Seeing science through a philosophical-artistic lens leads to useful allegories for understanding life. If we think of ourselves as beings working interdependently with the environment, we can emphasize biological relationships inside our own bodies to see how they contribute to wellbeing, which enhances the wellbeing of those we interact with. 

The beneficial bacteria in our digestive system regulate our immunity, protect us from pathogens and inflammation, and contribute to our energy and mood. Living symbiotically with them, we can engineer our lifestyles and diets to assist them so that they can more efficiently assist us.

Many bacteria species are beneficial because they produce short-chain fatty acids (SCFAs) which our body uses for important regulatory and metabolic processes.

Protection from stress

Both low and high doses of SCFAs significantly reduce the cortisol response to psychosocial stress compared to placebo. Know that what you put inside your body shapes the environment that predicts your physiological reactions to experiences in the world (Dalile, et al., 2020).

Rats with sterile guts are hypersensitive to stress and trauma. They are socially avoidant, anxious, and explore less than normal rats. When exposed to open-field stress, which is when they’re placed on a platform in a large box, their cortisol levels were 2.8-fold higher than normal rats. These behavioral issues are attributed to elevated gene expression for making corticotropin-releasing hormone, and inefficient dopamine metabolism in the brain (Crumeyrolle-Arias, et al., 2014).

Protection from inflammation and cancer

Probiotics reduce inflammatory cytokines in the body, partly by leading to a reduction in the expression of Toll-like receptors, TLR-2 and TLR4 (Plaza-Diaz, et al., 2017).

In Parkison’s (PD) patients, there is a reduction in SCFAs that corresponds to increased intestinal inflammation (Aho, et al., 2021). Patients with IBS and IBD also have reduced SCFAs compared to normal subjects (Venegas, et al., 2019). It’s important to note that other studies find an excess of SCFAs in PD, related to excesses of certain bacterial species and use of dopaminergic medications (Shin, et al., 2020). Deficiency and excess are both physiologically problematic and the issue is not usually black-or-white.

Escherichia coli live in healthy human guts and produce seven different SCFAs but mainly acetic acid. These were found to have potent ability to kill breast cancer cells while leaving normal breast cells alone. They also suppress inflammatory cytokines while promoting anti-inflammatory cytokines like interleukin-10 (Nakkarach, et al., 2021).

The presence of SCFAs seem to protect retinal cells in what is called the gut-eye crosstalk. SCFAs protect the eyes from endotoxin-induced inflammation (Chen, et al., 2021). Endotoxin is involved in the development of sensitization and allergies in tissues, such as irritation, itching, and sneezing. The beneficial bacteria are proposed as potential treatment for allergic conditions such as asthma and rhinitis, with L. casei and L. paracasei producing significant clinical results among others (Yang, et al., 2013).

Gut barrier maintenance

The short-chain fatty acid butyrate protects the gut by upregulating the tight junction proteins claudins-1, 3, and 4 (Wang, et al., 2012). Butyrate protects against endotoxin-induced cell damage and downregulation of intestinal protein synthesis, which is how “leaky gut” happens. Butyrate increases intracellular adenosine triphosphate (ATP). Yan and Ajuwon propose that butyrate serves as a nutrient substrate for ATP (2017). 

Bacteroidetes help mitigate endotoxin’s effects and maintain the gut barrier. A high intake of sugar increases proteobacteria and decreases bacteroidetes, threatening the gut mucosa and increasing inflammation and endotoxin leakage into the bloodstream (Satokari, 2020).


Acetate created by colonic bacteria travels to the brain, where it leads to the activation of acetyl-coenzyme-A carboxylase and shifts neuropeptides like glucagon-like peptide-1 and ghrelin, which suppresses appetite (Frost, et al., 2014). Rats that were fed fermentable carbohydrates for 3 weeks had substantially lower post-meal ghrelin, ate less calories, and lost significant weight and body fat, compared to control rats (Cani, et al., 2004).

Muscle strength

Removal of the gut microbiome leads to muscle loss and muscle atrophy and changes the composition percentage of muscle fiber type. The body weight and lean mass of the sterile-gut piglets were ~40% lower than normal piglets. Absence of microbiota caused an absence of short-chain fatty acids (“post-biotics”) and impaired muscle mitochondria. Re-colonization of gut microbes via fecal microbiota transplant partly restored the growth and function of muscle tissue (Qi, et al., 2021). 

