The Microbiome’s Role in Physical and Mental Health

The following information is derived from the highlights of my work for my independent research project my senior year at SIU-Carbondale. This presentation was directed and presented by the director of the Nutrition Program at SIUC for the ACHA. It focused on the role of the microbiome in relation to physical and mental health, especially regarding the college student population. 

If this is your first exposure to the world of the microbiome please click here to be directed to my blog discussing a beginner’s guide to understanding probiotics and the microbiome. 

Did You Know: The intestines of newborns are almost entirely sterile but become colonized immediately after birth; meaning we all start with a clean slate, and how we colonize that bacteria determines a vast amount about our futures, our personalities, and how we experience the world

The gut microbiome, through interactions with the gut epithelial lining and entire circulatory system, impacts nearly every part of the human body’s health, mentally and physically.

-Colonization of the gut microbiome

  • “Hygiene hypothesis”
  • Originated in 1989
  • “Reduced contact with microorganisms, especially during childhood, lifestyles away from nature and settlement mainly in large cities have resulted in an increased prevalence of allergic disease”
  • Emphasis on “hygiene” has led to reduced contact with helpful bacteria and has reduced colonization of beneficial bacteria in the gut


  • “Old Friends Hypothesis”
  • Concept that homo sapiens have been evolving  and interacting for thousands of years with friendly microorganisms and have grown to depend on their presence for healthy biological functioning
  • “Metabolites & nucleic acids produced by these microorganisms  are transported into human systemic circulation and lead to activation of inactive genes through epigenetic mechanisms”
  • Effects of decreased human-microbiota interactions (over hygienic environments) and changing diets are seen in developed countries where incidences of allergic diseases and autism are increasing

-Typical Bacterial species found in GI and their functions

  • The human gut microbiota contains more than 1,000 species and over 7,000 subspecies
  • Typical adult microbiome comprised of approximately 6 or 7 different bacterial phyla, dominated by Bacteroidetes and Firmicutes
  • Metabolite byproducts of these organisms used in human biological functions
  • Lactobacillus and Bifidobacterium synthesize gamma-aminobutyric acid (GABA) from monosodium glutamate, E. Coli, Bacillus, and Saccharomyces produce norepinephrine, Candida, Streptococcus, Escherichia, and Enterococcus produce serotonin, and Bacillus and Serratia produce dopamine
  • Lactobacillus casei, Lactobacillus helveticus, Lactobacillus Bulgaricus, and Bifidobacterium longum have all been shown to improve mental health upon oral administration

-How bacteria interact w/ our bodies (systemically through byproducts)

  • The bacteria in the gut interact with human cells. Interactions occur via one of the pattern recognition receptors (PRRs), namely the toll-like receptor (TLR). Ten TLRs have been identified in the immune system.  These receptors are the first steps in the cytokine production pathways
  • Inflammatory cytokines such as “interferon-alpha” are known to cause depression
  • Type 1 interferons (IFN-1) not only function as signaling molecules of innate immunity but also promote the activation of adaptive immunity
  • Systemic IFN-1 can influence CD4+ T Cell differentiation and function via their effects on dendritic cells

-Physical repercussions that have been connected to microbiota disruptions from modern lifestyles:

  • Due to microdamage to the gut epithelium walls caused by changes in the microbiota and increased permeability of the gut epithelium, harmful substances produced by microorganisms enter systemic circulation (a.k.a Leaky Gut Syndrome)
  • Clostridium difficile infections
  • IBS
  • Pathogen colonization (i.e. vancomycin resistant Enterococcus)
  • Autoimmune and allergic Diseases
  • Obesity and metabolic disorders
  • Neuropsychiatric disorders such as autism

-Mental health and the microbiome

  • The gut microbiota affects brain development and plasticity by secreting various neurotrophins and proteins such as brain-derived neurotrophic factor, synaptophysin, and postsynaptic density
  • The use of probiotics on mice has been proven to dramatically shift results of emotional reactivity tests, anxiety, and aggression

