Microbiome Data is FUZZY not fixed

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.
My DNA from Ancestry
My DNA from 23AndMe

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.

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