Here’s something wild: You have about 39 trillion microorganisms living in your gut right now.

That’s more microbial cells than you have human cells in your entire body.

And these tiny organisms? They’re not just along for the ride. They’re actively controlling your metabolism, your cravings, your inflammation levels, and even your mood.

Researchers now call your gut microbiome your "second brain" - and it has a HUGE say in whether your body stores fat or burns it efficiently.

So when we talk about metabolic health, we’re not just talking about what YOU eat. We’re talking about what you FEED those 39 trillion helpers.

Your Gut Microbiome: The Metabolic Control Centre

Here’s what your gut microbes do for you:

Regulate Metabolism: They help extract energy from food and decide whether to store or burn fat.
Control Inflammation : A healthy microbiome reduces chronic inflammation (which blocks fat loss).
Produce Essential Nutrients: They create vitamins (like B vitamins and vitamin K) and short-chain fatty acids that fuel your cells.
Regulate Hunger Hormones : They influence ghrelin (hunger) and leptin (fullness).
Protect Gut Barrier : They prevent “leaky gut” which triggers inflammation and metabolic dysfunction.
Communicate with Your Brain: Via the gut-brain axis, influencing mood, stress, and food choices.

Research shows: A diverse, healthy gut microbiome is associated with better metabolic health, lower inflammation, and easier weight management.

But when your microbiome is out of balance (dysbiosis)? You get:

❌ Increased inflammation
❌ Insulin resistance
❌ Fat storage (especially around the middle)
❌ Increased cravings for sugar and processed foods
❌ Poor nutrient absorption
❌ Low energy

So How Do You Feed Your Microbiome?

Your gut bacteria thrive on ONE thing above all else: FIBRE.

Not protein. Not fat. Not carbs. Fibre.

Specifically, prebiotic fibre – the kind of fibre that YOU can’t digest, but your gut bacteria can.

When your gut bugs ferment this fibre, they produce short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate.

These SCFAs:

→ Fuel your gut lining cells
→ Reduce inflammation throughout your body
→ Improve insulin sensitivity
→ Signal your brain that you’re full
→ Support metabolic health

But here’s the problem: Most people eating a Western diet get only 10-15g of fibre per day.

The optimal amount? 30-40g per day from diverse plant sources.

The Best Foods to Feed Your Microbiome

Here’s what to focus on:

Vegetables: Especially leafy greens, broccoli, Brussels sprouts, artichokes, asparagus
Fruits: Berries, apples, pears – with the skin on!
Nuts and Seeds: Almonds, walnuts, chia seeds, flaxseeds
Legumes: Lentils, chickpeas, black beans, kidney beansWhole Grains: Oats, quinoa, brown rice, barley
Healthy Fats: Olive oil, avocados – support gut barrier
Fermented Foods: Yogurt, kefir, kimchi, sauerkraut, miso – add beneficial bacteria

What to Limit (Your Gut Bugs Hate These)

❌ Ultra-processed foods – Damage gut lining and reduce microbial diversity
❌ Artificial sweeteners – Disrupt gut bacteria balance
❌ Excess sugar – Feeds harmful bacteria and yeast
❌ Refined grains (white bread, white rice) – Lack fibre, don’t feed good bacteria
❌ Excessive alcohol – Damages gut lining and reduces beneficial bacteria

Research shows: Ultra-processed foods are associated with reduced gut microbiome diversity and increased metabolic dysfunction.

Hydration Matters Too

Water isn’t just for quenching thirst. It’s essential for metabolic processes, nutrient transport, and keeping your digestive system moving.

Research shows: Even mild dehydration can slow metabolism, impair cellular function, and reduce exercise performance.

How much? Aim for 2-3 litres (8-12 cups) per day, more if you’re active or in a hot climate.

Signs you’re well-hydrated:

✓ Pale yellow urine (not dark)
✓ Regular bowel movements
✓ Good energy levels
✓ Skin elasticity

Your Action Plan:

Don’t try to overhaul everything at once. Pick ONE of these:

Option 1: Add Fibre Gradually

Add ONE high-fibre food to each meal:

• Breakfast: Add berries and chia seeds to your yogurt
• Lunch: Add a side of lentil soup
• Dinner: Add roasted Brussels sprouts or broccoli

Option 2: Eat the Rainbow

Track how many different coloured plant foods you eat each day. Aim for 5+ colours daily (red, orange, yellow, green, purple/blue).

