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How To Enhance Your Gut Microbiome For Brain & Overall Health

Key Takeaways

  • “Our body is shaping the decisions that our brain is making and we’re not aware of it, at all.” – Dr. Andrew Huberman

  • What you do, eat, think, and feel influences your microbiome

  • Some microbiota make enzymes locally to digest food, others make neurochemicals that impact brain function and mood

  • Our experience with and desire for certain foods involves how the food tastes, texture, and subconscious processing of taste in our gut which signal certain neuromodulators

  • The gut communicates to the brain to change what we think we want or to change our actual behaviors around food

  • Food and eating is not just about the food and nutrients we need or don’t need, there are subconscious signals and waves of nerve cells always coming from our body and changing the way our brain works

  • “Our brain is very carefully paying attention to whether the levels of dopamine that are being triggered are within a normal range or whether we gorged ourselves.” – Dr. Andrew Huberman

  • Creating the correct environment for microbiota to thrive enhances mood and behavior

  • Parents: the more diversity you can create early, the better chance you’re giving your child at healthy brain-gut signaling and immunity

  • In general, to create a healthy gut microbiome: eat the right foods, consume pro- and pre-biotics sparingly unless going through periods of high stress, travel, or significant change to diet

  • Though fasting has a lot of benefits – we don’t know whether it promotes or degrades the microbiome over time but it seems to cause disruption when prolonged

  • Non-diet related ways to enhance microbiome: get deep sleep, maintain proper social interactions, limit prolonged stress and stressors

  • To really improve microbiome diversity through diet, consume 4-6 ounces of fermented foods per day – start with 1 and work your way up to avoid gastric distress

Defining Key Terms

  • Gut: we’re not just talking about the stomach; the gut includes the entire digestive tract from start to finish

  • Microbiota: bacteria in the gut

  • Microbiome: bacteria in the gut AND genes the bacteria make

  • The micro-bacteria are so tiny, you could fit several thousand on the head of a pin

Architecture Of Digestive Tract

  • The gut and the brain are a bidirectional biological circuit

  • Your gut and brain are always in communication: your gut influences your brain and the brain influences your gut

  • Your digestive system begins at your mouth and ends at your anus, sectioned off by sphincters

  • Microbiotas live in the lumen of the digestive tract and thrive to varying degrees along the length of the path depending on the acidity and environment

  • You’re constantly making and excreting micro-bacteria

  • Behaviors and experiences alter microbiota – literally the hands that are on you at birth, how you were born (i.e., C-section versus vaginal), whether you have pets, whether you were allowed to play outside in the dirt, etc.

  • One of the major determinants of our microbiome is who we interact with and the environment we’re in – including whether we live with animals


  • Microbiota contribute to the digestion of nutrients

  • Enzymes are largely responsible for digestion and catalyzation of other cellular events in the digestive pathway

  • Microbiota changes the way your brain functions by metabolizing or facilitating the metabolism of neurotransmitters

  • Certain microbiota can improve or diminish your mood: microbiota are converted into various neurochemicals such as gabba and influence the way your brain functions

  • The more diverse one’s microbiome, the less lonely – read more: Association Of Loneliness And Wisdom With Gut Microbial Diversity And Composition: An Exploratory Study – and here – Emotional Well-Being And Gut Microbiome Profiles By Enterotype

Brain-Gut Connection

  • Neurons activated in the gut are activated when sugar, fatty acids, and amino acids are present

  • Nerve cells (specifically called neuropod cells) in the gut are collecting information about what’s there and sending that information up to the brain via the vagus nerve

  • Neuropod cells sense nutrients, particularly sugar, which activates areas of the brain that cause you to seek out more of that food

  • The selective preference for seeking out sweet foods occurs even if you can’t taste the food and it is injected straight into the gut

  • We don’t just like sweet foods – we have a gut sensation below conscious detection

  • Dopamine in the context of feeding: causes us to seek out more of the sensation of delight and satisfaction from what we ate

  • The gut is communicating by way of neurons – some of which also release hormones (e.g., PYY, glucagon, etc.)

  • Ghrelin levels increase with fasting and stimulate the feeling of driving you to seek out food by inducing hormones like epinephrine

  • Glucagon-like pathway (GLP-1): made by neurons in the gut and brain; it inhibits feeding and reduces appetite (can stimulate with yerba mate tea, avocado, eggs, ketosis, and other food and drink)

  • GLP-1 and ghrelin are examples of gut-brain signaling mechanisms that adjust appetite and are dependent on diet

  • Signaling from gut to brain can be chemical (e.g., hormonal) or mechanical

  • If you eat or drink too much so you’re full and distended, information travels to the brain via mechano-sensors and activate areas of the brain involved in stopping eating and the “vomit center”

  • Chemical and mechanical signals are always working in tandem, sending signals to the brain to eat more or stop eating

Direct & Indirect Signaling

  • Gut microbiota are capable of influencing metabolic events and synthesizing neurotransmitters

  • Indirect signaling: the food you eat and the environment of the gut microbiome can create chemical substrates that allow your brain to feel one way or another

  • Particular gut microbiota can create dopamine in the gut which enters the bloodstream and changes baseline levels of dopamine in the brain and body

  • Other microbiota can create serotonin and determine levels of serotonin released during certain events

  • The majority of serotonin is manufactured in the gut and released by neuromodulators in the brain in response to touch or social experiences

  • Creating the correct

Non-Diet Related Ways To Create A Healthy Gut Microbiome

  • The things we come into contact within the first three years of life has a profound impact on the microbiota we carry within our body

  • Babies do not get much, if any, exposure to microbiota in the womb

  • The gut microbiome is established in days and weeks following delivery – vaginal birth versus C-section, breastfed versus bottle, held by multiple caregivers or just one, pets at home or not, premature baby in NICU or not, etc.

  • The diversity you create early in life for your children is critical for establishing a healthy gut-brain connection and immunity

  • Fecal transplants are being performed in research settings to explore the effects of the microbiome for health – for example, transferring fecal matter of a healthy individual into someone with colitis to reset microbiota

  • The complexity of probiotics:

  • Gut microbiome diversity is critical – but excessive intake of probiotics can induce brain fog – check out: Brain Fogginess, Gas And Bloating: A Link Between SIBO, Probiotics And Metabolic Acidosis

  • Most probiotics don’t actually increase the gut microbiota you need most – unless you’re eating the right foods which can encourage the proliferation

  • Probiotics can be useful during prolonged periods of fasting which disrupts the microbiome – BUT – when you eat, there may be a compensatory mechanism

  • How to enhance microbiome: get deep sleep, maintain proper social interactions, limit prolonged stress and stressors