Microbiome Diversity Explained: Why Variety Is One of the Best Things You Can Feed Your Gut
Microbiome Diversity Explained: Why Variety Is One of the Best Things You Can Feed Your Gut
A Broth & Co guide to fibre, resistant starch, colourful plants, fermented foods, quality protein, bone broth meals and everyday habits for a more diverse gut ecosystem.
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Key takeaways Microbiome diversity refers to the variety of microorganisms living in the digestive tract. A diverse gut ecosystem is shaped by many everyday factors, especially dietary variety. Fibre, resistant starch, colourful plant foods, herbs, spices, fermented foods where suitable, quality protein, hydration, movement, sleep and stress management can all support the environment in which gut microbes live. |
Your Gut Is a Living Ecosystem
Inside every person is a remarkable community of microscopic life. The gut microbiome is made up of bacteria, fungi, viruses and other microorganisms that live mainly in the large intestine. Although invisible, this ecosystem interacts with digestion, nutrient metabolism, immune function, the gut barrier, metabolism and communication with the brain.
The microbiome is not separate from us. Humans and microbes have evolved together, forming a complex partnership that changes throughout life. Like a garden, rainforest or reef, the health of this ecosystem depends not only on which organisms are present, but also on the environment that allows them to thrive.
That environment is shaped by everyday life: food, sleep, movement, stress, medications, age, early life, travel, pets, outdoor exposure and health status. This is one reason microbiome science is exciting but also nuanced. There is no single perfect microbiome and no single food that creates one.
Why Gut Health Is About More Than Digestion and The Complete Guide to Healthy Digestion: How Your Body Breaks Down Food, Absorbs Nutrients & Supports Whole-Body Health give broader context for why gut health matters across the body.
What Does Microbiome Diversity Mean?
Microbiome diversity refers to the variety of different microorganisms living within the gut, along with the balance between them. Different microbes perform different jobs. Some ferment fibre. Some interact with the immune system. Some help produce compounds that nourish the cells lining the colon. Others metabolise plant compounds or interact with nutrient pathways.
A diverse ecosystem has more potential functions. In nature, a forest with many species is usually more adaptable than a single-species plantation. The gut is not exactly the same as a forest, of course, but the idea helps: a wider range of microbes may support a wider range of microbial activity.
Every person has a unique microbiome. Genetics, birth, early life, diet, sleep, stress, medications, physical activity, environment and age all influence the community that develops. Two people can both have healthy gut ecosystems while having different microbial profiles.
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Microbiome factor |
What it means in everyday life |
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Diversity |
A wider variety of microbial species and functions within the gut ecosystem. |
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Resilience |
The ability of the gut ecosystem to adapt after changes such as travel, illness or diet shifts. |
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Substrates |
The foods and compounds microbes can use, especially fibres, resistant starches and polyphenols. |
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Environment |
The wider conditions that shape microbes, including food, sleep, stress, movement and medication use. |
Your Microbiome Is Always Changing
Unlike your genes, your microbiome is dynamic. It changes from infancy through childhood, adulthood and older age. It also responds to short-term changes such as travel, illness, sleep disruption, antibiotics, stress and shifts in diet.
This can feel daunting, but it is also encouraging. The gut ecosystem is not fixed. Everyday habits can help shape the conditions in which microbes live. A week of meals rich in vegetables, legumes, whole grains, herbs and fermented foods creates a different microbial environment from a week built mostly around low-fibre convenience foods.
The aim is not to control every variable. It is to build a steady pattern that gives the gut ecosystem a range of useful inputs over time.
Every Meal Feeds Two Ecosystems
When we eat, we feed ourselves and we also influence the microorganisms living inside us. A colourful soup with vegetables, legumes, herbs and whole grains provides nutrients for human cells while also supplying fibres and plant compounds that microbes can use.
A repetitive diet made mostly from the same low-fibre foods provides fewer opportunities to nourish a broad microbial community. This does not mean every meal needs to be perfect. It means that variety over weeks and months matters.
A practical question is not 'What is the single best gut food?' but 'How many different nourishing foods am I eating across the week?' This shift makes gut health feel more flexible and more food-positive.
