A post on Facebook reminded me of an update from a recent data addition. We have added the prevalence of each condition. If you are at 75% ile for a condition that impacts only 5% of the population — there is low risk. But if the conditions impacts 50% of the population, you are at a significant risk.

Actions?

First, you should inform your medical professional that you are concerned about elevated risk for conditions that you do not have and inquire about any testing. Do not be surprised at some “rolling of the eyes” on how this risk was determined. Remember — many of the drugs prescribed for conditions do alter your microbiome in a favorable way (academic question: is this a possible mechanism of action?)

Second, for items of the greatest concern, you may wish filter by the bacteria associated with this condition to get suggestions that may shift your microbiome away from this profile.

Click on that link and then

You may wish to play around with different filtering criteria

One reader keep coming back to me wanting definitive comprehensive answers. There is no such thing.

Let us walk thru all of the layers of randomness..

• Your stool sample will vary according to time of day. The bacteria will change according to the last meal and the time since the last meal.
• Where you sample your stool (outside, inside, front, back) will have different bacteria
• The amount/quality of your sample will vary. uBiome did an informative: Count and then Count_norm
  • Count_norm is the count scaled to out of one million
  • Count is actual detected count… I have see that vary between 80,000 and 800,000
• There is differences between the machines used (different primers etc) by the lab
• The raw data file, FASTQ, (like a personal DNA sample) is interpreted by software.
  • If you have done your personal DNA, various sites will interpret what your ethnic inheritance is. The same applies to the software used to read the FASTQ file. See example below
  • Ombre and BiomeSight uses the same lab service but different software (in fact, Biomesight gives an option of a third software for interpretation.
• Labs software disagrees about amount of each type of bacteria and even which ones are reported!
• When we apply KEGG data, we have two randomness:
  • Does KEGG have data on the bacteria reported…. for some yes, at the strain level. We estimate genus level from strains… these are rough estimates and not necessarily accurate
  • Does the Lab report on those bacteria. In some cases yes, in other cases no.
• Percentiles are based on the uploads. There is no question that there will be some bias in the samples, thus percentiles are reasonable but not accurate. When the number of samples with a specific bacteria is less than 200, then the percentiles reported may be easily off by 5-10%ile. This is due to the small sample size.

Bottom Line

I understand that people want definitive, cast in bronze, answers. What is available is a fuzzy answer. IMHO, a fuzzy answer is far better than no answer or an answer by random reading of a posting on the web.

I describe the suggestions coming off Microbiome Prescription as being more lively to make the desired changes than trying random items or items suggested by web-self-reporting experience. It is like the stock market, AI can suggest stocks that are more likely to go up than down in purchase value. Buying gold or putting money under your mattress is also subject to changes in purchase value. Life is a random number generator, when you understand that, you can make better choices once you have done your homework.

Often I am faced with requests to keep things simpler of the Microbiome Prescription site while getting requests to give more choices (often arising from people’s belief of what may work). I have just finished a revision attempting to balance these two (and set up infrastructure to give more choices in the future)

The Expert Criteria takes you to a new page that has many criteria listed:

There will be differences from each choice, because the bacteria selected will likely be different. For one sample:

•  Use JasonH (15 Criteria) – 7 bacteria
•  Use Medivere (54 Criteria) – 7 bacteria
•  Use Metagenomics (59 Criteria) – 7 Bacteria
•  Use Nirvana/CosmosId (36 Criteria) – 7 Bacteria
•  Use XenoGene (22 Criteria) – 7 Bacteria
•  Standard Lab Ranges (+/- 2 Std Dev) – 9 Bacteria
•  Box Plot Whisker – 59 Bacteria
•  Kaltoft-Moltrup Normal Ranges – 64 Bacteria
•  Percentile in top or bottom %
  • 10% — 127 Bacteria
  • 5% — 55 Bacteria
  • 1% — 6 Bacteria

Why the differences? With only a few dozen bacteria with ranges, the chance of being picked is low. Box Plot and KM are computed for almost every bacteria. So with 700 bacteria, we have around 10% picked. With just 50 bacteria to be examined, we have around 14% picked.

These choices are also available in Advance Suggestions

On facebook, I was asked:

Can you guys tell us beginners what do you guys do for gut health

If in unhealth…

My approach is simple, get a 16s (Biomesight or Ombre) microbiome test. Transfer or upload the data to https://microbiomeprescription.com/, get suggestions and do them for 4-8 weeks. Retest and repeat.

Here is an example of my applying this method (with 8 blog posts)

• Report #1
• Report #2
• Report #3
• Report #4
• Report #5
• Report #6
• Report #7
• Report #8

A key item is to rotate, rotate, rotate. Take the list of take suggestions and break into 4 groups. Do each for 2 weeks and then change to the next group. Attempt to remove ALL of the avoids (at least those with a value of 0.4 and higher). Simple enough? (Apart from the methodology to select the bacteria to alter — a new video on methodology is in progress)

If in health

Every 6-9 months, My approach is simple, get a 16s (Biomesight or Ombre) microbiome test. Transfer or upload the data to https://microbiomeprescription.com/, get suggestions. Look at rotating in (2 weeks on, 4 weeks off) any items over 0.8 on the take. Try to reduce any items on the avoid over 0.4.

If I am prescribe an ongoing medicine, then I will take a sample after 4 weeks and make modifications to counter any adverse effects. If the medication is in the existing database, I would check if there is an excessive shift (in terms of percentile) of the bacteria that it is known to shift.

For items like vaccinations and short term antibiotics, I will wait at least 8 weeks, preferred 12 weeks, to allow my immune system to settle down.

Bottom Line

That’s it. I do not do items exclusively from suggestions. I may take other items for diverse reasons — if they are not high in the avoid list, I just keep taking them.

Q&A

Q: Do you drink Kefir in general for gut health?

A: No, unpredictability of which bacteria are in it. I tend to keep to researched strains only. For yogurt: Activa is an example, or Yakurt probiotic drink. Custom Probiotics is a regular source.