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Your Gut Has a Clock: Why When You Eat May Matter More Than What You Eat

  • July 2, 2025
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You’ve been choosing the right foods. 
Watching your sugar. Buying organic. Upping your greens. 
And yet… you still feel bloated. Sluggish. Tired. Foggy. 
Like something’s just not clicking — even when you’re doing “everything right.” 

 

If that feels familiar, here’s a little-known truth that could change everything: 

Your gut — just like your hormones and your brain — runs on a circadian rhythm. 
In fact, every part of your body is governed by an internal clock. 

 

And when your meal timing is out of sync with that natural rhythm, even the healthiest food choices can leave you feeling heavy, inflamed, or out of balance. 

 

Let’s talk about why when you eat could be just as important — and sometimes even more important — than what you eat. 

Your Gut Has Its Own Clock (And It’s Set by More Than Just Food) 

Your body runs on a 24-hour light-and-dark cycle called the circadian rhythm. 

 
You have a “master clock” in your brain — the suprachiasmatic nucleus — which is regulated by light. But you also have peripheral clocks in your organs: the gut, liver, pancreas, adrenals, and even your ovaries. 

 

These clocks don’t just track the time — they control key body functions: 

 

  • When digestive enzymes are most active 
  • When insulin is most sensitive 
  • When your liver detoxes most efficiently 
  • When your gut bacteria are more or less active 
  • When your cells repair and rest 

 

So when your eating patterns go against these internal rhythms, your body doesn’t work as well. 
You might feel bloated, foggy, inflamed, anxious, hormonally out of whack — even if you’re eating well. 

The “Wrong” Times to Eat (and Why They Matter) 

This is where most women unknowingly disrupt their gut and hormone balance — by eating at the wrong time. 

 Here’s what to watch for: 

  1. Late-Night Eating (After 7:30–8:00pm)

 

Your digestive system slows down at night. After sunset, your body is designed to repair and detox — not digest and process food. 

Eating too late can: 

  • Trigger bloating, reflux, and poor sleep 
  • Disrupt melatonin (your sleep hormone) 
  • Spike insulin at the wrong time (leading to fat storage) 
  • Interfere with liver detoxification 

 

Studies show late eating is linked to insulin resistance, weight gain, and disrupted sleep cycles — even when eating the same food. 

 

  1. Skipping Breakfast or Delaying the First Meal Too Long

 

Some intermittent fasting advice skips breakfast altogether — but in perimenopause, this can backfire. 

Skipping the first meal can: 

  • Raise cortisol (your stress hormone) 
  • Slow thyroid activation 
  • Increase cravings later in the day 
  • Disrupt blood sugar control and energy balance 

 

Your gut microbiome is most active in the morning. Nourishing it early supports mood, metabolism, and digestion all day. 

 

  1. Grazing All Day (Frequent Snacking)

 

Snacking too often keeps your body in a state of constant digestion. 

This can: 

  • Block the migrating motor complex (MMC) from doing its cleaning job between meals (leading to bloating and SIBO) 
  • Keep insulin levels elevated 
  • Disrupt your hunger/fullness signals 
  • Contribute to inflammation and fatigue 

 

Your gut needs 3–4 hour breaks between meals to clean, reset, and reset motility. 

 

  1. Eating During Stress or While Multitasking

 

Your body can’t digest in “survival mode.” When you’re rushing, scrolling, or stressed, digestion literally shuts down. 

This leads to: 

  • Poor enzyme output 
  • Bloating or cramps 
  • Nutrient malabsorption 
  • Increased food sensitivities over time 

 

Eating in a calm state (even just taking a few deep breaths) helps activate your vagus nerve and shifts you into “rest and digest” mode. 

 

  1. Midnight or Post-Bedtime Snacking

 

Snacking after you’ve already gone to bed (or after your body thinks it’s bedtime) is a major circadian disruptor. 

This: 

  • Raises cortisol and insulin 
  • Blocks melatonin 
  • Signals to your body that it’s still “daytime” 
  • Increases fat storage and inflammation 
  • Can interfere with mitochondrial repair 

 

Your gut and liver need that overnight window (at least 12 hours) to clean and reset. 

