Quick Images of a Reader’s Progress

This is largely a visual post — showing the results of a reader who has taken frequent ubiome sample, uploaded them and then started following the suggestions generally. It appears to confirm that the microbiome may be manipulated. Dates of samples

  • 3/11/2018 – first set of suggestions tried
  • 8/25/2018 –
  • 3/26/2019 – symptoms got bad enough that ‘coasting’ was no longer acceptable. Regular testing started.
  • 5/7/2019
  • 6/12/2019
The big picture
Anti-Inflammatory: Polyamine
Anti-inflammatory: Propionate
Anti-inflammatory: Butyrate
Akkermansia went very high, change brought it back down.
The metabolism is becoming more balance
Major improvement in often co-morbid conditions — BUT depression has gone up

Bottom Line

Correcting the microbiome is not a one step-dance or a direct root. This person had things drop to avoid and then re-appear as take on a later sample. The WHY charts are a nice visual representation of the known dependencies. For example, we need to reduce most of the bacteria slowing Bifidobacterium (as shown below)

A walkthru with all of the new features

A reader asked me to look at their ubiome results. They were having trouble interpreting the data (Brain Fog: 1, Site: 0)

Preferred Approach

This reader has enter their symptoms AND we have some matches in terms of patterns associated with symptoms and their microbiome.

This always gives the most targeted list

So on the Custom Suggestion page, we select this and exclude things that we are not interested in:

When we get the suggestions, we see that no Flavonoids are listed.

Probiotics and Flavonoid foods

We also have a list of supplements etc showing up

There is a long list of Postive Impact Probiotics. We want to always go for the highest impact ones that are available to you. The best is available in Germany: Probiotic PUR (DE) / RealDose Nutrition : impact 5.4

At the bottom we have Flavonoid Foods

I checked Almonds, Walnuts and Oregano to see if they had any flavonoids in common and high. No luck.

Approach 2 – Outliers

This looks at outliers compared to other samples uploaded. In this case we see one family that is massively high — Eubacteriaceae. Being focused on this alone is in Approach 3 below (targeted).

We change to this method of selecting the bacteria to be concerned about.

In this case, we get all three links at the top

The list is very different — likely because Eubacteriaceae was NOT selected above.

Our probiotic list is much smaller.

For Flavonoid foods we see cumin and rice

The interesting list is the Flavonoids list

Catechol and Curcumin dominates.

Curcumin is found only in turmeric(22.14) and curry (2.85). Catechol only in coffee… However, checking the Flavoid page, we see there are three other forms of Catechol.

4-Methylcatechol
4-Ethylcatechol

3-Methylcatechol

At this point, we enter fuzzy territory. Did the study include all of these different forms under Catechol or not? Peeking into the database, it appears that all four variations are the same or similar. They are associated with the following foods:

Approach 3 – Targeted

We see above that Eubacteriaceae was very very high. We could just go to it’s page and look at what modifies it. This often results in saturation.

An easier path is to go to the [Other Lab Analysis] and select: All Bacteria [Family] Reported. On that page, select only this one (add more if you wish)

This gives a filtered list (Sorry, I have not updated this page to the above style yet).

The risk with this approach is that you may be missing the bacteria that supports this very high bacteria. Unfortunately, we do not know what feeds this bacteria (clicking on WHY on the sample page). What we do see are odd unexpected relationships which hints at a specific strain being the issue.

Looking at the drop down, we see a lot of species that are overgrown in this family.

We counld return to the Other Lab analysis page and pick: All Bacteria [Genus] Reported This may produce a different report because some studies reported on the family impact and other on the genus impact.

We get a similar list to the above, with a few variations.

Bottom Line

I know people want things to be ultra simple — having multiple ways of looking at stuff can be a challenge. Looking at commonality in the above reports, I would suggest discussing the following with your medical professional.

  • Vitamins B9,B12,B1,B7, B6
  • Probiotics: Bifidobacterium Bifidum and possibly include other Bifidobacterium (avoid all Lactobacillus)
  • Berberine
  • Melatonin
  • Rice with turmeric

Sniffing out more helpful items using flavonoids…

A few readers have severe diet restrictions (mast cells, etc), which contributed to my adding flavonoids and polyphenols data. Once added, I have been connecting them up (a slow manual process).

New Sections on Suggestions Page

At the top, there may be up to 3 onpage jumps such as shown below.

We have already cover probiotics in a prior post, so let us look at the two new one:

Flavonoid Foods

This is a match up with all of the positive modifiers (2x more good risk than harm risk) that are also in our flavonoid database.

Note that all of them are hyperlinked. Clicking on one, for example bananas — takes us to the details for banana.

We see that ONE of the items is very high. This may be what is causing the benefits from banana. Click it to see other foods with this flavonoid.

This list is full of familiar suggestions and a few new ones!

So, if you can’t eat bananas — this is a list of possible alternatives that may help. Some, like Carob, we have no studies on… but this suggests it may be logical to try it.

Flavonoids Suggested

These have been studied and are on your list above. A common problem is getting them. You can buy them as supplements (with huge markups) or you can get them from fresh food — but which foods?

Just click on one of them, say Quercetin,

Items like Capers have not been studied for it’s impact on the microbiome. Again, it is a logical suggestion.

