Gut Health Explained: How Your Microbiome Affects Digestion and Immunity
Discover how your gut microbiome influences digestion, mood, and overall health. Learn the science behind gut health, key microbes, and practical tips to restore balance naturally.
What is Human gut health
The human gut contains millions of microorganisms that together form a complex and diverse microbial community.
These microorganisms, which are mostly harmless, live in a symbiotic relationship with the host and help strengthen the immune system to protect against harmful pathogens.
In addition to nourishing the body, the food we eat also provides nutrients for these beneficial microbes living in our digestive system — collectively known as the gut microbiome.
Undigested food components are broken down into various useful substances called metabolites.
Therefore, our diet plays a key role in shaping the structure and function of the gut microbiome.
This microbiome interacts with the gut lining and immune system to keep the intestine healthy and balanced.
When the gut microbiome is disturbed, it can contribute to diseases such as inflammatory bowel disease (IBD).
Five major phyla for human gut microbiota
The human gut microbiome contains about 3.8 × 10¹³ microbes in an average adult male, which is even more than the total number of human cells in the body (around 3.0 × 10¹³).
There are five major phyla for the human gut microbiota, namely Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobe.
The two dominating phyla, Firmicutes and Bacteroidetes, representing 90% of the gut microbiota.
Pathogenic bacteria in gut
Some bacteria, known as “pathobionts,” are normally harmless but can become harmful under certain conditions.
For example, bacteria from the phylum Proteobacteria are considered pathobionts, and their overgrowth is often observed in people with inflammatory bowel disease (IBD).
Gut microbiota diversity depends on
- Diet
- Human lifestyle
- Age
- Environmental factors
Use of antibiotics and gut health
Antibiotics are commonly used to treat serious bacterial infections, prevent infections during surgeries, and manage certain microbe-related cancers.
However, overuse or misuse of antibiotics can harm the gut microbiome.
Firstly, it can cause bacteria to develop resistance, allowing antimicrobial-resistant genes to spread quickly to other microbes through horizontal gene transfer.
Secondly, antibiotics disturb the balance of the normal gut bacteria and reduce the production of important bacterial metabolites, which can affect the body’s protein functions.
Recovery of the gut microbiome after antibiotic use is usually slow and often incomplete, sometimes taking several years to return to normal.
Short-chain fatty acids (SCFAs)
Certain bacterial species in the gut can ferment dietary fibers — the indigestible carbohydrates — to produce substances such as short-chain fatty acids (SCFAs), branched-chain fatty acids, lactate, ethanol, hydrogen, and carbon dioxide. These products are either used by the body or eliminated.
Indigestible carbohydrates act as major dietary fibers that promote the growth of fiber-degrading bacteria, which in turn produce SCFAs.
The main SCFAs found in humans are acetate, propionate, and butyrate.
SCFAs and its function
Under normal conditions, short-chain fatty acids (SCFAs) are generally beneficial for maintaining gut health.
However, they are also linked to certain metabolic diseases such as obesity and type 2 diabetes.
The levels and ratios of different SCFAs can change depending on the types of bacteria present in the gut.
Effect of balanced and imbalanced diet on gut health
Balanced diet in gut health
A nutritionally balanced diet is essential for maintaining a healthy gut microbiome, a strong intestinal barrier, proper immune balance, and normal gut function.
Imbalance diet in gut health
Imbalance diet can reduce microbial diversity and cause gut dysbiosis, leading to a leaky gut and chronic inflammation, as commonly seen in conditions like inflammatory bowel disease (IBD) and other disease such as obesity, type 2 diabetes, and atopy.
Dysbiosis alter the composition of gut microbiota
Dysbiosis — a condition marked by reduced diversity and changes in the composition of gut microbes — is linked to several health issues, including obesity, diabetes, and gastrointestinal diseases like IBD.
There is increasing interest in improving gut health by targeting the gut microbiota through dietary and nutritional strategies, which can also serve as supportive therapies for treating IBD.
Eubiosis control various disease
Eubiosis, a balanced and healthy state of the gut microbiota, helps protect against various microbe-related diseases.
Dietary fiber plays an important role in maintaining this balance by supporting beneficial bacteria and promoting the production of metabolites like butyrate, which support gut health.
While a balanced diet is vital for overall well-being, a fiber-rich diet is especially important for preserving the diversity of gut microbes.
Eating a healthy diet and maintaining eubiosis together contribute significantly to better human health.
Gut microbiome in new born babies
Microbial colonization of the human gut starts at birth.
At first, the infant’s intestines are almost sterile or contain very few microbes, but the gastrointestinal tract is rapidly colonized during and after delivery.
As a baby passes through the birth canal, it is exposed to the mother’s vaginal microbes, which strongly influence the early development of the infant’s gut microbiota.
