If you had to choose between genetics or diet as having the bigger influence on your gut microbiome, which would you choose?
The answer isn’t quite as simple as one or the other.
Your gut microbiome is influenced by many factors, including your genetics, age, medications, environment, lifestyle and, importantly, what you eat.
However, research shows that diet is one of the factors you can actually change, making it a particularly interesting target for supporting your gut health.
Your Gut Microbiome Is Unique
Your gut contains a huge community of microorganisms, including bacteria, fungi and other microbes.
The combination of microorganisms living in your gut varies considerably from person to person.
Even identical twins, who share almost all of their genetic material, can have substantially different gut microbiomes.
One study involving 1,098 people, including twins and unrelated individuals, used detailed genetic, dietary, microbiome and metabolic information to explore these relationships.
The researchers found that identical twins shared around 34% of the gut microbial species assessed, compared with around 30% among unrelated individuals.
This is an interesting finding because it suggests that having the same genes doesn’t mean having the same gut microbiome. However, the small difference between twin and unrelated pairs does not mean that genetics is irrelevant.
In fact, the study found that monozygotic twins were somewhat more similar to each other than unrelated people, while dietary habits and other personal factors also contributed to differences in the microbiome.
Why is this exciting?
Unlike your genes, your gut microbiome can be influenced by lifestyle factors.
You can’t change your DNA, but your diet is something you can modify.
And research suggests that changing dietary patterns can change the composition and function of the gut microbiome.
Food and Your Gut Microbiome
Your gut microorganisms don’t all use the same foods as fuel.
The foods you eat provide different types of fibre, carbohydrates, fats and plant compounds that create different conditions within the gut.
For example, plant foods can provide:
- Dietary fibre
- Resistant starch
- Polyphenols
- Other compounds that interact with gut microorganisms
Some types of fibre are fermented by gut microorganisms, producing compounds such as short-chain fatty acids.
This is one reason why a varied diet can be so important.
Rather than trying to find one “best” food for your gut, think about creating variety in the foods you eat over the course of the week.
More Plant Variety May Mean More Microbial Variety
You may have heard the recommendation to eat 30 different plant foods each week.
Thirty is not a magic number or an official dietary requirement.
However, research has found an association between greater plant-food diversity and greater gut microbial diversity. In the American Gut Project, people who reported eating more than 30 different types of plants each week had greater microbial diversity than those reporting lower plant diversity.
So rather than stressing about reaching exactly 30, use it as a simple challenge:
How many different plant foods can you include this week?
For example:
- Oats
- Wholegrain bread
- Brown rice
- Quinoa
- Chickpeas
- Lentils
- Kidney beans
- Spinach
- Broccoli
- Carrots
- Tomatoes
- Capsicum
- Apples
- Bananas
- Berries
- Kiwi fruit
- Almonds
- Walnuts
- Chia seeds
- Pumpkin seeds
- Garlic
- Onion
- Ginger
- Cinnamon
- Turmeric
- Parsley
Even small amounts can contribute to variety.
Your Gut Microbiome May Help Explain Why People Respond Differently to Food
Here’s where the research becomes particularly fascinating.
Have you ever eaten the same meal as someone else and wondered why you felt completely different afterwards?
Research suggests that people can have very different metabolic responses to the same food.
In the PREDICT 1 study, researchers measured post-meal blood responses in more than 1,000 twins and unrelated adults.
Following identical meals, there was substantial variation between individuals in their post-meal:
- Blood glucose
- Triglycerides
- Insulin
For example, the coefficient of variation was approximately 68% for glucose and 103% for triglycerides after the same meals.
The gut microbiome was also associated with differences in fasting and post-meal cardiometabolic markers.
This is one reason researchers are so interested in personalised nutrition.
However, it doesn’t mean your microbiome alone determines how you respond to food.
Your genes, body composition, physical activity, sleep, meal composition, medications, previous meals and many other factors can all contribute.
