Exploring Probiotic Species for SIBO and Heart Health
Over the past few months, I’ve been diving deep into the science of probiotics and their potential to support gut health, particularly for conditions like SIBO (Small Intestinal Bacterial Overgrowth) and cardiovascular disease. My focus has been on specific bacterial strains that have shown promising effects on both gut microbiota balance and metabolic health.
Dr. William Davis’ Perspective
Dr. William Davis, author of Wheat Belly and Undoctored, has long advocated for using specific probiotic species to restore gut health. In his research and clinical experience, he emphasizes the role of Lactobacillus reuteri in particular, which he incorporates into homemade yogurts. Davis believes that high-count, strain-specific probiotics can help modulate inflammation, improve immune function, and even support cardiovascular health. His approach focuses less on “perfectly set yogurt” and more on ensuring sufficient bacterial counts for therapeutic benefit—a concept that aligns with modern microbiome research.
In Wheat Belly, Davis highlights the negative effects of processed grains and sugar on gut microbiota and heart health, while Undoctored expands on personalized strategies for reversing chronic disease, including gut-targeted therapies like probiotic supplementation. His yogurt recipes are designed to deliver high concentrations of beneficial strains such as L. reuteri for daily therapeutic use.
My Research & Experimentation
Inspired by Dr. Davis, I began experimenting with L. reuteri, L. gasseri, and even Bacillus subtilis in various dairy media. My goal was to create a reliable method to cultivate these probiotics at home while maximizing their survival and potency. Throughout the process, I experimented with different milk types, cream ratios, and prebiotics like inulin, while closely monitoring pH and fermentation times. One clear takeaway was that traditional visual cues for yogurt texture were less important than ensuring adequate bacterial growth for therapeutic purposes.
Introducing the Fermented Dairy Composition & CFU Estimator
To help others replicate and optimize these probiotic-rich yogurts at home, I developed a Fermented Dairy Composition & CFU Estimator. This tool allows you to enter different amounts of whole milk, evaporated milk, cream, and milk powder, then calculates the fat, protein, and sugar content of your mixture. It also gives visual feedback if your composition falls within the optimal range for probiotic growth and palatability.
The calculator makes it easy to experiment safely with your yogurt base while ensuring that your final mix supports the growth of the strains you’re targeting. This tool is particularly useful for anyone following Dr. Davis’ protocols and aiming to produce therapeutic yogurts at home.
Fermented Dairy Composition & CFU Estimator
Version 1.6
How to Use the Fermented Dairy Composition & CFU Estimator
This calculator helps you design a fermented dairy batch with the right fat, protein, and sugar levels to support probiotic bacteria growth — and then estimates how many colony-forming units (CFU) you’ll end up with after fermentation.
It was built with Australian home fermenters in mind. Unlike the US, Australia doesn’t have “half and half” — that familiar American product that sits halfway between milk and cream. Many probiotic yogurt recipes (particularly those following the L. Reuteri protocol popularised by Dr. William Davis) call for half and half as the base. Since we can’t buy it off the shelf here, the calculator lets you combine whole milk, cream, evaporated milk, and other ingredients to hit the same macro targets yourself.
The Two Sections
🧪 Growth Medium Composition
This is where you enter your ingredients. Each ingredient can be toggled on or off with its checkbox. When checked, you can enter the volume (in mL or grams for powder) and adjust the fat, protein, and sugar values to match the specific product you’re using — since these vary between brands.
Available ingredients:
- Whole Milk
- Evaporated Milk
- Pouring Cream
- Whole Milk Powder
- Water
- Prebiotic Fibre (Inulin or Potato Starch)
🧫 Fermentation Parameters
This is where you configure your bacteria strain, starting CFU, incubation time, and temperature. The calculator uses a logistic growth model — meaning growth accelerates early then slows as it approaches the carrying capacity of the medium, which is more realistic than simple exponential growth.
Target Ranges
After hitting Calculate, the composition results are colour coded:
- 🟢 Green — within the optimal range
- 🟡 Yellow — below optimal
- 🟠 Orange — above optimal
The targets used are:
| Macro | Optimal Range |
|---|---|
| Fat | 9–12% |
| Protein | 3.5–5% |
| Sugar | 4–6% |
These ranges are aimed at providing a rich substrate for probiotic bacteria while keeping sugar low enough to avoid feeding unwanted organisms.
Worked Examples
Example 1 — The Classic L. Reuteri Yogurt (Australian Style)
L. Reuteri is the most popular strain for home fermented yogurt, largely due to the work of Dr. William Davis whose protocol calls for a long 36-hour fermentation at body temperature to achieve very high CFU counts. His recipes typically use half and half as the base — which simply isn’t available in Australia.
The good news is that combining whole milk and pouring cream gets you right into the same fat range. Here’s a straightforward 1 litre batch:
| Ingredient | Amount |
|---|---|
| Whole Milk | 700 mL |
| Pouring Cream (35% fat) | 300 mL |
Fermentation settings:
- Strain: L. Reuteri
- Starting CFU: 10 billion
- Time: 36 hours
- Temperature: 37°C (use the Use Optimal button)
Result: ~11.5% fat, ~3.4% protein, ~3.9% sugar — sitting right in the optimal zone. L. Reuteri thrives in high-fat dairy and the 36-hour fermentation gives it plenty of time to reach a very high final CFU count.
