How to Optimize Your Gut Health – Nutrition

What to eat and drink to keep your microbes happy and healthy.

Dietary diversity

Diet as a key modifiable factor

Diet is a key modifiable factor when it comes to optimizing gut health. Eating a variety of fresh, whole foods such as fruits, vegetables, nuts and seeds can help promote the growth of beneficial bacteria in the microbiome. Fermented foods like yogurt and kimchi are also great sources of probiotics that can help maintain balance in the gut. Additionally, limiting processed foods high in sugar and saturated fat can reduce inflammation and improve overall digestive health.

Including dietary fiber from plant-based sources is essential for maintaining healthy levels of beneficial bacteria in the gut. Fiber helps feed these microbes which then produce short-chain fatty acids (SCFAs) that nourish cells lining our intestines and protect against disease-causing pathogens. Studies have shown that diets rich in SCFAs may even reduce risk factors associated with obesity, diabetes, heart disease and cancer! So make sure to include plenty of fiber-rich foods like legumes, oats and barley into your diet for optimal gut health!

Permanent versus acute changes to diet and impact on the gut microbiota

When it comes to optimizing gut health, permanent dietary changes are more effective than acute ones. For example, a study of over 1,000 people found that those who made long-term dietary changes had significantly higher levels of beneficial bacteria in their microbiome compared to those who only made short-term adjustments. This suggests that making sustainable lifestyle modifications is the best way to promote healthy microbial diversity and balance in the gut.

In addition, research has shown that certain foods can have an immediate impact on our microbiota composition. Eating probiotic-rich fermented foods like yogurt or kimchi can help increase levels of beneficial bacteria within 24 hours! Similarly, consuming prebiotics such as garlic and onions can stimulate growth of good microbes within just a few days. So while permanent diet changes are important for maintaining optimal gut health over time, incorporating these types of food into your daily routine may also provide quick relief from digestive issues or other symptoms associated with dysbiosis.

Focus on whole foods

When it comes to optimizing gut health, focusing on whole foods is key. Whole foods are unprocessed and contain all the essential nutrients our bodies need for optimal functioning. Eating a variety of fresh fruits, vegetables, nuts and seeds can provide an abundance of vitamins, minerals and fiber that help nourish beneficial bacteria in the microbiome. Additionally, these plant-based sources are rich in polyphenols which have been shown to reduce inflammation and improve digestive health.

Including healthy fats from sources like avocados, olive oil or fatty fish can also be beneficial for gut health as they provide energy for microbes to thrive. Studies have even found that omega-3 fatty acids may help protect against dysbiosis by reducing levels of pro-inflammatory molecules in the gut! So make sure you’re getting enough healthy fats into your diet for optimal microbial balance!

Fill up on fiber, part 1

Fiber is an essential part of a healthy diet and plays an important role in maintaining gut health. It helps to feed beneficial bacteria, which produce short-chain fatty acids that nourish the cells lining the intestine and reduce inflammation. Eating plenty of fiber can also help keep you regular by promoting bowel movements.

Good sources of dietary fiber include fruits, vegetables, legumes, nuts and seeds. For example, one cup of cooked lentils contains 15 grams of fiber – almost half your daily recommended intake! Other great sources are raspberries (8g per cup), black beans (15g per cup) and almonds (4g per ounce). Adding these foods to your meals will not only boost your fiber intake but also provide other essential nutrients like vitamins A & C as well as minerals such as iron and magnesium.

Including prebiotic fibers like garlic, onions or Jerusalem artichokes can be especially beneficial for gut health since they act as food for probiotics in the microbiome. Prebiotics have been shown to increase levels of beneficial bacteria while reducing levels of harmful ones – making them a powerful tool for optimizing gut health!


Polyphenols are a type of antioxidant found in many plant-based foods, such as dark chocolate, green tea and red wine. They have been shown to reduce inflammation and improve the diversity of beneficial bacteria in the microbiome. Polyphenols can also help protect against oxidative stress caused by free radicals, which can damage cells and lead to chronic diseases like cancer or heart disease.

In addition to their anti-inflammatory properties, polyphenols may also play a role in regulating blood sugar levels. Studies have shown that consuming polyphenol-rich foods can help reduce insulin resistance and lower fasting glucose levels. This is especially important for people with diabetes who need to keep their blood sugar under control.