Option 3: Add One Fermented Food Daily

Start with something simple:

• Morning: Greek yogurt or kefir
• Lunch: Kimchi on your salad
• Dinner: Sauerkraut as a side

Option 4: Hydration Check

Drink a full glass of water:

• First thing in the morning
• Before each meal
• Mid-morning and mid-afternoon

Start small. Build consistency. Your gut bugs will thank you.

A word about ketogenic and carnivore diets

I tried doing some research about whether keto and carnivore diets were healthy for your gut, but there were so many bits of conflicting information that I gave up on the idea of being able to provide any definitive message.

Carnivore

What a lot of people don’t know about sustaining long term health by eating a carnivore diet is that it’s not just about eating lots of steak. You need to eat the whole animal (nose to tail) which includes organ meats, connective tissue, and bone marrow. This provides a more complete spectrum of nutrients that muscle meat alone often lacks. Incorporating organ meats, marrow, and connective tissue provides essential nutrients (like collagen and glycine) that support the gut lining. Carnivore removes common plant-based triggers (like fibre, lectins, and oxalates) that cause bloating, gas, and irritation. But the long-term impact of a zero-fibre diet on the gut microbiome remains controversial.

Ketogenic

Ketogenic eating offers potential anti-inflammatory benefits and can help manage certain digestive issues improving symptoms of inflammatory bowel disease. But the restriction of fruits, vegetables, and grains can lead to a lack of prebiotic fibre, which is essential for feeding beneficial, gut-friendly bacteria. I personally followed a ketogenic diet without any problems for over 5 years and found it great for energy, mental clarity and weight management. Here is an article you can read if you want to dig deep on keto:

• Attaye I, van Oppenraaij S, Warmbrunn MV, Nieuwdorp M. The Role of the Gut Microbiota on the Beneficial Effects of Ketogenic Diets. Nutrients. 2021 Dec 31;14(1):191. doi: 10.3390/nu14010191. PMID: 35011071; PMCID: PMC8747023

The Bottom Line

I have always said that you need to know what is right for your body. What suits one person will not necessarily suit another. So I never make any blanket statements about nutrition and do not prescribe or promote any kind of diet or way of eating. My only nutrition advice is to eat whole natural foods. My main focus when working with clients is on identity transformation and the mental game.

This is true for everyone:

✅Your gut microbiome is like a garden. You can’t control every weed that pops up, but you CAN decide what you feed and water.

✅Feed it whole natural foods, and it will reward you with better metabolism, lower inflammation, and easier weight management.

✅Neglect it with processed foods and sugar, and it will sabotage your best efforts.

The choice is yours to make.

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References

• Chang L, et al. (2024). Gut micro-organisms associated with health, nutrition and dietary patterns. Nature. https://www.nature.com/articles/s41586-025-09854-7
• So D, et al. (2021). High-Fibre, Whole-Food Dietary Intervention Alters the Human Gut Microbiome. mSystems. https://journals.asm.org/doi/10.1128/msystems.00115-21
• McDonald D, et al. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. PMCID: PMC5954204
• Popkin BM, et al. (2010). Water, Hydration and Health. Nutrition Reviews. https://pmc.ncbi.nlm.nih.gov/articles/PMC2908954/ PMID: 20646222

Check out these other posts in the Metabolic Health Series:
⭐ Blog 1 https://www.coachingwithsuzi.com/scale-weight-metabolic-health/
⭐ Blog 3 https://www.coachingwithsuzi.com/the-protein-power-play-why-your-metabolism-needs-more-than-you-think/

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About Coach Suzi
Weight Loss Coach, Counsellor, Hypnotherapist
Author of The Balanced Mind Diet micro book
Creator of the Weight Freedom Mastery Academy
📧 Questions? Email Me: suzi@coachingwthsuzi.com
📅 Let’s chat: Book a time in my online calendar to discuss your goals (30 minutes)