Infants born through vaginal delivery have gut microbes similar to their mother’s vaginal microbiota, while those born by cesarean section tend to have fewer gut microbes in the first month. However, these differences usually disappear by around six months of age.
During the first year of life, the gut microbiota remains relatively simple and varies widely between individuals.
The early microbial colonization of the gut plays an important role in shaping the composition of the adult gut microbiota later in life.
Factor that affects microbiome in new born
The infant’s gut microbiota undergoes a succession of changes that are correlated with a shift in feeding mode from breast- or formula-feeding to weaning and the introduction of solid food.
Gut microbiota depends on different external and internal, host-related factors.
External factors
- Microbial load of the immediate environment
- Type of food eaten
- Feeding habits
- Composition of the maternal microbiota
- Dietary
- Temperature-related stresses can influence the succession of microbes
Internal factors
Internal factors include, but are not limited to,
- Intestinal pH
- Microbial interactions
- Environmental temperature
- Physiological factors
- Bile acids
- Host secretions and immune responses
- drug therapy
Functions of the Gut Microbiota
Human gut microbiota can synthesize essential vitamins, including biotin, folate, and vitamin K, and neutralize carcinogenic compounds.
In addition, the microbiome provides the vital biochemical pathways for the metabolism of nondigestible carbohydrates, such as resistant starches, cellulose, hemicellulose, pectins, and gums; some oligosaccharides that escape digestion; unabsorbed sugars and alcohols from the diet; and host-derived mucins.
This functionality results in the recovery of energy and absorbable substrates for the host and a supply of energy and nutrients for bacterial growth and proliferation.
The Gut–Brain Axis
The gut–brain axis is a system that allows the gut and the brain to talk to each other. They communicate through nerves, hormones, and immune signals.
This connection works in both directions — the brain can control how the gut moves food (called peristalsis), how it makes mucus to protect itself, and how the gut’s immune system works.
At the same time, the gut microbes (tiny bacteria living in our intestines) can send signals back to the brain. They do this by making chemicals called metabolites, which can affect how we feel and think.
Changes in gut bacteria can affect mood, stress, memory, and even mental illnesses. This means keeping our gut healthy may also help keep our mind healthy.
Intestinal bacteria prevent colonization of pathogens
Many bacteria in our intestines help protect us from harmful germs. They do this by competing for food and space on the gut lining, so harmful microbes can’t settle and grow. This protective action is called the barrier effect or competitive-exclusion effect.
Some good bacteria also make special chemicals called bacteriocins, which can kill or stop the growth of harmful bacteria, keeping our gut healthy and balanced.
Association between Gut Microbiota and Disease
The bacteria living in our intestines, called the intestinal microbiota, play an important role in keeping us healthy and can also be linked to many diseases.
Although research on this topic is still in the early stages, scientists are learning that changes in the gut microbiota can affect how our body works.
An imbalance in gut bacteria has been connected to several major diseases, including obesity, diabetes, heart problems, cancer, high blood pressure (hypertension), and inflammatory bowel diseases (IBDs).
The possibility of a link between the intestinal gut microbiota and
(1) Chronic gastrointestinal diseases such as
Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD), and
(2) Systemic metabolic diseases, such as
type 2 diabetes and obesity.
Gut microbiota and autoimmune disorders
Recent studies show that the early development of gut bacteria is very important for building a strong and healthy immune system.
The gut microbiota helps the immune system grow, mature, and learn how to respond properly to harmful germs.
This process starts at birth, when a baby’s body first comes into contact with these microbes.
Without these friendly bacteria, the immune system cannot develop fully.
A healthy balance of gut microbes early in life also helps prevent autoimmune diseases, where the body’s defense system mistakenly attacks its own cells.
Gut microbiota in malnutrition and fasting
What we eat has a big effect on the types and balance of bacteria in our gut. The foods and supplements we consume can change the gut microbiota over time.
A high-fat diet can increase the risk of diseases such as obesity, metabolic syndrome, and diabetes, and these conditions are often linked to major changes in gut bacteria.
Also, when the body’s natural day–night rhythm (circadian rhythm) is disturbed — for example, due to irregular sleep or eating patterns — it can upset the balance of gut microbes (intestinal dysbiosis).
This imbalance may lead to metabolic and inflammatory diseases, including diabetes, intestinal inflammation, and even cancer.
Malnutrition
Malnutrition affects the gut microbiota in many ways, but most studies on this topic have been done using laboratory animals because it is not ethical to test such conditions in humans.
Malnutrition is one of the main causes of death in children worldwide. To treat severe cases, doctors use nutrient-rich therapeutic foods.