Interestingly, some research suggests that polyphenols may even be able to cross the blood-brain barrier – meaning they could potentially influence brain health too! For example, one study showed that consuming cocoa flavanols (a type of polyphenol) improved memory performance in healthy adults aged 50–69 years old. So if you’re looking for an excuse to indulge in some dark chocolate every now and then – this might just be it!

Dietary diversity

The key to keeping our colony of gut microbes healthy and happy through diet is diversity.

In *The Diet Myth*, Tim Spector points out that our forager ancestors probably regularly ingested around 150 ingredients in a week. These days, most people consume fewer than twenty separate food items in a week, many of which are artificially refined, and “come depressingly from just four main ingredients: corn, soy, wheat or meat.”

According to Spector, the trend towards highly restrictive eating plans that we’ve observed in the last few decades – first by eliminating fat, then carbohydrates – is harmful to our health as it depletes the diversity of our resident microbes.” The exception to this, he claims, is intermittent fasting, which has the potential to stimulate friendly gut microbes, provided the ‘background diet’ is healthy and diverse.

Reduce your intake of red and processed meat

Vegetarians have different resident microbes than omnivores, and some studies have shown that a plant-based diet may benefit the gut microbiome. However, it’s unclear whether this is due to a lack of meat or the high fiber content that a plant-based diet provides.

Researchers have found that heme iron found in red meat increases the abundance of bacteria that can permeate the immunity-protective mucosal layer of the colon. Red and processed meats also have high levels of saturated fats, which increase the secretion of bile acids.

Those that aren’t absorbed in the small intestine are converted into secondary bile acids in the colon, which can trigger DNA damage and resistance to apoptosis (programmed cell death). Apoptosis resistance is associated with the development of cancer cells. Sulfur – present in amino acids from red meat and used as a preservative in processed meat – can also promote cancer development.

Prebiotics and probiotics

Probiotics are live cultures that provide health benefits by improving or restoring gut flora. They can take the form of foods (such as yogurt, kombucha and miso) or supplements – but many supplements claiming to confer probiotic health benefits have not been subjected to rigorous testing by regulatory bodies.

Tim Spector offers the following helpful analogy to describe prebiotics: “Whereas probiotics are selected microbes that benefit the health of the host, prebiotics are the constituent parts of foods that act as fertilisers for the microbes in the colon. These largely non-digested fibres allow beneficial microbes to thrive, and they come in several forms.”

The first prebiotics we’re exposed to are the oligosaccharides in breastmilk (see “How microbiotas benefit the body”). Most prebiotics come in the form of resistant starches – dietary fibers found in certain fruits, vegetables and other plant-based foods. Some studies have shown that eating specific prebiotics can reduce cortisol levels in humans.


Omega-3 is an essential fatty acid that we can’t make ourselves, belonging to the group of fats known as polyunsaturated fatty acids (PUFAs).

The main dietary sources of Omega-3 are oily wild fish, leafy greens, and certain plants such as linseed (flaxseed). These appear to be beneficial for the heart as they reduce lipids and inflammation, dampening the body’s reaction to threats of infection in the process.

According to Ruairi Robertson, the typical western diet is deficient in Omega-3 – and this imbalance in dietary fat can contribute to a number of chronic diseases, especially across generations. Research on mice fed a diet deficient in Omega-3 found changes to the microbiota that included an abundance of bacteria associated with metabolic diseases. The studies also showed decreased production of the metabolites, SCFAs, in Omega-3-deficient mice.

Fermented foods and synbiotics

Fermented foods such as kimchi, sauerkraut and tempeh tend to be rich in the beneficial bacteria, Lactobacilli. Apple cider vinegar is a fermented liquid that is high in the SCFA, acetate. The fermentation process enhances the number of live cultures, or beneficial organisms, particularly Lactobacillus.

People who eat these foods typically have lower levels of Enterrobaccae in their guts. This is a type of microbe associated with inflammation and chronic disease – so having lower levels of it makes you less at risk of developing chronic illness.

The traditional Japanese diet (which is rich in fermented foods) and the Mediterranean diet (which is rich in polyphenols) are good examples to follow, as they resemble the prehistoric human diet most closely.

Fermented foods also belong to a group of foods known as ‘synbiotics’. Synbiotics are foods that contain a mix of prebiotics and probiotics. Other sources of synbiotics are onions and garlic, which are a good source of prebiotics.

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