The effects of microbiota are transferable from animals to people. When mice are colonized with the gut bacteria of high-functioning older adults, their muscle strength increases from baseline (Fielding, et al., 2019). We already know that humans share their gut bacteria with those they live with, including their pets, so this gut-muscle axis has far-reaching implications (Song, et al., 2013). For example, when babies are raised with a furry pet in the household, the bacterial strains oscillospira and ruminococcus are doubled in their guts. These two strains confer protective effects against allergies and obesity (Tun, et al., 2017). 


Chronic early life sugar consumption disrupts the microbiome and subsequently impairs memory by negatively affecting the hippocampus. This happens regardless of body weight. The sugar supported the growth of two species, Parabacteroides distasonis and P. johnsonii. When these species were transplanted into healthy rats who didn’t grow up on sugar, they developed the same hippocampus dysfunction and memory impairment (Noble, et al., 2021).

Synbiotics and sulfoquinovose

The eating of leafy greens provides the molecule sulfoquinovose, which prominent beneficial bacteria species use as energy, for example, E. coli. Dr. Goddard-Borger describes the intestinal lumen as finite real estate: if there is ample beneficial bacteria being consistently fed, the pathogenic bacteria have less space to colonize or grow (2016).

Without the symbiotic relationship of our gut microbiome, we are rendered helpless inside and out. The “good” bacteria not only protect us against the bad, but also enable essential bodily processes to be carried out. Our very anatomy depends on their presence.

Foods that lead to acetate, propionate, and butyrate production [source]

  • Honey
  • Squash
  • Apples
  • Oranges
  • Peaches
  • Carrots
  • Raspberries
  • Peas
  • Onions
  • Chicory
  • Garlic
  • Asparagus
  • Banana
  • Artichoke
  • Beans
  • Broccoli
  • Lettuce
  • Seaweed
  • Mushrooms
  • Dairy (not recommended)
  • Grains (not recommended)

Works Cited

Aho, Velma T, et al. “Relationships of Gut Microbiota, Short-Chain Fatty Acids, Inflammation, and the Gut Barrier in Parkinson’s Disease.” 2021, doi:10.21203/

Byrne, C S, et al. “The Role of Short Chain Fatty Acids in Appetite Regulation and Energy Homeostasis.” International Journal of Obesity, vol. 39, no. 9, 2015, pp. 1331–1338., doi:10.1038/ijo.2015.84.

Cani, Patrice D., et al. “Inulin-Type Fructans Modulate Gastrointestinal Peptides Involved in Appetite Regulation (Glucagon-like Peptide-1 and Ghrelin) in Rats.” British Journal of Nutrition, vol. 92, no. 3, 2004, pp. 521–526., doi:10.1079/bjn20041225.

Chen, Nu, et al. “Short Chain Fatty Acids Inhibit Endotoxin-Induced Uveitis and Inflammatory Responses of Retinal Astrocytes.” Experimental Eye Research, vol. 206, 2021, p. 108520., doi:10.1016/j.exer.2021.108520.

Crumeyrolle-Arias, Michèle, et al. “Absence of the Gut Microbiota Enhances Anxiety-like Behavior and Neuroendocrine Response to Acute Stress in Rats.” Psychoneuroendocrinology, vol. 42, 2014, pp. 207–217., doi:10.1016/j.psyneuen.2014.01.014.

Dalile, Boushra, et al. “Colon-Delivered Short-Chain Fatty Acids Attenuate the Cortisol Response to Psychosocial Stress in Healthy Men: a Randomized, Placebo-Controlled Trial.” Neuropsychopharmacology, vol. 45, no. 13, 2020, pp. 2257–2266., doi:10.1038/s41386-020-0732-x.

Fielding, Roger A., et al. “Muscle Strength Is Increased in Mice That Are Colonized with Microbiota from High-Functioning Older Adults.” Experimental Gerontology, vol. 127, 2019, p. 110722., doi:10.1016/j.exger.2019.110722.