However, even after treatment, many children do not fully recover their normal body weight and growth.
This may be because their gut microbiome remains immature, which affects how their bodies absorb and use nutrients.
Intermittent fasting (IF) regimens
Intermittent fasting helps shape the gut microbiota by changing how and when nutrients are available for digestion. This, in turn, affects the immune responses in the intestines and can influence conditions such as heart disease, high blood pressure, and diabetes.
Studies also show that using antibiotics to change the gut microbiota can help children with severe malnutrition live longer.
However, if their gut microbiome stays immature, the malnutrition often returns.
This suggests that a mature and balanced microbiota is important for long-term recovery.
Overall, diet and lifestyle habits, such as fasting or time-restricted eating, play a key role in determining the composition and health of the gut microbiota.
Effect of Foods on the Gut Microbiome
Dietary fiber benefit
Having low diversity of gut bacteria is linked to several long-term diseases, such as obesity, diabetes, and inflammatory bowel disease (IBD).
Eating habits play a big role in this. A low-fiber, high-fat, and high-protein diet can reduce the number of fiber-degrading bacteria in the gut, which is common in people from industrialized countries.
Even short-term changes in diet can have quick effects — for example, eating a high-fat, high-protein, low-fiber diet can reduce gut bacteria diversity within a single day.
Not eating enough fiber can cause lasting damage to gut bacteria. Adding fiber back into the diet can help restore these bacteria in the first generation, but if the low-fiber diet continues for many generations, the loss becomes permanent.
Dietary Fat on Gut Microbiome
A high-fat diet reduces the variety of gut bacteria compared to a low-fat diet, no matter what type of fat is eaten — whether it comes from lard, milk, safflower oil, or palm oil.
Different fats affect gut bacteria in different ways because each type of fat has a different fatty acid makeup.
Palm oil greatly increases a group of bacteria called Verrucomicrobia, mainly due to the rise of Akkermansia muciniphila, which lives in the gut’s mucus layer.
Taking omega-3 fatty acids (PUFAs) — about 4 grams daily — in healthy adults can increase certain helpful bacteria such as Bifidobacterium, Roseburia, and Lactobacillus.
A diet high in milk fat (which contains many saturated fatty acids) can cause an increase in certain sulfate-reducing bacteria in the gut. This effect is not seen with fats like safflower oil, which are rich in n-6 polyunsaturated fatty acids.
However, adding dietary fiber can help reverse the negative effects of a high-fat diet.
Fiber supports healthy gut bacteria and helps prevent metabolic and immune system problems caused by unhealthy fat intake.
Dietary Protein and Certain Amino Acids
Not all the protein we eat gets completely digested. Animal proteins are digested very well (over 90%), while plant proteins are a bit less digestible (about 70–90%).
In a regular mixed diet, it’s usually the amount of protein eaten, not where it comes from, that affects how much undigested protein reaches the colon.
The protein that isn’t digested travels to the lower part of the colon (distal colon), where gut bacteria ferment it. This process produces many complex by-products, including short-chain fatty acids (SCFAs), branched-chain fatty acids, carbon dioxide, hydrogen, hydrogen sulfide, ammonia, phenols, and indole compounds.
These substances can influence gut health in both positive and negative ways.
The amount and type of protein in our diet affect the kinds and amounts of substances made by gut bacteria.
Eating a high-protein diet causes gut bacteria to focus more on breaking down proteins instead of carbohydrates.
This shift can disturb the balance of the gut lining (mucosal homeostasis) and may negatively affect gut health if it continues for a long time.
High sugar intake
Eating too much sugar is common in the Western diet, and studies in animals have shown a connection between high sugar intake and inflammatory bowel disease (IBD).
In healthy mice, eating large amounts of glucose or fructose for a short time doesn’t cause gut inflammation. However, in mice that already have a weakened gut barrier (leaky gut), high sugar intake makes colitis (gut inflammation) worse.
A high-sugar diet increases the number of mucus-eating bacteria like Akkermansia muciniphila and Bacteroides fragilis, which damage the gut’s protective mucus layer. It also reduces the diversity of gut microbes and changes their balance.
Too much glucose or fructose can also increase gut inflammation and make the gut lining more leaky by lowering the levels of tight junction proteins that hold the intestinal cells together.
Overall, these findings suggest that a high-sugar diet harms gut bacteria, weakens the intestinal barrier, and may increase the risk of developing IBD.
References:
Afzaal, Muhammad, et al. “Human gut microbiota in health and disease: Unveiling the relationship.” Frontiers in microbiology 13 (2022): 999001.
Zhang, Ping. “Influence of foods and nutrition on the gut microbiome and implications for intestinal health.” International journal of molecular sciences 23.17 (2022): 9588.