Requirements for any Microbiome Provider to make their data accessible.

Web Site to assist with becoming a provider

Provider Motivations NOT to support

The following has become apparent from dialogs with some providers:

  • They are not willing to spend money to get a suitable file created
  • They do not have programming staff to code, i.e. they will need to hire a developer.
  • They do not want to have their advice question by allowing second or third opinions of what people should take.
    • Often they perceive this as generating support calls (paying more staff) dealing with customers’ questions
  • Their business model depend on up-selling probiotics (huge profit margins), supplements, or meal plan. Customers getting second or third opinions risk lost of these profits
  • Pure Ego issues.

Directly sending the file

This should only be done by their client (owner of the microbiome sample) from the provider site. This simplifies the transfer (more client friendly) and usually results in good will for the provider (as well as repeat business). Many people have switched to supported providers for subsequent tests because they wish to use the features on the Microbiome Prescription site.

The simplest format is a very very simple upload (post) a text file consisting of nothing more than:

Line 1: Email Address of user
Line 2-N: NCBI Taxon Number, Percentage

That is it!!! We have a test page available for people who wish to try it (data is not saved).

When you wish to enable it so that it is saved, we will provide a key to you so that we know where the data is coming from. THERE IS NO COST. See statistics on uploads here.

This also clarifies to users whether they should or could be seeing a specific species, genus or family on their report.

Lactobacillus reuteri: NCBI 1598

Route 1: Giving the client a file to download and then upload

This may be as simple as a CSV file illustrated below, or rich in other data. Once we have a sample of the file, we will code an import routine (no cost to the provider).

Line 1-N: NCBI Taxon Number, Percentage

356, 0.004
468, 0.002
469, 0.002
506, 0.373
543, 0.338
551, 0.002
561, 0.311
562, 0.025
613, 0.019
712, 0.05
713, 0.002
724, 0.0429
729, 0.0429
766, 0.003
775, 0.003
780, 0.003
815, 35.804
816, 35.804
817, 0.002
818, 4.764
820, 4.165
821, 0.011
823, 3.028
830, 0.002
836, 0.015
838, 0.032
841, 2.608
853, 11.933
872, 0.039
904, 0.025
905, 0.025
906, 0.008
970, 0.045
976, 46.664
1030, 0.018
1046, 0.002
1047, 0.002
1051, 0.002

Why NCBI Numbers?

https://www.ncbi.nlm.nih.gov/

The reasons are simple:

  • various bacteria have dozens of names — on occasion, the name was deprecated and assigned to a different bacteria. It assures us that we have the right bacteria.
  • We use the KEGG: Kyoto Encyclopedia of Genes and Genomes, and their data is all keyed to NCBI Taxon numbers
  • It allows data to be stored in a more compact fashion (up to 60x smaller database) and allows faster processing of data (saving operating costs).

Please note that there are open source tools available to assist with finding the correct NCBI numbers, see  https://youtu.be/VMi0dOeNQFA and https://youtu.be/B0zOSF8f0mo for an illustration.

Alternative: Use the NCBI Names

We have 3,635,527 names from NCBI in our database and can do a lookup of NCBI numbers by name. This is less precise — however, some providers use this route with over 99% of their names matching.

We request all taxonomic ranks to be specified

Our experience is that percentages become distorted (under reported) when we rollup from species to genus to family etc. Typically, there will be some undetermined species in each genus, family, etc. These will often be referred to as “unclassified Lactobacillus” etc.

Example of a walk thru complete test file:

Ken@lassesen.com
356, 0.004
468, 0.002
469, 0.002
506, 0.373
543, 0.338
551, 0.002
561, 0.311
562, 0.025
613, 0.019
712, 0.05
713, 0.002
724, 0.0429
729, 0.0429
766, 0.003
775, 0.003
780, 0.003
815, 35.804

Example of CSV file to be pasted

A download will start

The file will show the NAME for each of the taxon, so you can verify that the numbers are correct.