Our gut is often called the second brain because it communicates closely with the central nervous system and influences many aspects of our health. Advances in research have revealed how the gut affects digestion, mood, immunity, and even the development or progression of certain diseases.
I’m genuinely glad the gut is finally getting the attention it deserves for the everyday work it does. Talking about gut health is important and worthwhile.
Let’s begin. The gut manages a wide range of bodily functions. It contains a network of nerve cells comparable in size to the spinal cord and hosts more neurons within its walls than are found in the brain—one reason it earns the nickname “second brain.” Neurotransmitters produced in the gut, such as serotonin, dopamine, glutamate, and norepinephrine, transmit signals throughout the body. About 90% of the body’s serotonin is produced in the gut, where it helps regulate mood, gastrointestinal motility, appetite, and sleep. Even slight imbalances in gut serotonin can contribute to constipation or diarrhea. Like serotonin, the gut is influenced by many internal and external factors.
Our bodies harbor both beneficial and harmful bacteria that together form the microbiome. Maintaining a favorable balance of beneficial bacteria is essential because a large portion of the immune system resides in the gut—roughly 70%—where it helps identify and eliminate foreign invaders. Feeding the body properly supports immune function and improves the ability to neutralize toxins. The gut also plays a central role in digestion, helping the body absorb nutrients, eliminate waste, and even produce certain vitamins.
Antibiotics
Antibiotics affect gut health significantly. While they can be lifesaving when used appropriately, antibiotics tend to kill both harmful and beneficial bacteria. That’s why probiotic use is often recommended during and after antibiotic courses: to help restore beneficial microbes lost during treatment. Disruption of the microbiome increases the risk of infections, allergies, and other health problems, and can encourage antibiotic-resistant bacteria to emerge. Given how commonly antibiotics are used in many countries, it’s not surprising that disturbances to the microbiome are linked with rising rates of illness and immune-related conditions. Antibiotics have an important role when medically necessary, but their impact on the microbiome should be considered.
As one study noted:
Gut bacteria exhibit reduced capacity to produce proteins and show deficiencies in key metabolic activities during and after antibiotic treatment. The microbiota also demonstrates diminished ability to absorb iron, digest certain foods, and synthesize essential molecules, suggesting that antibiotic therapy may negatively affect colonic metabolic status (Pérez-Cobas et al., 2013).
Most antibiotic exposure is not only from prescriptions. Antibiotics are routinely used in industrial animal farming to promote growth and compensate for crowded, unsanitary conditions. According to data cited by advocacy groups, a large proportion of antibiotics in the U.S. are administered to livestock. This means consumers of conventional meat, fish, and dairy may also be exposed to antibiotic residues and to antibiotic-resistant bacteria, which is why choosing organic, wild-caught, and pasture-raised animal products can reduce some of that risk.
Balancing Bacteria
An imbalance in gut bacteria can trigger inflammation and allow partially digested food particles to pass into the bloodstream, potentially creating food sensitivities and contributing to gastrointestinal disorders. A poorly nourished or under-diverse microbiome has been associated with chronic and degenerative conditions, including irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and autoimmune conditions like rheumatoid arthritis.
Many factors influence the microbiome: diet, sleep, stress, and environmental exposures all play a role. The human body is well suited to a diet rich in fiber and nutrients, yet the typical modern diet often falls short, favoring processed foods high in trans fats and added sugars that harm microbial balance.
Tips to Keep Your Gut Healthy
To support a thriving microbiome, consider these practical steps:
- Increase probiotic-rich foods such as sauerkraut, kimchi, yogurt, kefir, and miso. Choose products labeled “active cultures” or “contains live cultures.” Probiotics can be especially helpful while taking antibiotics to replenish beneficial bacteria.
- Reduce processed foods and favor whole, nutrient-dense options.
- Choose wild-caught fish, pasture-raised eggs, and grass-fed or pasture-raised meats when possible.
- Avoid artificial sweeteners, which can disrupt gut flora and may contribute to weight gain. Limit added sugars and use natural alternatives like cinnamon, honey, maple syrup, or dates in moderation.
- Eat more fiber—aim for roughly 25–30 grams per day from diverse sources such as vegetables, fruits, legumes, nuts, seeds, and whole grains.
- Increase omega-3 fatty acids to help balance excessive omega-6 intake and reduce inflammation. Good sources include wild-caught seafood, flaxseed oil, chia seeds, avocados, olive oil, coconut oil, and grass-fed butter in moderation.
References:
Pérez-Cobas, A. E., Gosalbes, M. J., Friedrichs, A., Knecht, H., Artacho, A., Eismann, K., Moya, A. (2013). Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut, 62(11), 1591–1601.
Human Microbiome: How It Works + a Diet for Gut Health. (2016).
Foundation, G. C. Antibiotics. Retrieved December 23, 2016.