Food Is More Than Nutrition | Health, Communities & the Planet and Why Nutrition Is About More Than Calories: Understanding Food Quality, Nutrient Density & Long-Term Health support this wider food-quality view.
Modern Diets Can Become Narrow
Many households rotate through the same few breakfasts, lunches and dinners each week. Favourite meals are not a problem, but when the diet becomes very narrow, the gut microbiome receives a narrower range of fibres, resistant starches, polyphenols and plant compounds.
Traditional food patterns often included greater natural variation. Meals changed with seasons, regions, family gardens, markets, harvests, seafood availability and cultural cooking methods. Slow-cooked soups, broths, legumes, grains, herbs, spices and fermented foods were ordinary parts of many kitchens.
A modern approach can borrow from that wisdom without becoming complicated. Add a new vegetable to a familiar soup. Rotate oats, brown rice, barley and potatoes. Try lentils in a sauce. Use fresh herbs. Keep frozen vegetables on hand. These small choices gradually widen the diet.

Fibre: One of Your Microbes' Favourite Foods
Fibre is often discussed in relation to bowel regularity, but its role is much bigger. Many forms of dietary fibre travel through the small intestine largely undigested. They reach the large intestine, where gut microbes can ferment them.
During fermentation, microbes produce short-chain fatty acids such as butyrate, acetate and propionate. These naturally occurring compounds are an active area of research because they interact with the gut lining, immune system, metabolism and communication between the gut and other organs.
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Short-chain fatty acid |
Why it matters |
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Butyrate |
An important energy source for cells lining the colon and studied for gut barrier and immune signalling roles. |
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Acetate |
The most abundant short-chain fatty acid in circulation and involved in energy and signalling pathways. |
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Propionate |
Studied for roles in metabolism, appetite-related pathways and nutrient utilisation. |
Different fibres feed different microbial groups. Oats, barley, legumes, apples, berries, carrots, sweet potato, nuts, seeds and vegetables all bring different fibre structures. This is why eating a range of plant foods is more useful than relying on one high-fibre option every day.
Gut Health Is Not Just About Probiotics: Why Feeding Your Microbiome Matters and The Complete Guide to Gut Biotics. explain the difference between feeding microbes and simply adding microbes.
Resistant Starch: A Helpful Carbohydrate for Gut Microbes
Resistant starch is a fibre-like carbohydrate that resists digestion in the small intestine. Instead of being fully broken down and absorbed, it travels to the large intestine where it can be fermented by gut microbes.
Food sources include cooked and cooled potatoes, cooked and cooled rice, cooked and cooled pasta, green bananas, rolled oats, barley, lentils, beans and chickpeas. Cooling certain cooked starches changes part of their structure through a natural process called retrogradation. That means yesterday's potato salad or rice salad can offer a different starch profile from the same food served hot.
Fibre and resistant starch complement one another. One microbial group may prefer oat beta-glucans, another may thrive on resistant starch, while others may ferment pectin from apples or fibres from legumes. The more variety you include, the more opportunities different microbes have to participate.
Colourful Plants, Polyphenols, Herbs and Spices
Colour matters because different colours often reflect different plant compounds. Polyphenols are naturally occurring compounds found in plants that contribute to the colours, flavours and aromas of fruit, vegetables, herbs, spices, tea and cocoa.
Many polyphenols are not fully absorbed in the small intestine. A significant proportion continues to the large intestine, where they interact with the gut microbiome. Gut microbes can help break polyphenols into smaller compounds, while polyphenols may also influence the growth of particular microbial communities.
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Colour group |
Examples |
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Red |
Tomatoes, strawberries, cherries, red capsicum and watermelon. |
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Orange and yellow |
Pumpkin, sweet potato, carrots, corn, mango and yellow capsicum. |
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Green |
Spinach, kale, broccoli, rocket, parsley, basil and coriander. |
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Blue and purple |
Blueberries, blackberries, purple cabbage, eggplant, purple carrots and plums. |
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Herbs and spices |
Turmeric, ginger, cinnamon, oregano, rosemary, thyme, dill, mint, garlic, cloves and black pepper. |
Herbs and spices are especially useful because small amounts still add diversity. Parsley in soup, cinnamon on porridge, coriander in a broth bowl or rosemary in a stew all increase the range of plant compounds in the meal.

