Not only do they provide all of the supplies to create a burlap sack garden, they also help to install it, and have exciting ideas for the future.