7 Surprising Signs Your Gut Microbiome Is Out of Balance (And What to Do About It)
What If Your Gut Is Trying to Tell You Something?
As a gut health naturopath, I see it time and time again: clients come to me with frustrating symptoms including fatigue, bloating, brain fog, skin issues and they’ve been told their blood tests are normal. But when we look deeper into their gut microbiome, the picture becomes clear.
Your gut isn't just responsible for digestion. It's your second brain, a key part of your immune system, and a silent driver of your overall health.
So how do you know if your gut needs support? Let’s explore 7 lesser-known signs your microbiome might be out of balance and what you can do to restore harmony from within.
1. You Get Sick More Often Than Others
Your microbiome is your immune system's first line of defence. When it’s disrupted, your body becomes more vulnerable to colds, flus, and lingering infections.
Try this: Incorporate fermented foods like sauerkraut or kefir.
2. Your Mood Feels Unpredictable
Over 90% of serotonin (the feel-good hormone) is produced in the gut. If your gut bacteria are out of balance, it can trigger anxiety, low mood, or emotional ups and downs.
Natural support: Increase your vegetable intake and ensure regular movement to support the gut-brain axis.
3. You Struggle With Skin Breakouts or Eczema
The gut-skin connection is real. Dysbiosis (an imbalance of gut bacteria) can increase inflammation and permeability in the gut lining, allowing toxins to trigger skin flare-ups.
Naturopath tip: Heal the gut lining with bone broth and zinc-rich foods.
4. Your Sleep Is Restless or Interrupted
Your circadian rhythm is influenced by gut microbes. If you're waking between 2-4am or finding it hard to fall into deep sleep, your microbiome may be struggling.
Restore balance: Eat dinner at least 2–3 hours before bed, limit alcohol, and include prebiotic fibres like cooked oats or stewed apples in your diet.
5. You Have Intense Sugar or Carb Cravings
Blood sugar regulation issues can lead to insatiable cravings and can wreak havoc on your gut health.
What helps: Increase bitter greens like rocket, dandelion and radicchio to retrain your taste buds and starve off unhelpful microbes. Ensure you get protein in every meal.
6. You React to “Healthy” Foods
If you’ve suddenly developed food sensitivities or feel bloated after eating nourishing meals, your gut may be inflamed or "leaky."
My approach: Temporarily remove reactive foods and seek naturopathic support.
7. Your Bowel Habits Are Inconsistent
You don’t need to live with bloating, constipation or urgent dashes to the loo. Irregular bowel movements are often the first clue your gut is asking for help.
Start here: Hydrate, chew thoroughly, and include resistant starch (like cold cooked potatoes) to feed beneficial bacteria.
Ready to Heal Your Gut (For Real)?
If these signs resonate with you, you’re not alone. The good news? Your microbiome is incredibly responsive to natural interventions. With the right support, you can begin to feel more energised, clear-headed, and balanced within weeks.
💚 Want expert guidance? Join my free ‘Heal Your Gut Microbiome’ masterclass here a powerful starting point for anyone ready to understand and restore their gut from the inside out.
Final Thoughts
Symptoms are your body’s language, gentle nudges asking for attention. When we listen to the gut, we unlock a deeper level of health and healing.
As a naturopath trained in microbiome science and holistic health, I’m here to guide you back to balance, one step at a time.