Bottom Line

The early users of these new features have been delighted. It has open up new choices that are logical and reasonable. Whether they work — that is to be determined.

Sun Genomics – Preliminary Thoughts

I have been getting several messages a day from readers about this firm that has started to aggressively advertise on facebook etc. I have had messages, emails and telephone conversations with Sunny Jain , M.S. (Molecular Medicine and Cell Biology) – the founder and CEO. His Linked In profile. and crunchbase profile Like me and my multiple sites, his business grew out of personal family issues with the microbiome.

Fortunately, there has been no NDA requested or “off the record” requests. I am a blogger, which means that I am also a Journalist (see this court ruling), thus whatever was share is technically free game.

Waiting for … from Sunny

The following is an existing request to him:

  • An example of some of their 16s samples with the probiotic mixture generated for each. Sample to be in ‘ubiome json’ format
    • Why? We are using different methods and our recommendations may be radically different.
    • This may open up a can of worms — I can provide citations for all of my recommendations to show my logic. SunGenomics may be working off a lot less citations.

Requests to Sunny

  • Can you custom mix probiotics from a formula created and sent from my site? This would solve a lot of challenges people have.
    • No, the issue of liability if they do not come up with the formula based on their analysis. This explanation makes no sense.
  • Can you provide single strain probiotics, especially for strains where there are no single source providers on the market?
    • He is looking at it. Probiotics are very high markup.

Another struggling Ubiome?

The financial basis of the company is Venture Capital (the same type of situation that drove Ubiome into ‘pushing things‘ to satisfy the venture capitalists.

https://www.crunchbase.com/organization/sun-genomics

For myself and my sites — it is totally self funding (i.e. my own wallet and paycheck from the day job); old school ‘garage startup‘. Garage startup worked for Amazon, Apple, Google, etc. (Reference).

SunGenomics was founded in 2016, Sunny and his wife are scientists (I do not believe either are physicians) working full time for the firm. There are 11 people showing on the team page. Three million divided by 11 over 3 years, means $90,000/employee. Translation: they may be running financially lean/under-funded/over-grown. A scenario similar to Ubiome. Sunny indicated that the team is stretched/stressed (a.k.a. under-staffed)

Speculation On Internal Process

Their technology appears overhyped and may be using alternative wordings to obfuscate what they do. This can be a good marketing ploy — their direct competitors use different terms — hence they are doing something different!

from https://sungenomics.com/

Some key points, they use a patented technology. There is no claim of having the patent on it. This will be missed by most people who will conclude that it is THEIR patented technology – it’s wordsmithing! They also emphasis “DNA” excessively, I believe it is actually rDNA (i.e. 16s)

Correction: Sunny emailed, they are not using 16s (72K) but Whole Genome Microbial Sequencing (2421). The numbers are the number of articles using each term on PubMed. 16s is more common and have had many more studies.

16s vs Whole Genome Sequencing

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

In terms of results, there can be differences. They agree on the ones that they have in common, but WGS reports about 50% more:

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

”  In summary, our study demonstrates that WGS has multiple advantages compared with the 16S rRNA amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. “

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

At 1888 species vs 3239 species, the differences appear to be major — the reality is that apart from names — we know almost nothing about how to increase or decrease these additional bacteria. For our purposes at hand, it gives academic knowledge but not practical clinical knowledge, IMHO.

Given the expressed concerned over liabilities; I believe they are ultra-conservative (a.k.a. Standard of Care) in their suggestions. I would not be surprised if their selection of probiotic strains and application to each consumer is just a rehash of information from either of these two excellent guides prepared by Dragana Skokovic-Sunjic .

These guides ranks what we know about each probiotic in a solid objective manner. I strongly recommend them.

Bottom Line

I have reservations about using this firm. If someone out there wishes to give them a trial ($800 to do below!l, I would love to get the following for a followup post:

  • Ubiome done from the same sample that is shipped to them.
  • List of probiotic strains in the probiotic delivered to them
  • Their report on your sample
  • Ubiome done on a followup same sample that is shipped to them.
  • Their report on your followup sample

I see too much risk of ‘resampling until you get positive results’ to report to the customer to show that an impact was made (a.k.a. Repeat business – which is what Venture Capitalist are looking for!). This risk is expected whenever a venture capitalist is backing a company.

I would love to give a thumbs up to this firm — conceptually it is on target. However I am an evidence based person and well aware of the reality of venture capitalist backed firm from years in Information Technology. Until there is evidence — I must give a thumbs down because of the costs involved and the risk of not targeting the entire microbiome due to following a conservative approach.

Flavonoids Library Is Up

I still have some more features to add and references to add. All of the information is coming from 2018 report by United States Department of Agriculture – Agricultural Research Service.

http://microbiomeprescription.azurewebsites.net/Library/Flavonoids

This takes you to the main listing — there are some names that you may not recognize,

Clicking on any will list the foods containing them and amount.

http://microbiomeprescription.azurewebsites.net/library/flavonoidDetails?fid=789

A few will have a link to bacteria impacted by it.

Stage #1 Complete

Stage #2 will be similar to what I did for probiotic mixtures — if there are multiple flavonoids in the suggestions, then the foods containing them will be examined and a relative weighing of the foods will be done (Take, Mix, Avoid).