Overview

Bacteria are microscopic organisms found all over the world, including in the human body. They are present on your skin, mouth, gut, airways, reproductive system, and urinary tract. The human body hosts trillions of microbial cells, most of them important for good health. The bacteria that reside in our body are called the resident flora or microbiome. They play a key role in the fundamental process of life. 

How do we get the right types from the thousands of different microbes in the world? The answer: other humans. Newborns get their first microbes from the mother’s birth canal, breast milk, and the ones who touch them. As the infant grows up, they encounter microbes from their environment and diet.¹

We encounter hundreds of microbes every day in our lives. So how to promote the good ones among them, and keep the bad ones at bay? Let us explore the microbial world for an answer to this question.

Understanding the microbiome

The human microbiome consists of a set of organisms, including bacteria, archaea, viruses, and eukaryotes, which live within or outside the body. They can impact human life in terms of health and disease, by colonising and adapting to different sites on the body.¹

From the moment a child is born, the symbiotic association, or mutual interaction, between the body and the microbes begins. This association helps in the overall health and well-being of the living body.¹

The human microbiome is evolving constantly in response to factors like age, lifestyle, nutrition, hormonal changes, inherited genes, and underlying diseases. There should be a balance in the microbiome for the sustenance of life, and an alteration in this balance may result in life-threatening diseases.² Hence, it is important to maintain the beneficial bacteria and check on the harmful ones for the overall health of the body.

The benefits of good bacteria

The diverse microbial community in the human body has many roles that promote health. They help digestion, nutrient absorption, immunity, vitamin production, etc. The beneficial bacteria maintain the intestinal epithelium (the lining of your intestines) by providing energy in the form of short-chain fatty acids and releasing antimicrobial substances against pathogens.^1,2

Role in digestion and nutrient absorption

The beneficial bacteria in the gut help break down complex dietary carbohydrates and proteins consumed. Most of the nutrient digestion and absorption take place in the stomach and small intestine. However, about 10-30% of the total ingested energy reaches the large intestine in indigestible form.³ Bacteria in the large intestine mainly depend upon these undigested dietary substrates to survive.

Without these bacteria and the limited digestive capability of the large intestine, the energy in the undigested food would be wasted during elimination through stool. These bacteria break down the undigested substrates (food) into simple units like monosaccharides and short-chain fatty acids that can be absorbed by the intestinal mucosa.^3,4

Immune system support and disease prevention

The microbiome plays a crucial role in the development of the immune system. Most of the critical events in the development of immunity happen during the first three years of life. It starts with the first encounter of microbes during birth in the birth canal and the mother’s skin.

The window of opportunity in the first three years of life makes children more susceptible to environmental microbes, with long-term impacts on immunity. Studies show that microbial diversity during early life is important in establishing an immunoregulatory network by host-immune-microbial interaction.⁵

Beneficial bacteria are linked to multiple immune functions, like the production of cytokines, maintenance of homeostasis, T cell production, and regulation of the immune system. The beneficial microbiome provides resistance against colonisation by harmful bacteria.⁶

Production of essential vitamins and other beneficial compounds

Vitamins are micronutrients that help in cellular metabolism, and some of the gut bacteria, like lactic acid bacteria and bifidobacteria, can synthesise vitamin B and vitamin K groups. Also, the gut bacteria help transform vitamin A into its active metabolite—retinoic acid, which can be used by the body. It is also found that vitamins can modulate the microbiome of the gut.⁷

Contribution to mental health through the gut-brain axis

Maintaining a healthy gut enables the brain to tackle stress and emotional pressure in life. Studies have shown there is bidirectional communication between the gut microbiome and the central nervous system (CNS), known as the gut-brain axis.

It has been found that hormones, neurotransmitters, and immunological factors from the gut send signals to the brain. There is an association between the loss of balance in the gut microbiome and mental illness, including anxiety and depression.⁸

The dangers of harmful bacteria

Dysbiosis is the imbalance in the microbiome due to various factors like dietary change, increased sugar or protein intake, chemical food additives, alcohol abuse, improper usage of antibiotics, infections, and inflammation. Due to dysbiosis, there may be a decrease in the diversity of the microbiome, a loss of beneficial bacteria, and growth of harmful bacteria.⁹ 

Some of the common harmful bacteria include E. coli, Salmonella, and C. difficile. These bacteria may grow in the intestine and release harmful toxins, causing abdominal pain, diarrhoea, and nausea. Bacteria in the gut can play a role in conditions like inflammatory bowel diseases (IBD), obesity, and type 2 diabetes.¹⁰

Promoting good bacteria

Diet and nutrition

A balanced diet provides nutrients to the body and promotes the beneficial microbiome in the gut. A balanced diet is rich in fibre, fruits, vegetables, and whole grains. For the normal development and function of the intestinal epithelium, bacterial stimulation is essential. A low-fat, high-fibre diet has a strong impact on the gut microbiome.¹¹ 

Prebiotics are a group of nutrients that can be broken down by the gut bacteria. Fructo-oligosaccharides, galacto-oligosaccharides, and inulin are the most common types of prebiotics. These are non-digestible foods that can stimulate gut bacterial growth, thus improving overall health.

