Evaluation of Microbiome 16s and shotgun providers

This post describes the scoring system that I will use in evaluating providers. It includes suggestions from other people active in this area. Not every item is important to every one. This represents what would should make everyone happy.

  • Accessibility to your own data
    • A: FastQ and Csv/Json (with Taxon No) available on the site
    • B: Csv (with Taxon No) available on the site
    • C: All taxa and amounts are available as PDF or web page
      • + if with Taxon No
    • D: Partial data only available
  • Significance of Deviations
    • A: A full distribution for each taxa in the reference set is provided
    • B: A range of normal values for each taxa is provided
    • C: The average and standard deviation for each taxa is provided
    • D: Only an average is provided
  • Reference Groups
    • Add 1 for each of the following available
      • By Gender
      • By Age (10 years bucket or less, under 10, 2 years buckets or less)
      • Diet Style
      • Geographical location
      • ICD Codes
      • 5=A+, 4=A, 3=B, 2=C, 1=C-, 0=D
  • Recommendations of Actions to correct
    • A: Over 1000 actions available
    • B: Over 350 Actions Available
    • C++: Over 180 Actions Available
    • C: Over 100 Actions Available
    • D: Below 100 Actions
    • a + or even a level higher if there is evidence of significant professional researchers involved (not rubber stampers)
  • Supporting Evidence
    • A: All information is footnoted with citations. + if linked to PubMed or actual study, at least 100 citations
    • B: Key information is footnoted with citations. , at least 40 citations
    • C: 90% correct but general information without supporting evidence sources, at least 20 citations
    • D: Below 75% correct or below 10 citations
  • Benevolence (No Conflict of Interest)
    • A: Works with University or Significant Research Group (Ideally making tests available for free)
    • B: No side business (“Just the microbiota, Ma’am, Just the microbiota”)
    • C: Sells diet plans etc with an average monthly cost of $10 or less
    • D: Sell proprietary products (i.e. their custom probiotics)
  • Customer Support (subjective)
    • A: Prompt correct answers within one business day, Order are done right the first time
  • Promptness of Data (in US, most are sent with tracking numbers)
    • A: 7 days from receipt of sample until report
    • B: 14 days from receipt of sample until report
    • C: 21 days from receipt of sample until report
    • D: 28+ days from receipt of sample until report
  • Additional Metadata Provided
    • A: Estimates of Metabolites produced (i.e. using KEGG )
    • B: Estimates of butyrate and similar compounds produced
    • C: Identification of pathogenic taxa (at strain level)
    • D: No additional information
  • Ability to see changes over time
    • A: Support for Charts, Tables and CSV Downloads
    • B: One of the above is missing
    • C: Two of the above is missing
    • D: None of the above is supported.
  • Taxa Coverage – uBiome Taxa report is used as a reference
    • % Score – the number of taxa that matches those reported by uBiome
      • Thryve Inside: 1798 -> 40%
      • American Gut: 134 -> 4%
      • XenoGene: 70%
      • SequentiaBiotech (on FastQ files): 2477 -> 82%
      • BiomeSight (on FastQ files): 2436 -> 81%
    • Taxa Scope %– the number of taxa reported compared to the number reported from uBiome (3013). At this point of time we have:
      • Thryve Inside: 3339 -> 111%
      • American Gut: 146 -> 5%
      • XenoGene: 4739 -> 157%
      • SequentiaBiotech (on FastQ files): 930-> 31%
      • BiomeSight (on FastQ files): 8066 -> 267% (based on access to their DB)

Accessibility to your own data

This means that you can get second, third and fourth opinions on what you should do to address any issues that you have. This may mean using resources such as Jason Harwelak, BiomeSight or MicrobiomePrescription. In some cases, your own physician may wish to use this data.

Significance of Deviations

The classic question is “Is this value significant?” If it is a value seen in the middle 80% of people, it is likely just a natural, not condition related, variation. Having your value and the average cannot answer that. In general you need a range. This is often a judgement call. MicrobiomePrescription use the actual percentile, thus if you are not in the top or bottom 6%, you are assumed to be normal (with the ability to extend to 12% if desired)/