Inside the ‘Second Brain’: The science behind gut health and the microbiome
Dr Neerja Hajela
We usually picture the gut as just the body’s digestion centre, a system that breaks up food and takes in nutrients. But science gives us a much more intriguing image. Lurking deep inside our gut is a huge, dynamic community of microbes – trillions of bacteria, fungi, yeasts, and viruses — that collaborate not only to facilitate digestion but to shape our immunity, metabolism, and even mood. This complex network, called the gut microbiome, has earned the gut an amazing new name: our second brain.
The Gut–Brain Axis: A Two-Way Conversation
Ever had “butterflies” before a big event or felt your stomach tighten during stress? That’s your gut-brain axis talking, an actual communication system between your gut and brain via a sophisticated network of nerves, hormones, and immune signals. The key to this connection is the vagus nerve, a major highway that transmits signals both directions: from your brain to your gut and vice versa.
Within the gut is the enteric nervous system (ENS), a complex of approximately 500 million neurons that operates independently of the brain”. The ENS secretes many of the same neurotransmitters as the brain, including serotonin and dopamine that control mood, motivation, and overall sense of well-being. In fact, almost 95% of the body’s serotonin, the so-called “happiness hormone” is secreted in the gut. The secretion of these neurotransmitters are determined by the type of microbes which harbour the gut.
While the gut’s serotonin does not directly enter the brain, it can indirectly influence mood and behaviour through mechanisms such as immune response and the vagus nerve. It is not surprising that an imbalance in gut bacteria has been associated with anxiety, depression, and even neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease.
Microbiome Health: The Conductor of the Body’s Systems
Your gut microbiome acts as a kind of internal orchestra conductor, regulating the body’s various systems to keep everything in balance and healthy. When these microbes work together, they help in digestion, boost the immune system, and safeguard against inflammation. But when this balance is broken, dysbiosis is what ensues. Dysbiosis has been associated not just with gastrointestinal disorders like IBS (IrritableBowel Syndrome) but also with autoimmune disorders, obesity, diabetes, and even eczema and acne.
A healthy gut microbiota has three important features: diversity, stability, and resilience. It means having a large array of good bacteria that can respond to change in diet, stress, or environment. Diet has the ability to influence this ecosystem and it is here that probiotics and prebiotics come into the spotlight.
Probiotics are live, healthy bacteria that restore and balance the gut flora. They are especially formulated as probiotic foods which contains the scientifically tested bacteria which imparts the health benefit. Regularly consuming probiotics can support digestion, strengthen the intestinal barrier, and may even have mood-stabilising effects.
Prebiotics, on the other hand, are considered as the “food” that the good bacteria consume. The indigestible fibres that comprise prebiotics are found in various sources such as bananas, onions, garlic, oats, asparagus, legumes, and whole grains. Probiotics and Prebiotics work together and therefore help maintain a healthy gut ecosystem.
The Gut’s Wider Influence: Immunity, Metabolism, and Beyond
It’s estimated that up to 70% of our immune cells reside in the gut, learning from and responding to the microbiota. The gut is the body’s frontline defence, educating immune cells to differentiate between friendly bacteria and disease-causing pathogens. A healthy microbiome not only protects against infections but also regulates inflammation, helping prevent autoimmune responses in which the immune system mistakenly attacks the body’s own tissues.
The gut plays a vital role in metabolism by secreting hormones that regulate appetite, insulin sensitivity, and fat storage. Research shows that as gut bacteria ferment dietary fibers, they produce short-chain fatty acids (SCFAs)—bioactive compounds that help reduce inflammation and benefit metabolic health.
Equally intriguing is the connection between the gut and the skin, often referred to as the gut-skin axis. Imbalances in the gut microbiome can manifest externally, contributing to conditions like acne and other inflammatory skin issues. A healthy, balanced gut microbiome helps modulate systemic inflammation, promoting clearer, healthier skin.
Nourishing the Gut Brain Connection
To nurture a strong gut-brain connection, return to the basics: diet and lifestyle.
- Nourish with diversity: Fill your plate with a rainbow of fruits, vegetables, legumes, whole grains, and fermented foods. A Mediterranean-style diet—rich in fiber, omega-3 fatty acids, and polyphenols—has been shown to support both gut health and cognitive function.
- Supplement with probiotics and prebiotics: Incorporate probiotic-rich foods like Probiotic fermented milk drinks or other scientifically tested probiotic foods. Don’t forget prebiotics—found in garlic, leeks, onions, asparagus, and oats—which fuel the beneficial bacteria in your gut.
- Stay active: Consistent physical activity enhances microbial diversity and helps regulate stress hormones like cortisol.
- Prioritize stress management and sleep: Practices such as mindfulness, deep breathing, and yoga calms the nervous system and supports a balanced microbiome. Aim for 7–9 hours of high-quality sleep each night to allow your body and brain to reset.
Conclusion: A New Way to Think About Health
The science is clear — your gut is far more than a digestive organ; it’s a central hub that connects the mind, body, and immune system. By nurturing this inner ecosystem, you can not only support better digestion but also enhance your mental clarity, mood, and resilience.
Your gut is indeed your second brain, and like any great mind, it needs balance, nourishment, and care. By fuelling it with the right foods, using probiotics and prebiotics, and practicing mindfulness, you can help your microbiome bring together harmony in every system of your body, from your gut to your brain and beyond.
Dr. Neerja Hajela is Head – Science and Regulatory Affairs,
Yakult Danone India Pvt. Ltd