Prebiotics improve gut bacteria, regulate bowel movements, produce neurotransmitters and hormones to stimulate the gut-brain axis, help calcium and phosphorus in the bone mineralisation, and improve anti-inflammatory responses and immunity.¹²

The food items that contain these prebiotics include chicory root, dandelion greens, garlic, onion, leeks, asparagus, bananas, barley, oats, apples, cocoa, flax seeds, yacon root, wheat bran, seaweed, avocado, and wild yam.

Live microbes known as probiotics, typically found in fermented food, provide numerous health benefits when consumed. The frequently used ones are Bifidobacterium and Lactobacillus.

Probiotics mainly act by competitive exclusion of the pathogenic microorganisms, improving intestinal epithelium, producing neurotransmitters, and modulating the immune system. They compete with the pathogenic bacteria for nutrients, making their survival difficult.¹³

Probiotic sources are fermented foods like yoghurt, kombucha, kefir, pickles, miso, kimchi, sourdough bread, dairy foods, like buttermilk, fermented milk, and cottage cheese.

Lifestyle choices

The microbiome architecture can be influenced by physical activity. Studies have shown that aerobic exercises can induce a metabolic shift that can improve the beneficial bacteria in obese individuals.¹⁴

The gut is also responsible for stress. In turn, the psychological factors may affect the gut microbiome, intestinal epithelial (lining) integrity, and metabolites.¹⁵

Try to identify and understand the stress factors and manage those triggers. Stress can be managed by practicing meditation, yoga, and regular exercise. Getting adequate sleep is also important for reducing stress and balancing the microbiota.

Avoiding overuse of antibiotics

Improper use of antibiotics—repeated usage, overdosage, underdosage, and an incomplete course—can result in dysbiosis, an imbalance in the bacterial microbiome. Dysbiosis can result in the degradation of beneficial bacteria in the gut. In the absence of competition, the pathogenic microbes find it easy to attack the body, resulting in diseases.⁹ 

There is also the danger of antibiotic resistance due to the overuse of antibiotics, where many pathogenic strains of bacteria have become resistant to antibiotics, making the infection challenging to treat.

Hygiene practices

It is important to practice good hygiene, and safe food handling, to avoid contamination by harmful bacteria. Also keep in mind that oversanitisation, fastidious washing, and overuse of antibacterial sprays can also be detrimental to beneficial bacteria in the body.

Keeping bad bacteria at bay

Identifying and avoiding sources of harmful bacteria

One of the most common sources of pathogenic bacteria is through contaminated food and water. The other ways include close contact with the affected person, direct contact with an infected animal, or its environment.

Always try to drink boiled water and practice safe handling of food. Wash vegetables and fruits before consuming, practice good personal hygiene and sanitation.

Strengthening the immune system

A strong immune system can help us keep the harmful bacteria at bay. Eating healthy food, exercising regularly, and choosing a healthy lifestyle can improve your body's immunity level.

Vaccinations targeting the bacterial pathogens help to reduce the infections caused by antibiotic-resistant and other susceptible pathogens. 

Regular health check-ups

Routine medical check-ups help to detect and treat infections at an early stage. Always pay close attention to your general health, and if you suspect any symptoms, seek medical advice immediately.

Practical tips for everyday life

• Incorporating prebiotics and probiotics into the daily diet
• Include a microbiome-friendly diet, especially the fibre intake
• Eat as many fruits and vegetables as possible
• Choose food items that have a high level of antioxidants like seeds, berries, coffee, green tea, and olive oil
• Regular exercising
• Drinking plenty of water
• Limit alcohol
• Avoid unnecessary antibiotics
• Practice mindfulness and relaxation techniques^12,13,14,15

Summary

Trillions of microbial friends reside on our skin, mouth, gut, airways, urinary tract, and reproductive system, they help in the digestion and absorption of nutrients, vitamin production, and immunity. Out of the thousands of varieties of bacteria, it is important to promote the growth of the beneficial ones and keep the harmful ones at bay. Fostering the growth of beneficial microbes can be achieved by eating a healthy diet rich in fibre, prebiotics, and probiotics; adopting a healthy lifestyle; regular physical activity; practicing good hygiene; and strengthening the immune system.