Comparing Taxons on same FastQ file

David Morrison requested this feature. The FastQ file is produced by the physical lab machine. This file is then pushed thru software to produce a list of taxonomies. Different 16s retail providers use different software and as a result – different reports. For back ground see this “Taxonomy Nightmare before Christmas” post.


This feature is available only for those that sign on securely (i.e. request a login link to be sent by email).

On the samples page you will see some new buttons

Items are disabled if you use legacy login
Buttons enabled with secure login

Define FastQ files

Simply Click [FastQ Catalog] and create records for each FastQ file you are going to work with.

Identifying sample with FastQ file

Return to the Samples page, and click [Update of Delete Samples]

You may now assign the FastQ file to the sample intrepretation


You need at least 2 sample to be linked to a FastQ file. Returning to the Samples page, click the [FastQ Set Comparison] button

Select the FastQ file that you are interested in, click Compare button.

You will now see the results reported. Some taxonomy will be very similar and others very different.

What’s next?

Once sufficient users link their files, we can start doing the various analysis that David was asking for.

Post-Covid19 Syndrome

Most of the Post-Covid19 Syndrome symptoms has a strong match to the symptoms seen with Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). This condition has no conventional medical treatment known. Treatments attempt to mitigate symptoms.

There is evidence that some people develop a long-term fatigue syndrome from coronavirus infections, Dr. Anthony Fauci said Thursday.

“There may well be a post-viral syndrome associated with Covid-19,” Fauci told a news conference organized by the International AIDS Society. The group is holding a Covid-19 conference as an add-on to its every-other-year AIDS meeting.

Fauci said the symptoms resemble those seen in patients with myalgic encephalomyelitis, or ME, once known as chronic fatigue syndrome.

“If you look anecdotally, there is no question that there are a considerable number of individuals who have a post-viral syndrome that in many respects incapacitates them for weeks and weeks following so-called recovery,” Fauci said.CNN

I am very familiar with ME/CFS as anyone who knows my story can attest. And I believe that while the model of why these symptoms are there is simple, the treatment is complex, not cookbook and must be individualized for each person.

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Persistent Symptoms in Patients After Acute COVID-19

The Model

COVID19 sends out chemical signals to the body to produce chemicals (metabolites) that its need OR which create a friendlier environment for it. The signals alters the microbiome (gut bacteria) to be a factory for its needs (Viralforming the gut). Once COVID is eliminated, the alterations should return to the prior state overtime— unfortunately a percentage that take a long time or never return. The best documented example is the Bergen’s Giardia Infection.

“Gastrointestinal symptoms are common in patients with COVID-19, and had an increased prevalence in the later stage of the recent epidemic in China. SARS-CoV-2 enters gastrointestinal epithelial cells, and the faeces of COVID-19 patients are potentially infectious.”Review article: gastrointestinal features in COVID-19 and the possibility of faecal transmission

The microbiome consists of many co-operations between bacteria. Often there are over 2000 bacteria involved in various dialogs. Identifying the bacteria that are at abnormal (too high or low) is the start. The next step is modifying the bacteria by drugs, diet, supplements. At this point, we need to point out that there may be 100 or more abnormal bacteria that needs to be adjusted. Naive adjustments may make more bacteria abnormal.

My Proposed Process

This is the process that I have done with ME/CFS and it is likely that it may also work for many people with post-covid syndrome:

  • Obtain a 16s analysis from an appropriate source
  • Look at the suggestions for correcting and make appropriate changes
  • Two+ weeks after making changes, repeat the 16s analysis and make the next set of changes.

This is an iterative process. Often the suggestions will cause one symptom to lessen or disappear while leaving others untouched. This is to be expected.

For more information, see

BiomeSight (UK) is now integrated with Microbiome Prescription

Rose Walbrugh and I are proud to announce one click sending of data from based in the UK to After you get your BiomeSight data processed, you can send the data across without needing to download and upload. You will be sent an email with an automatic login link (no more making up and remembering passwords!).

How to Do It and get Expert System Suggestion

Log in to Biomesight then on left Menu:

  • Click Third Part App
  • Click Microbiome Prescription

Find the sample that you wish to send:

If you need to RESEND sample, see the bottom — there is an alternative way. A rotating circle will appear

When Complete, you will see this shown

Check your email. You should get one like below (it is sent to the email used by biomesight)

Click Link. You should see a page like below

Click on my Profile and then click “Just give me suggestion”

After a few minutes of calculation (over 2 million pieces of information is evaluated), a page like this will appear with usually 1-2000 items listed. Click on what type of item interests you most, for example [Probiotics] and they will be shown…. By default, best items are at the top and worse at the bottom but by clicking table titles you can change the sort order.

If you click the “books” on the right, you will see the precise logic used with links to clinical studies.

Other Options

The transfer is available as an external application on a mobile device, as shown above
Or with more details in a web browser.

Once the [Send] button is clicked, you will get an email like shown below that allows you to login and explore your data deeper.

Clicking the link will log you in automatically, and you will see your sample and it’s identified as originating with BiomeSight.

BiomeSight specific distributions of bacteria will automatically become available once there is a large enough sample.


As part of this celebration, a discount code “MICRO” is offered on BiomeSight services. This results in £60 off, which brings the price down to £89 per kit ($110). Local USA fulfillment is now setup. Expedited 2 day delivery at £4.95.

Resend Sample

From Biomesight Support:

To be clear, there’s 2 ways to send it – on the row itself, the button will not be available it was sent already. But you can also do it by selecting the rows and using an alternative button that will send it again regardless. The screenshot below shows both.

New Feature

After transferring the data you will get two emails. One to log into the site. The second is a PDF analysis with suggestions and literature supporting the suggestions.

Bottom Line

Microbiome Prescription is dedicated to working with labs to enrich user experience and knowledge. BiomeSight has stepped up to the plate for cooperation and win-win attitude.