Plant-Forward Eating for Healthy Ageing | Colourful Foods, Protein & Longevity gives more ideas for colourful, plant-rich eating.
Traditional Cuisines Often Build Diversity Naturally
One reason traditional cuisines remain so useful is that they often combine many ingredients in one meal. A Mediterranean-style soup might include onion, garlic, celery, carrot, tomato, beans, herbs and olive oil. An Asian-inspired broth bowl might include mushrooms, bok choy, ginger, garlic, spring onion, coriander and noodles or rice. A family stew might include root vegetables, legumes, herbs, spices and broth.
These meals are not built around a single ingredient. They work because they combine protein, plants, fibre, flavour and cooking methods that make nourishing food satisfying. That is exactly the kind of pattern that can help microbiome diversity feel achievable.
From Australia to Asia: A Journey Through Traditional Soups, Broths & Nourishing Recipes and Mediterranean Bone Broth Recipes show how traditional food cultures can make variety feel natural.
Should You Aim for 30 Plant Foods Each Week?
Aiming for around 30 different plant foods each week has become a popular way to think about diversity. It is not a strict rule, and it is not a magic number. It is simply a practical prompt to rotate beyond the same few vegetables and grains.
Plant foods include vegetables, fruit, legumes, whole grains, nuts, seeds, herbs and spices. Small ingredients count. Basil, parsley, cinnamon, black pepper, chia seeds, lentils, oats, berries and leafy greens all add to the weekly mix.
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Meal |
Plant diversity examples |
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Breakfast |
Oats with blueberries, chia seeds, walnuts and cinnamon. |
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Lunch |
Soup with pumpkin, carrot, onion, garlic, celery, lentils, spinach, thyme and parsley. |
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Snack |
Natural yoghurt with kiwi fruit and pumpkin seeds. |
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Dinner |
Fish, tofu or chicken with brown rice, broccoli, red capsicum, mushrooms, bok choy, ginger, garlic and sesame seeds. |
This is not about counting forever. It is about noticing variety and making it easier to add another colour, herb, seed, legume or whole grain where it fits.
A Sample Day of Microbiome-Friendly Eating
A diverse day does not need to be elaborate. It can be built from ordinary foods that repeat in different combinations.
· Breakfast: porridge with oats, blueberries, strawberries, chia seeds, walnuts and cinnamon.
· Morning snack: natural yoghurt with kiwi fruit and pumpkin seeds.
· Lunch: vegetable and lentil soup made with bone broth, pumpkin, carrot, onion, garlic, celery, spinach, thyme and parsley.
· Afternoon snack: apple with almond butter.
· Dinner: fish, tofu or chicken with brown rice, broccoli, red capsicum, mushrooms, bok choy, ginger, garlic and sesame seeds.
This kind of day can include more than 20 different plant foods without feeling restrictive. The exact number matters less than the habit of rotating plants, fibres, herbs and grains across the week. Variety is built meal by meal.

Fermented Foods Add Variety Alongside Fibre
Fermented foods such as natural yoghurt, kefir, kimchi, sauerkraut, miso and tempeh are traditional foods that can add flavour and dietary variety. Some contain live microorganisms when consumed, while others are valued for the changes fermentation creates in the food itself.
Fermented foods can sit beautifully within a balanced eating pattern. They work best alongside the fibre-rich plant foods and resistant starches that help nourish existing microbial communities.
The Gut Ecosystem: Why No Single Food or Supplement Can Do It All is a useful companion for keeping this balanced.
Quality Protein Still Matters
Gut health conversations often focus on plants, but humans also need adequate protein. Protein provides amino acids for muscle maintenance, connective tissue, skin, enzymes, hormones, immune proteins, tissue repair and growth across life.
Good protein sources include fish, eggs, poultry, lean meat, dairy foods, legumes, soy foods, nuts, seeds and broth-based meals. A balanced gut-supportive meal can include both protein and fibre-rich plant foods; the two are complementary.
Protein Throughout Life: Why Your Protein Needs Change With Age and High-Protein Foods: The Foundation of Muscle, Healthy Ageing & Recovery Nutrition place protein in a life-stage context.