What to Do Instead: Sync With Your Gut’s Natural Rhythm

  1. Eat With the Sun

 

Start your eating window within 1–2 hours of waking. Have your largest meals earlier in the day when your digestion and metabolism are most active. 

 
Aim to finish eating 2–3 hours before bed to give your gut space to rest. 

 

  1. Create a Gentle Overnight Fast

 

A simple 12–14 hour overnight fast (e.g. dinner at 7pm, breakfast at 7–9am) allows your gut lining, microbiome, and mitochondria to reset. 

 

  1. Eat Mindfully

 

Sit down. Breathe. Chew. Give yourself time to chew and digest. Even if it’s just for 10 – 15 minutes — this simple shift activates the parasympathetic nervous system and improves digestion. 

 

  1. Keep Consistent Meal Timing

 

Eat around the same times each day. This trains your body and gut clocks to expect and prepare for nourishment — improving enzyme output, blood sugar, and hormonal balance. 

 

Over the years, I’ve discovered something powerful — both in myself and in my clients….. 

 

When I eat just because the clock says it’s lunchtime or dinner time, or because I “should,” I often end up feeling bloated, heavy, and flat. 

 

But when I eat in rhythm with my body — when I tune in to real hunger, natural light, and flow with my day — I feel energised, clear, and nourished. 

 

So often, the missing piece in gut healing isn’t just what you’re eating — it’s when you’re eating it. 

 

When you support your body’s internal clocks, your digestion improves. Your hormones stabilise. Your sleep deepens. Your cravings fade. Your mind clears. 

 

You feel like yourself again — because your body is finally in rhythm. 

Want help resetting your gut rhythm? 

I’ve created a Free Gut & Circadian Reset Checklist with simple daily actions to help you sync your digestion, hormones, and energy with your body’s natural timing. 
 
This checklist is here to help you reconnect with your natural rhythm. Because true nourishment isn’t just about what’s on your plate — it’s about when and how your body is ready to receive it.

→ Grab Your Copy Here ←

And if you’d like personalised support, you can book a Naturopathic Consultation with me — where we’ll look under the hood and build a tailored plan to get your spark back. 

 

Teressa
Naturopath + Biochemist

Click here to Book a Consultation

Ready to kick start Gut Health? Book a Call!

Teressa Todd - Australia’s #1 Naturopath, Biochemist and Microbiologist

 

This is how gut microbes can influence weight! 

 

Probiotics can help you gain weight or lose weight by interacting with our genetics, food and metabolism.  

 

And yes, I did say lose or gain weight…….. 

 

Firstly, let me explain that the trillions of microbes in the gut need to be varied, meaning that there should be a large variety of species. There are many different species (or breeds) of microbes, and they all have their place in aiding health — the more variety and balance, the better health results. 

 

Back to the weight loss or weight gain issue…. 

   

Do you eat yogurt and berries for breakfast? Thinking that it’s helping you lose weight?   

 

Well, Lactobacillus acidophilus (like the species found in yoghurt) has been connected to weight gain.  

I am not saying throw your yoghurt and berries in the bin. Instead, I am suggesting looking at the overall picture. If Lactobacillus acidophilus is the predominant micro-organism of the gut, then weight gain can result. 

It is about the variety of species of gut microbes. Imagine if we only have trained german shepherd guard dogs in the world. It may be a safe world, but I am sure that other breeds may be more suitable as a family pet. 

  

While Lactobacillus acidophilus is associated with weight gain, other Lactobacillus species correlate with weight loss.   

Species like Lactobacillus plantarum, Lactobacillus gasseri, and Bifidobacteria animalis have been found to support weight loss.  

 

 

Want to lose weight?

Look at your gut flora to support your goal.  

Tests can be performed to identify the predominant species of the gut, and specific species can be utilised to support weight changes.  

   

Want more information about your gut health?  

Or want to look at all the factors contributing to weight gain, I’d love to be able to help.  

 

Click here to book your appointment!

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Teressa Todd and My Naturopath Gold Coast acknowledges and pays respect to the past, present and future Traditional Custodians and Elders of this nation and the continuation of cultural, spiritual and educational practices of Aboriginal and Torres Strait Islander peoples.

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