What Did the Microbiome Study Find?
The 2021 Nature Medicine study found many associations between gut microorganisms and:
- Dietary patterns
- Specific foods and nutrients
- Body composition
- Blood glucose
- Blood lipids
- Inflammatory markers
- Post-meal metabolic responses
The associations were particularly strong around healthy and plant-rich dietary patterns.
The study also identified particular microorganisms associated with more favourable metabolic markers.
Two interesting examples were:
Prevotella copri
People carrying Prevotella copri had, on average, lower estimated visceral fat and more favourable post-meal glucose responses in this study.
However, P. copri is not simply a universally “good bacterium.”
Previous research has produced conflicting findings, and different strains or subtypes may behave differently.
The important point is that the presence of P. copri was associated with more favourable metabolic measures in this particular population. It does not prove that P. copri itself caused the improvements.
Blastocystis
The study also found that people who had Blastocystis in their gut had, on average, more favourable glucose responses and lower estimated visceral fat.
Interestingly, Blastocystis is not a bacterium. It is a single-celled eukaryotic microorganism that can be found in the human gut.
Its role is complex and still being investigated, so it would not be appropriate to describe it simply as a “good probiotic”.
Again, the study found an association, not proof that introducing Blastocystis would improve health.
What Does More Recent Research Tell Us?
We now have much larger datasets to build on the original findings.
A major 2026 Nature study analysed microbiome, dietary and health data from more than 34,000 people in the UK and United States.
The researchers identified gut microorganisms that were consistently associated with different dietary patterns and cardiometabolic health markers.
Importantly, they also examined people participating in two dietary intervention trials. In 746 participants, microorganisms considered more favourable according to their health-associated ranking increased following dietary interventions, while some less favourable species decreased.
This provides additional evidence that the gut microbiome can be modified through dietary intervention.
However, the researchers were careful to point out that these studies cannot completely determine whether microbiome changes are the reason diet improves health. More causal research is still needed.
This is an important distinction:
Diet can influence your microbiome, but your microbiome is only one part of the relationship between diet and health.
What Kind of Diet Is Associated With a Healthier Gut Microbiome?
Across these studies, dietary patterns containing more plant foods are repeatedly associated with a more favourable gut microbiome.
A practical pattern can include:
Wholegrains
- Oats
- Wholegrain bread
- Brown rice
- Quinoa
- Wholegrain pasta
Fruit and Vegetables
Aim for variety rather than focusing on one “superfood”.
Legumes
- Chickpeas
- Lentils
- Beans
- Peas
Nuts and Seeds
- Almonds
- Walnuts
- Chia seeds
- Pumpkin seeds
Other Foods
Research has also identified associations involving foods such as yoghurt, seafood and unsaturated fats, including extra virgin olive oil.
The goal isn’t to create a perfect microbiome diet.
It’s simply to build a varied, balanced eating pattern that gives your gut microorganisms plenty of different substrates to work with.
What About Red Meat and Processed Foods?
It is easy to look at microbiome research and conclude that individual foods are either “good” or “bad” for your gut.
The reality is much more complicated.
Some dietary patterns higher in highly processed foods, added sugars or lower in fibre are associated with less favourable microbiome profiles. But this doesn’t mean that one food automatically damages your gut.
Likewise, eating red meat doesn’t mean you have an unhealthy microbiome.
The overall dietary pattern matters.
A person can enjoy red meat while also eating plenty of vegetables, wholegrains, legumes, nuts and fruit.
There is no need to remove an entire food category simply because one study found an association with a particular microorganism.
Your Microbiome Isn’t Something You Need to “Perfect”
The term “healthy gut microbiome” can be misleading.
There isn’t one universal collection of microorganisms that every healthy person needs.
Microbiomes differ substantially between individuals, and the same microorganism can potentially have different associations depending on the surrounding microbial community, diet and host environment.
Researchers are increasingly interested not just in which microorganisms are present, but also in what they are doing and the metabolites they produce.