Where Bone Broth Fits
Bone broth has been enjoyed across many cultures as a base for soups, stews, noodle bowls, sauces and slow-cooked meals. It contributes naturally occurring protein, minerals present in the finished broth, collagen-derived amino acids, warmth, hydration and savoury flavour.
Bone broth is not a significant source of dietary fibre, so it does not feed fibre-fermenting microbes in the same way legumes, vegetables, oats or resistant starch do. Its strength is that it helps build meals that include those foods.
For example, bone broth can become the base for a vegetable and lentil soup, a bean minestrone, a mushroom and bok choy noodle bowl, or a slow-cooked stew with herbs, spices and whole grains. In that context, it supports a diverse meal rather than acting as a standalone gut-health solution.
Bone Broth Benefits: The Complete Guide to Gut Health, Protein, Recovery & Healthy Ageing, Bone Broth Clinical Study: Digestive Wellbeing & Intestinal Permeability Research | Broth & Co and Bone Broth, Collagen & Functional Nutrition provide more Broth & Co context.

Whole Dietary Patterns Matter Most
Microbiome science can feel technical, but the practical message is familiar: the overall pattern matters most. Vegetables, fruit, legumes, whole grains, nuts, seeds, herbs, spices, fermented foods where suitable, quality protein and broth-based meals can all sit together in a balanced routine.
This is also why home cooking is so useful. A single soup can include broth, onion, garlic, pumpkin, carrot, lentils, spinach, parsley and black pepper. A tray bake can include chicken or tofu, sweet potato, broccoli, capsicum, red onion, olive oil and herbs. A lunch bowl can include brown rice, chickpeas, cucumber, tomato, leafy greens, seeds and yoghurt dressing.
These meals are simple, but they do several things at once: provide protein, add fibre, increase plant diversity, reduce waste, support hydration and make leftovers easier.
Lifestyle Shapes the Microbiome Too
Food is powerful, but it is not the only influence on the microbiome. Regular movement, sleep, stress, medications, time outdoors and everyday routines all help shape the environment in which gut microbes live.
· Movement supports overall health, metabolic function, gut motility and communication between body systems.
· Sleep supports repair, appetite regulation, immune function and daily biological rhythms.
· Stress and digestion are closely connected through the gut-brain axis.
· Time outdoors, gardening and contact with natural environments may increase everyday microbial exposure while supporting wellbeing.
· Antibiotics remain important medicines and should be used as directed by a qualified healthcare professional.
Sleep, Gut Health & Brain Function, Neurotransmitters and Gut Health | Understanding the Gut-Brain Axis, The Gut-Mitochondria Connection: How Gut Health Influences Energy, Ageing & Metabolic Wellness and The Gut–Mitochondria–Brain Connection: How Cellular Energy Links Digestion, Brain Function & Whole-Body Health connect the microbiome with wider systems.
Gut Diversity and Whole-Body Health
The gut microbiome is often introduced as a digestion topic, but it is also connected with immune activity, metabolic health, brain signalling, skin pathways and muscle-supporting routines. These relationships are complex and still being researched, so they should be described carefully. The useful takeaway is that gut health sits within whole-body wellbeing.
The immune system is closely connected to the gastrointestinal tract, where it continually monitors what passes through the digestive environment. The gut and brain communicate through nerves, hormones, immune signals and microbial metabolites. Metabolic health is influenced by many factors, including diet quality, movement, muscle, sleep and the gut environment.
This is why a diverse, food-first routine can support more than digestive comfort. It helps create a dietary pattern that also supports energy, meal satisfaction, protein intake, fibre intake, immune wellbeing and long-term health habits.
Microbiome Diversity Across Life
Microbiome diversity matters across life, not only during healthy ageing. A baby's microbiome begins developing around birth and continues maturing through infancy and childhood. Children benefit from repeated exposure to a variety of foods, textures, flavours and family meals. Adults need practical routines that support energy, digestion and metabolic health. Older adults may need extra attention to protein, fibre, hydration, appetite, muscle and social connection around meals.
Children's Nutrition: Building Healthy Eating Habits for Life, The Gut-Brain Connection in Children: How Gut Health May Influence Mood, Behaviour & Development and Gut Health & Healthy Ageing: How the Microbiome Influences Longevity give more life-stage context.