Frost, Gary, et al. “The Short-Chain Fatty Acid Acetate Reduces Appetite via a Central Homeostatic Mechanism.” Nature Communications, vol. 5, no. 1, 2014, doi:10.1038/ncomms4611.

Giovannini, Marcello, et al. “A Randomized Prospective Double Blind Controlled Trial on Effects of Long-Term Consumption of Fermented Milk Containing Lactobacillus Casei in Pre-School Children With Allergic Asthma and/or Rhinitis.” Pediatric Research, vol. 62, no. 2, 2007, pp. 215–220., doi:10.1203/pdr.0b013e3180a76d94.

Joseph, Jamie, et al. “Modified Mediterranean Diet for Enrichment of Short Chain Fatty Acids: Potential Adjunctive Therapeutic to Target Immune and Metabolic Dysfunction in Schizophrenia?” Frontiers in Neuroscience, vol. 11, 2017, doi:10.3389/fnins.2017.00155.

Nakkarach, Atchareeya, et al. “Anti-Cancer and Anti-Inflammatory Effects Elicited by Short Chain Fatty Acids Produced by Escherichia Coli Isolated from Healthy Human Gut Microbiota.” Microbial Cell Factories, vol. 20, no. 1, 2021, doi:10.1186/s12934-020-01477-z.

Noble, Emily E, et al. “Gut Microbial Taxa Elevated by Dietary Sugar Disrupt Memory Function.” 2020, doi:10.1101/2020.06.16.153809.

Plaza-Díaz, Julio, et al. “Evidence of the Anti-Inflammatory Effects of Probiotics and Synbiotics in Intestinal Chronic Diseases.” Nutrients, vol. 9, no. 6, 2017, p. 555., doi:10.3390/nu9060555.

Qi, Renli, et al. “The Intestinal Microbiota Contributes to the Growth and Physiological State of Muscle Tissue in Piglets.” Scientific Reports, vol. 11, no. 1, 2021, doi:10.1038/s41598-021-90881-5.

Satokari, Reetta. “High Intake of Sugar and the Balance between Pro- and Anti-Inflammatory Gut Bacteria.” Nutrients, vol. 12, no. 5, 2020, p. 1348., doi:10.3390/nu12051348.

Shin, Chaewon, et al. “Plasma Short‐Chain Fatty Acids in Patients With Parkinson’s Disease.” Movement Disorders, vol. 35, no. 6, 2020, pp. 1021–1027., doi:10.1002/mds.28016.

Song, Se Jin, et al. “Cohabiting Family Members Share Microbiota with One Another and with Their Dogs.” ELife, vol. 2, 2013, doi:10.7554/elife.00458.

Tun, Hein M., et al. “Exposure to Household Furry Pets Influences the Gut Microbiota of Infants at 3–4 Months Following Various Birth Scenarios.” Microbiome, vol. 5, no. 1, 2017, doi:10.1186/s40168-017-0254-x.

Unger, Marcus M., et al. “Short Chain Fatty Acids and Gut Microbiota Differ between Patients with Parkinson’s Disease and Age-Matched Controls.” Parkinsonism & Related Disorders, vol. 32, 2016, pp. 66–72., doi:10.1016/j.parkreldis.2016.08.019.

Venegas, Daniela Parada, et al. “Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases.” Frontiers in Immunology, vol. 10, 2019, doi:10.3389/fimmu.2019.00277.

Wang, Hong-Bo, et al. “Butyrate Enhances Intestinal Epithelial Barrier Function via Up-Regulation of Tight Junction Protein Claudin-1 Transcription.” Digestive Diseases and Sciences, vol. 57, no. 12, 2012, pp. 3126–3135., doi:10.1007/s10620-012-2259-4.

Yan, Hui, and Kolapo M. Ajuwon. “Butyrate Modifies Intestinal Barrier Function in IPEC-J2 Cells through a Selective Upregulation of Tight Junction Proteins and Activation of the Akt Signaling Pathway.” Plos One, vol. 12, no. 6, 2017, doi:10.1371/journal.pone.0179586.Yang, Ping-Chang, et al. “Treatment of Allergic Rhinitis with Probiotics: An Alternative Approach.” North American Journal of Medical Sciences, vol. 5, no. 8, 2013, p. 465., doi:10.4103/1947-2714.117299.

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