Example 2 — L. Reuteri Large Batch with Evaporated Milk
For a thicker, more set yogurt with better body, adding evaporated milk boosts the protein without dramatically changing the fat profile. This is a great approach if you find the basic milk and cream version too thin.
| Ingredient | Amount |
|---|---|
| Whole Milk | 2000 mL |
| Evaporated Milk | 384 mL |
| Pouring Cream | 600 mL |
Fermentation settings:
- Strain: L. Reuteri
- Starting CFU: 10 billion
- Time: 36 hours
- Temperature: 37°C
Result: Fat lands around 10.8%, protein around 4.1%, sugar around 4.8% — all green. The higher protein content from the evaporated milk gives the yogurt a noticeably better texture while keeping everything in the optimal fermentation range. This is roughly the default batch the calculator opens with.
Example 3 — L. Casei Shirota Using Yakult® as Your Starter
L. Casei Shirota is the probiotic strain found in Yakult®, the small red-topped bottles available at Woolworths and Coles. Rather than sourcing a commercial starter powder, you can use a bottle of Yakult directly as your inoculant — it contains billions of live L. Casei Shirota cells and works very well as a starter culture, making it one of the most accessible and affordable ways to get started.
One 65 mL bottle of Yakult contains approximately 6.5 billion CFU, so use that as your starting CFU value in the calculator.
| Ingredient | Amount |
|---|---|
| Whole Milk | 1500 mL |
| Evaporated Milk | 375 mL |
| Pouring Cream | 300 mL |
Fermentation settings:
- Strain: L. Casei Shirota
- Starting CFU: 6.5 billion (one bottle of Yakult)
- Time: 36 hours
- Temperature: 37°C (use the Use Optimal button)
Result: L. Casei Shirota is a good sugar utiliser and handles dairy very well. After 36 hours you’ll end up with a mild, slightly tangy yogurt with a very high CFU count — at a fraction of the cost of commercial probiotic supplements.
Note that Yakult itself is quite high in sugar (about 11g per bottle), but this is actually a non-issue for two reasons. First, you’re diluting it across roughly 2 litres of dairy so the contribution to the starting sugar percentage is minimal. More importantly, L. Casei Shirota is a strong sugar fermenter — it will actively consume the sugars in the medium (including whatever came from the Yakult bottle) and convert them into lactic acid over the course of fermentation. By the time your 36 hours are up, the finished yogurt will have a significantly lower sugar content than the raw starting mix. The calculator shows the composition of the medium going in, not what comes out the other end.
Example 4 — B. Longum with Inulin for Prebiotic Support
B. Longum is a slower-growing strain but it is exceptionally good at fermenting prebiotic fibres — particularly inulin. Adding inulin to a B. Longum batch provides a significant substrate boost and supports the broader gut microbiome through short-chain fatty acid production during fermentation.
| Ingredient | Amount |
|---|---|
| Whole Milk | 2000 mL |
| Evaporated Milk | 384 mL |
| Pouring Cream | 600 mL |
| Inulin | 30 g |
Fermentation settings:
- Strain: B. Longum
- Starting CFU: 10 billion
- Time: 36 hours
- Temperature: 37°C (use the Use Optimal button)
Result: The inulin provides a 1.30× substrate boost for B. Longum — the largest fibre boost of any strain in the calculator. Despite being a slower divider, the extended fermentation time and the prebiotic advantage mean B. Longum still produces a high-CFU end product. Try comparing the result with and without inulin by toggling the amount between 0 and 30g to see the difference.
Tips
Use the “Use Optimal” button. Each bacteria strain has a different ideal temperature — L. Bulgaricus and S. Thermophilus prefer 42°C, while most Lactobacillus strains prefer 37°C. Clicking Use Optimal fills in the right temperature automatically. You can still override it manually if your incubator runs slightly warm or cool.
The recommended temperature is shown next to the label. Even before clicking the button, you’ll see the strain’s optimal temp displayed in green next to the Temperature field — handy as a quick reference.
Adjust the macro values to match your actual product. The default values are reasonable averages, but full-cream milk from Pauls vs. a home-brand can differ noticeably in fat content. Check the nutrition panel on your carton and update the fields accordingly for a more accurate result.
Prebiotic fibre only boosts CFU if you enter an amount. Selecting Inulin or Potato Starch from the dropdown reveals an amount field. If you leave it at zero, no boost is applied. Different strains respond differently — B. Longum gets the biggest lift from inulin (1.30×), while L. Gasseri also responds well (1.20×).
The CFU estimate is a model, not a lab result. It uses established growth parameters and a logistic growth curve, but real-world results will vary based on starter culture viability, actual incubator temperature consistency, and individual batch conditions. Use the numbers as a guide for comparing recipes and strains rather than as absolute values.
Understanding the CFU Results
After calculating, the fermentation results show:
- Starting CFU — your inoculation amount
- After X hrs — estimated total CFU at the end of incubation
- Final CFU / mL — how concentrated the culture is
- Doublings achieved — how many times the population doubled
- CFU per 125 mL serving — a practical per-serve estimate
- Temperature efficiency — how close your set temperature is to the strain’s optimal, expressed as a percentage
If your temperature is outside the viable range for the selected strain, the calculator will warn you and return zero growth.