How the Gut Microbe Affects the Brain and Mind
A Boy with Rocky Mountain Spotted Fever / The Link Between Microbes and the Brain / Gut Microbes and Memory / Cognitive and Physiological Impact of Microbes / Gut Microbes and Behavior / Neurotransmitters Produced by Bacteria / Microbiota, Antibiotics, and Autism / Microbiota and Human Health
A few days ago, my eldest child shared a highly interesting YouTube video titled “How the Gut Microbe Affects the Brain and Mind,” published by the channel What I've Learned. (It was posted on February 19, 2018, and runs for 13 minutes and 22 seconds.)
It felt too valuable to watch alone, so I made time to summarize it. I’ve long suspected that certain microorganisms might influence not only the human body but also our mental and emotional states. I do not mean in the general sense of psychological damage caused by the COVID-19 pandemic, but rather in the more direct form of microbes affecting the brain and mind. After watching this video, that idea feels far more plausible. It is, without question, a video worth watching.
Microorganisms: Generally include fungi, protozoa, bacteria, viruses, and algae (Wikipedia).
A Boy with Rocky Mountain Spotted Fever
Dr. Martin Blaser (Director of the NYU Human Microbiome Program and a renowned researcher in microbiology) recalled an afternoon during his time in medical school when he was called to examine an 11-year-old boy who had suddenly fallen ill and been hospitalized. Just two days earlier, the boy had appeared perfectly healthy before developing acute fever and gastrointestinal symptoms. On the second day, his fever worsened, and by the third day, bluish-purple spots appeared on his skin. Emergency room physicians quickly diagnosed him with Rocky Mountain Spotted Fever.
This disease is caused by a bacterium known as Rickettsia, transmitted through the bite of an infected tick. Rickettsia invades endothelial cells lining blood vessels, inducing a severe immune response. Because this affects cerebral vasculature, the boy developed symptoms of encephalitis, including intense headaches caused by cerebral edema. When Dr. Blaser entered the room with the other doctors, the boy was in such pain that the room had to be darkened due to photophobia. His body was covered in purplish rashes, and he was drenched in sweat, thrashing on the bed and screaming incoherently in a hallucinatory state. As Dr. Blaser recounts in his book Missing Microbes, the boy recovered and was discharged just five days after initiating treatment with the antibiotic tetracycline.
The Link Between Microbes and the Brain
Recently, microbes inhabiting the human gut have drawn growing interest for their relevance to overall health. While there are pathogenic microbes like Rickettsia, many microbes are beneficial. Approximately 500 to 1,000 bacterial species exist in the human body. Ongoing research has increasingly highlighted the significance of these beneficial bacteria. However, determining how microbes in our gut affect cognitive functions and brain activity remains a challenge.
As shown in the boy’s case, bacterial infections can clearly alter mental states. Thus, it becomes less surprising to consider a possible link between gut microbes and brain function.
Gut Microbes and Memory
Researchers observed that germ-free laboratory mice (raised in sterile environments without any gut flora) exhibited distinct behaviors compared to those with normal microbiota. These germ-free mice showed reduced threat perception and roamed freely without caution—behavior that would render them easy prey in natural settings. Moreover, they displayed impairments in memory-related tasks.
In their book The Good Gut, Erica and Justin Sonnenburg describe an experiment comparing normal mice with germ-free mice using a memory test. First, two objects—a plain ring and a large checkered ring—were placed in the enclosure for five minutes. Twenty minutes later, the checkered ring was reintroduced alongside a novel star-shaped cookie cutter. As expected, normal mice explored the novel object more, ignoring the familiar ring. However, germ-free mice spent comparable time examining both, indicating they failed to remember the checkered ring from earlier.
Cognitive and Physiological Impact of Microbes
These memory deficits are likely related to lower levels of BDNF (Brain-Derived Neurotrophic Factor) in germ-free mice. BDNF is a protein crucial for the generation and maintenance of neurons and is vital for learning and memory. Reduced BDNF levels are associated with depression and anxiety.
Though human trials are ethically constrained, one documented case involved a woman who underwent Fecal Microbiota Transplantation (FMT) using stool from her healthy, albeit overweight, 16-year-old daughter to treat intestinal disease. While her condition improved, she gained 34 pounds (15.4 kg) over the following 16 months despite diet, exercise, and even protein-based medical nutrition interventions.
Conversely, experiments have shown that transplanting microbiota from lean mice into other mice can inhibit weight gain. This suggests microbiota can influence body phenotype—and perhaps even personality.