A Simple Microbiome Diversity Routine
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Habit |
How to make it practical |
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Add one new plant food each week |
Try a new vegetable, bean, whole grain, herb, spice, nut or seed. |
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Rotate grains and legumes |
Swap between oats, barley, brown rice, lentils, chickpeas, beans and wholegrain pasta. |
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Build diverse soups |
Use broth with vegetables, legumes, herbs, spices and whole grains. |
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Use herbs generously |
Add parsley, coriander, dill, mint, basil, thyme, rosemary, ginger or turmeric. |
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Include protein |
Pair plant-rich meals with fish, eggs, poultry, dairy, tofu, legumes, nuts, seeds or bone broth. |
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Support the rhythm |
Prioritise sleep, movement, hydration and stress-management habits that suit your routine. |
Food First: 10 Daily Habits for Gut Health, Energy & Long-Term Wellbeing and Daily Gut Health Routine: Simple Habits for Digestive Wellbeing, Energy & Microbiome Health offer more everyday structure.
Common Gut Diversity Misunderstandings
Gut health can become confusing because the topic is often surrounded by strong claims. A more useful approach is to keep the basics steady.
· You do not need the same microbiome as someone else; healthy microbial communities vary between individuals.
· Fermented foods can be useful, but they do not replace fibre-rich plant foods.
· A probiotic does not replace a varied diet, and different strains have been studied for different purposes.
· Bone broth can support gut-friendly meals, but it should be paired with fibre-rich ingredients such as vegetables, legumes, herbs and whole grains.
· Microbiome diversity is built over time through repeated habits, not one perfect meal.
This balanced view makes the science more practical. Instead of trying to control every detail, focus on the foods and routines you can repeat.
Recipe Inspiration
This article does not need a new standalone recipe to be useful. The most practical next step is to use meals that naturally combine broth, vegetables, legumes, herbs, spices and whole foods.
· collection of nourishing recipes
· Vegetable Forward Soups and Broths
· The Power of Soup: How One Pot Can Support Immune Health, Eat More Vegetables & Reduce Food Waste
· Mediterranean Bone Broth Recipes
· From Australia to Asia: A Journey Through Traditional Soups, Broths & Nourishing Recipes
· Healthy Kids Recipes with Hidden Vegetables
· How to Flavour Bone Broth: Herbs, Spices & Gut-Friendly Ingredients
Frequently Asked Questions
What is microbiome diversity?
Microbiome diversity refers to the variety of microorganisms living within the digestive tract. A diverse microbiome is generally considered a feature of a resilient gut ecosystem, although every person's microbiome is unique.
How can I support microbiome diversity naturally?
Focus on variety: vegetables, fruit, legumes, whole grains, nuts, seeds, herbs, spices, resistant starch, fermented foods where suitable, quality protein, hydration, movement, sleep and stress management.
Do frozen vegetables count?
Yes. Frozen vegetables can contribute nutrients, fibre and plant diversity and are often a practical, affordable option.
Do herbs and spices count as plant foods?
Yes. Fresh and dried herbs and spices each contribute plant compounds and can help increase dietary variety.
Is bone broth good for the microbiome?
Bone broth can be part of a microbiome-friendly pattern by contributing protein and serving as a base for meals rich in vegetables, legumes, herbs and whole grains. It is not a significant source of dietary fibre on its own.
Do I need expensive supplements?
Not necessarily. For many people, the biggest opportunity is improving dietary variety and everyday habits. Personal medical concerns should be discussed with a qualified healthcare professional.
Summary
Microbiome diversity is about creating a gut environment where many different microbial communities can coexist and perform different roles. Food is one of the most powerful ways to shape that environment, but lifestyle matters too.
The most practical approach is simple: eat a wider variety of whole plant foods, include fibre and resistant starch, use herbs and spices, enjoy fermented foods if they suit you, include quality protein, stay hydrated, move regularly, prioritise sleep and manage stress where possible.
Bone broth fits best as part of a diverse meal pattern. It brings savoury flavour, warmth, protein and collagen-derived amino acids, and it can help turn vegetables, legumes, whole grains and herbs into meals that nourish both you and your gut ecosystem.
