Step 1 - Begin Here | How to Track Digestion
- therhythmofhealth
- Nov 21, 2025
- 6 min read
You don’t need fancy testing to begin, one of the easiest ways to start the healing journey is to simply track your digestion. So, for the next three days, keep a diary so you can see your baseline. Three days is enough to see patterns, but feel free to track longer if your symptoms are unpredictable. Keep meals simple and consistent during this time. The goal is to see when symptoms happen, not just what they are. That’s it. You’ll start to see timing clusters, maybe your symptoms always come right after meals, maybe always two hours later, maybe always the next morning. Once you know the timing, you’ll know where to look.
Continue the diary as your move through the steps. It will help you map progress, know when to move to the next stage and if you need to circle back at any point. But you don’t need to fill every column every day, consistency matters more than perfection.
Gut Diary | What Your Stool Tells You
One of the best tools for understanding your gut is something no one likes to talk about: your stool. It’s not glamorous, but it’s the most honest feedback your body gives you. Once you know what to look for, you can tell which part of digestion is off, how well bile and acid are working, and whether things are moving too quickly or too slowly. Think of your stool as the report card for your gut.
Gut Diary PDF Download
1. Colour
Colour says a lot about upper digestion and bile flow.
Medium brown | This is your goal. It means bile is flowing normally and your digestion is on track.
Pale, clay-coloured, or greyish | Not enough bile reaching the intestines. Could mean sluggish bile or weak stomach acid.
Yellow or mustard | Bile is moving too fast through the gut and irritating the colon.
Dark brown or almost black | Food moving slowly or too much iron. If jet black, get checked medically.
Green | Food passing too quickly through the intestines; sometimes after diarrhoea or lots of leafy greens.
Colour can vary | Certain foods like beetroot, blueberries, and iron supplements can temporarily change stool colour, this is normal.
2. Form
Form shows how long food stayed in the colon and how hydrated you are.
Smooth, formed, easy to pass | Balanced digestion.
Soft, mushy | Food is moving too fast or bile is irritating the colon.
Watery diarrhoea | Dumping, often bile acids, stress, or too much magnesium.
Hard, cracked, or pellet-like | Slow transit or dehydration, can also mean too little bile or fibre.
Fluffy and floats | Often mean your body didn’t absorb fat fully. This is usually linked to bile or enzyme timing.
3. Smell and Surface
Your stool can also indicate how food is being broken down and absorbed.
Strong, sour, or rancid smell | Fermentation or incomplete digestion in the upper gut.
Greasy or oily surface | Fat malabsorption, usually bile or enzyme related.
Undigested bits of food | Low stomach acid or rushed eating.
4. Timing
Paying attention to timing helps you find the root cause of your symptoms.
Regular morning movement | Healthy motility and rhythm.
Skipping days | Motility slowing, dehydration, or underactive bile flow.
Urgent trips | Colon irritation, overactive gastrocolic reflex, or bile dumping.
Within 30 Minutes of Eating | The Nervous System or Stomach Stage: If you feel full too quickly, get reflux, nausea, tightness under the ribs, or even anxiety soon after eating, that’s usually a signal from the top of the chain. It means your body wasn’t ready to receive food. The brain and stomach didn’t line up. Your nervous system might still be in “alert mode” (sympathetic state), or your stomach acid just didn’t switch on properly.
One to Three Hours After Eating | The Bile and Enzyme Stage: If you start to feel heavy, gurgly, or queasy an hour or two later, or you notice your stool turns softer, lighter, or oilier. that’s the middle of digestion. It often means your bile flow or enzyme release is off. Either the bile came out too late or not enough of it was released. Fats don’t break down properly, and the small intestine struggles to move things along.
Three to Eight Hours After Eating | The Microbiome Stage: If you’re fine at first but get bloated or gassy hours later, that’s a sign food is fermenting. This usually means your microbiome is off. The bacteria in your gut are working on leftovers that didn’t break down properly earlier.
Next Morning | The Colon and Motility Stage: If your stool is urgent, loose, or oddly timed the next morning, that’s a downstream issue. Your colon might be too sensitive or getting hit with bile at the wrong time, or your gut’s motility is out of sync. This stage often reflects issues that began earlier but only show up after the full wave passes through.
Your body is giving you real-time updates every day. When you learn to read them, you can adjust and stay in balance long before things spiral into major symptoms.
What About Lab Testing?
You can do lab testing at some point, but you don’t need it to begin. In fact, most people get far clearer results if they wait a little. Right now, you’re just learning your body’s signals, that matters more than any lab result. Once you’ve calmed the system and restored the top of the chain (nervous system and stomach acid), your digestion becomes more stable, and that’s when testing becomes more accurate and actually worth the money.
If you ever decide to do testing later on with a practitioner due to persistent bloating, nausea and fatigue, these are the ones people usually find most helpful:
Comprehensive Stool Test | Looks at bacteria, H. pylori, yeast, inflammation, and digestion markers.
Organic Acids Test (OAT) | Shows deeper patterns like yeast metabolites, oxalate markers, and energy pathways.
Blood work | Basic vitamins and minerals that reflect digestion (iron, B12, folate, electrolytes, liver markers). If energy stays low and bowels stay slow, checking thyroid can be helpful.
Bile and liver markers | Useful if you’ve had long-term issues with fats, nausea, or pale stools.
But here’s the key part, testing is most accurate and most helpful once your system has settled a bit. If you test too early, you’re basically getting a snapshot of chaos, and that doesn’t tell you much. So a good rule of thumb is to spend 8 to 12 weeks stabilising the foundations first. Calm the system. Track your timing. Support stomach acid. Let things settle. Then, if symptoms aren’t shifting the way you expect, that’s the time to consider testing. Think of testing as something you might add later, once the basics are working and you want a deeper look.
When to Get Help
Even though most gut problems can be improved with rhythm, and time, there are moments when it’s wise to get proper medical testing. Getting help doesn’t mean you’ve failed, it means you’re being thorough. Sometimes, extra information can point to something deeper that needs attention. You should always get checked if you notice:
Ongoing or severe pain
Unexplained weight loss or fatigue that isn’t improving.
Persistent pale stools, dark urine, or yellowing of the skin or eyes (possible liver or bile issue).
Blood or black streaks in stool.
Constant nausea or vomiting.
Night-time pain that wakes you from sleep.
Fever or signs of infection.
Pain or difficulty swallowing.
In the next section, we’ll start at the very top of the chain: Step 2 | Calm the System. Because if the nervous system is off, nothing below it can work properly. Even if you think your issue is further down, always start at the top. Fixing the nervous system often corrects what’s happening later.
→ Step 2 - Month 1 | Calm the System ← Up Next
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