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How processed foods influence the gut microbiome: Doctor explains

The gut is not just a digestive organ — it contains trillions of microbes collectively known as the gut microbiome. These microbes can affect digestion, immunity, metabolism and even mood. Diet has a powerful imprint in this community, where fibrous foods help preserve balance and processed ones disrupt it, so gut health is key to overall well-being.

September 17, 2025 / 13:19 IST
Processed foods can disrupt the balance of the gut microbiome, affecting digestion, immunity, and overall health.(Image: Pexels)

Most people think of the gut and assume that it only functions in digestion, a center for nutrients to be absorbed. But scientific studies in recent decades have demonstrated that the gut has a far more significant role in overall health and wellness. At the heart of this new vision is the gut microbiome, a vast and largely uncharted network of bacteria — as well as viruses, yeasts and fungi — that live in your digestive system. These little critters are not mere tenants but rather active players in various systems of the body.

They help to digest those challenging foods, make important vitamins, manage metabolism and improve the immune system. The gut is literally tied to brain function and even mood regulation (as in this thing called the gut-brain axis).

Also read: 9 blood-sugar-friendly fruits for people with diabetes and prediabetes

“Diet is an important factor for optimal functioning and balance of the microbiome. Whole, fiber-rich foods nourish good bugs to keep the balance in check, but when a diet consists of higher amounts of processed foods, added sugars and unhealthy fats it can throw that balance off and cause inflammation - not ideal for your gut or overall health,” Dr Ankur Jain, Associate Director & Unit Head - Gastroenterology, Hepatology & Endoscopy, Max Super Speciality, Dwarka, told Moneycontrol.

When we recognize gut health to be more than just digestion, the concept of mindful eating and maintaining microbial biodiversity become crucial for overall well-being.

Processed Foods

Processed foods are items that have been drastically changed from their natural state. Examples include:

  • Packaged snack foods

  • Soft drinks

  • Instant noodles

  • Refined breakfast cereals

While convenient, these foods typically are high in sugar, salt, damaging fats, and preservatives, and low in fiber and micronutrients—the nutrients needed to promote healthy gut bacteria.

How Processed Foods Attack the Gut

  • Fiber Deficiency

Helpful microbes feed on dietary fibers and ferment the fibers into SCFAs (short-chain fatty acids) that feed the gut lining and regulate inflammation. Fiber deficiencies from non-fiber foods represent a loss of nutrients needed by beneficial bacteria. This often contributes to leaky gut syndrome, weight gain, and metabolic disease.
  • Additives and Artificial Sweeteners

The presence of emulsifiers, sweeteners, and preservatives in packaged foods upsets the microbial equilibrium within the gut. Research indicates that emulsifiers and artificial sweeteners can promote pro-inflammatory bacteria in the gut, which can lead to conditions such as fatty liver, inflammatory bowel disease, and insulin resistance. Addictive sugars promote dysbiosis beyond any other food.
  • Toxic By-products

Certain highly processed meats and fried foods can produce toxic chemicals in the gut, damaging associated tissues and promoting inflammation. These also contributed to the disruption of the gut–brain axis, meaning poor gut health can (and does) promote anxiety and depression, as well as impairing immunity.

Also read: OMAD diet: 10 proven benefits of eating one meal a day for health and weight loss

The Good News: The Gut Can Heal

The gut microbiome is resilient, and returning to natural, whole foods will help to regain the balance and diversity amongst the microbiome. Specifically, natural foods include:

  • Fresh fruits and vegetables.

  • Pulses and whole grains

  • Nuts and seeds
  • Fermented foods including yogurt and kefir

Even if you can only make small changes to your diet and do it consistently, your gut health should greatly improve, as well as your long-term health status.

Quick, processed foods are currently convenient and easy; however, the long-term impact on your gut health is concerning. Gently tending back to fibrous, whole and natural foods may be the most prudent way to protect your gut microbiome and long-term health.

Disclaimer: This article, including health and fitness advice, only provides generic information. Don’t treat it as a substitute for qualified medical opinion. Always consult a specialist for specific health diagnosis.

Nivedita is a Delhi-based journalist who writes on health, fashion, lifestyle and entertainment. Views expressed are personal.
first published: Sep 17, 2025 01:19 pm

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