This is why gut health is much broader than simply counting bacteria.
So, How Much Control Do You Have?
You have some influence, but not complete control.
Your microbiome is shaped by:
- Genetics
- Diet
- Age
- Medications
- Health conditions
- Physical activity
- Sleep
- Environment
- Other lifestyle factors
The exciting part is that some of these factors—particularly diet and lifestyle—are modifiable.
Research increasingly supports the idea that dietary changes can alter the gut microbiome, although people can respond differently to the same dietary changes.
This is encouraging because it means you don’t need to buy expensive microbiome tests or supplements to start supporting your gut.
You can start with the foods on your plate.
Five Simple Ways to Support Your Gut Microbiome
1. Increase Plant Variety
Try adding a new fruit, vegetable, wholegrain, legume, nut or seed each week.
2. Include Fibre-Rich Foods Regularly
Choose foods such as oats, wholegrains, legumes, vegetables and fruit.
3. Include Different Colours
Orange carrots, green spinach, purple cabbage, red tomatoes and blueberries all provide different combinations of plant compounds.
4. Include Fermented Foods You Enjoy
Yoghurt containing live cultures, kefir, kimchi, sauerkraut, tempeh and other fermented foods can be included as part of a varied diet.
Remember that fermented foods are not automatically probiotic foods.
5. Focus on Your Overall Diet
Don’t worry about creating the perfect meal for your microbiome.
Your gut microorganisms are exposed to your diet over and over again, so the overall pattern you follow most of the time is much more important than one individual meal.
Take Home Message
Your genetics may influence your gut microbiome, but they aren’t the whole story.
Research involving twins demonstrates just how individual our microbiomes can be, while studies of diet and microbiome relationships show that what you eat is one of the important factors that can influence your gut microbial community.
More recent research involving tens of thousands of people provides further evidence that diet and the gut microbiome are closely connected and that dietary interventions can change aspects of the microbiome. However, scientists are still working to understand exactly how these changes translate into health benefits.
You can’t change your genes — but you can influence some of the factors that shape your gut microbiome.
So rather than searching for one “perfect” probiotic or gut-health food, focus on variety.
Eat plenty of plant foods. Include fibre-rich wholegrains, legumes, fruit, vegetables, nuts and seeds. Enjoy fermented foods you like. And remember that no single food determines the health of your gut.
Your gut microbiome is individual — and your diet is one practical way you can support it.
How Feed Your Future Dietetics Can Help
Gut health advice can quickly become confusing when social media promotes microbiome tests, expensive supplements and lists of foods you supposedly need to eliminate.
At Feed Your Future Dietetics, I help you separate emerging gut-health research from established nutrition advice and turn the evidence into practical eating strategies.
Whether you’re looking to improve your gut health, increase dietary variety, manage gastrointestinal symptoms or simply build a healthier eating pattern, nutrition can be tailored to your individual needs without unnecessary restriction.
With over 10 years of experience supporting Australians with their nutrition and health goals, Feed Your Future Dietetics provides individualised dietetic support Australia-wide via Telehealth using Zoom or Microsoft Teams.
To learn more or book an appointment:
ashleigh@feedyourfuturedietetics.com
References
- Asnicar F, Berry SE, Valdes AM, et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nature Medicine. 2021;27:321–332.
- Berry SE, Valdes AM, Drew DA, et al. Human postprandial responses to food and potential for precision nutrition. Nature Medicine. 2020;26:964–973.
- Asnicar F, Manghi P, Fackelmann G, et al. Gut micro-organisms associated with health, nutrition and dietary interventions. Nature. 2026;650:450–458.
- McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3.
- Millman JF, Okamoto S, Teruya T, et al. Extra-virgin olive oil and the gut-brain axis: influence on gut microbiota, mucosal immunity, and cardiometabolic and cognitive health. Nutrition Reviews. 2021;79(12):1362–1374.