Click here to watch a video about Resistant Starch (prebiotics)

-Foods that fuel good bacteria (resistant starch, prebiotics, etc)

  • Planted based foods – fruits, vegetables, legumes – are ideal sources of resistant starch and complex carbohydrates to fuel microbiome
  • Diversity of diet is beneficial to nurturing a diverse gastrointestinal microbiome
  • Increased consumption of fiber, fruits, and vegetables in proportion to saturated fats and red meats – counteract disproportionate ratio of saturated fat in Westernized diets
  • Examples of resistant starches are beans, bananas, yams, corn, and brown rice
  • Preparation is key in resistant starches – their formation comes when a food is cooked and then cooled allowing the starch to absorb water and crystallize into a form that resists digestion

-Foods that fuel bad bacteria (simple carbs, etc)

  • Foods that are high in microbial richness in people who consume an agrarian plant-based vs a Western diet, which is high in meat and fat
  • Diet overly abundant in red meats and saturated fats
  • Foods that are processed and contain very simple starches and simple carbohydrates
  • Examples are enriched wheat containing simple carbs such as crackers, white bread, and pastries

-Suggestions for change in operations on campus to offer opportunities for healthier food choices

  • The diversity of the gut microbiota can change under stress, drugs, and diet
  • Establish curriculum in general education courses (i.e. Nutrition 101) that cover the topic
  • Invest money in raising awareness via lectures, posters, and social media campaigns
  • Invest money in restaurants and food service providers that offer pre and probiotic foods at an affordable price
  • Avoid investing money if possible in restaurants and food service providers that promote foods that inhibit this goal
  • Raise awareness about the importance of stress management and mental health. Encourage students to reach out and utilize programs that will allow them to receive help with any mental health issues they are experiencing and help keep stress levels under control

The nature of the Westernized diet and the stressful lifestyles of college students has created an epidemic of poor gastrointestinal microbiome health and in turn has impacted the mental and physical health of this population. In order to assist students in succeeding at Universities during a time of drastic shifts in independence and responsibility is occurring in their lives, it is vital to comprehend the importance of the impact of the gastrointestinal microbiome and its far-reaching effects throughout the entire body both physically and mentally. 

Dalhamer JM, Zammitti EP, Ward BW, Wheaton AG, Croft JB. Prevalence of Inflammatory Bowel Disease Among Adults Aged ≥18 Years — United States, 2015. MMWR Morb Mortal Wkly Rep 2016;65:1166–1169. DOI:
Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease. Albenberg, Lindsey G. et al. Gastroenterology , Volume 146 , Issue 6 , 1564 – 1572
Kutikhin, A. G., & Yuzhalin, A. E. (2015). Recent Discoveries in Evolutionary Genomic Microbiology (Vol. 1). Frontiers Media SA. doi:978-2-88919-617-3
Thakur, A. K., Shakya, A., Husain, G. M., Emerald, M., & Kumar, V. (2014). Gut-microbiota and Mental Health: Current and Future Perspectives. Journal of Pharmacology and Clinical Toxicology,25(1), 4-15.
Evrensel, A., & Ceylan, M. E. (2015). The Gut-Brain Axis: The Missing Link in Depression. Clinical Psychopharmacology and Neuroscience,13(3), 239-244. doi:10.9758/cpn.2015.13.3.239
Kotredes, K. P., Thomas, B., & Gamero, A. M. (2017). The Protective Role of Type I Interferons in the Gastrointestinal Tract. Frontiers in Immunology,8. doi:10.3389/fimmu.2017.00410
Bested, A. C., Logan, A. C., & Selhub, E. M. (2013). Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: part III – convergence toward clinical trials. Gut Pathogens,5(1), 4. doi:10.1186/1757-4749-5-4
NIH Human Microbiome Project. (2009). Microbe Magazine,4(9), 393-393. doi:10.1128/microbe.4.393.1

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