Gut Microbes and Behavior
In a 2011 study at McMaster University, two mouse groups were studied—one cautious and hesitant, the other outgoing and sociable. They were placed on elevated platforms, and the time taken to descend was measured. The cautious group took an average of 4 minutes and 30 seconds, while the bold group jumped down in seconds. After microbiota transplantation between the groups, cautious mice became faster, and bold mice became more hesitant. The results suggest that gut microbial composition can affect behavior and anxiety levels.
Neurotransmitters Produced by Bacteria
Microbiota transplantation also raised BDNF levels in anxious mice, suggesting not only behavioral changes but also chemical changes in the brain. In fact, many neurotransmitters originate in the gut. For instance, approximately 90% of serotonin (a neurotransmitter involved in mood regulation) is produced in the gut. Bacteria such as Candida, Streptococcus, Escherichia, and Enterococcus have been identified as producers of serotonin. Lactobacillus and Bifidobacterium synthesize gamma-aminobutyric acid (GABA), the chief inhibitory neurotransmitter that reduces stress and anxiety. Bacillus and Serratia are known to produce dopamine, which is linked to motivation and reward.
Effectively, the gut acts as a massive pharmaceutical factory producing chemicals that affect the brain.
Some preclinical studies in rodents have shown that specific probiotics can function similarly to antidepressants or anxiolytics. One study demonstrated that Bifidobacterium infantis had an effect comparable to the antidepressant citalopram. Previously, I believed dietary fiber’s only benefit was aiding bowel movements. But recognizing that a fiber-rich diet supports gut bacteria reframes it as a mental health intervention as well.
Microbiota, Antibiotics, and Autism
This raises the question of how many psychological disorders may stem from dietary fiber deficiencies, refined carbohydrate intake, or indiscriminate antibiotic use. As seen in the aforementioned case, antibiotics can be life-saving, but broad-spectrum antibiotics kill both harmful and beneficial bacteria indiscriminately.
In the United States alone, tens of millions are prescribed antibiotics for minor infections. Between 60–80% of children with ear, nose, or throat infections are sent home with antibiotic prescriptions. It is estimated that individuals receive around 30 antibiotic courses by age 40. Infants under age 2 receive the most, with 1,365 prescriptions per 1,000 children. What effect might this have on gut microbiota and neurodevelopment?
Dr. Derrick MacFabe’s 2012 paper described injecting propionic acid (PPA) into rodents, causing neuroinflammation, oxidative stress, and glutathione depletion. These mice exhibited abnormal movement, repetitive interests, cognitive deficits, and impaired social interaction—mirroring autism-like symptoms. PPA is a byproduct of bacterial fermentation by Desulfovibrio, Bacteroidetes, and Clostridia. Children with autism often harbor elevated levels of Clostridium and show high PPA concentrations in fecal samples. One-third of autistic children show no symptoms until after 18–24 months of age.
According to some parents, their children’s development regressed only after being treated with antibiotics for ear infections. Dr. Sidney Finegold noted that while antibiotics suppress most gut flora, Clostridia tends to survive. In CBC’s 2011 documentary Autism Enigma, Ellen Bolte recounted how her son Andrew, after receiving six antibiotic courses for ear infections within the first few months of life, exhibited drastic behavioral changes and was diagnosed with severe autism.
After discovering research on Clostridia, she sought a physician willing to try vancomycin—an antibiotic specifically targeting Clostridia. The result was astonishing.
“Within weeks, Andrew calmed down. He became aware of his surroundings. He started doing puzzles again.”
Vancomycin brought temporary but remarkable improvements. Inspired by her case, Drs. Finegold and R. Sandler conducted a small trial on 10 autistic children, where 8 showed significant but transient improvement after vancomycin treatment. Although premature conclusions are dangerous, evidence increasingly supports a theory that autism may, in part, be rooted in gut dysbiosis. Up to 70% of children with autism are believed to suffer from gastrointestinal issues.
Microbiota and Human Health
Autism is just one of many conditions potentially linked to gut health. Research on gut microbiota is accelerating rapidly—between 2010 and 2015, over 3,600 related articles were published. To say “gut microbes are important to health” is a massive understatement. Dr. Blaser stated that “losing one’s gut microbiota may be comparable to losing a kidney or liver.” But unlike those organs, we can reshape our gut microbiome through food.
Hippocrates once said:
“All disease begins in the gut. Let food be thy medicine.”
He may have known exactly what he was talking about.
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