Back Story

I heard from a group of long covid patients that you’re offering specific recommendations after they provide you results from a microbiome sample analysis. Would you happen to still be offering those?

My partner and I have had covid 8 times, and unfortunately have over 20 cardiovascular, neurological and pulmonological long covid symptoms. I had my sample analyzed through BiomeSight(attached below).

Happy to follow any process that you may have for this.

The process is simple

• Upload (Ombre or Thorne) your data to Microbiome Prescription upload page, OR
  • Transfer your data from BiomeSight. 📹 PC, 📹 Phone
• Send me an email (Ken /at\ Lassesen.com with:
  • Your Back Story
  • Permission to use the above information anonymously for a blog post
    • This is required to avoid issues with Health Insurance Portability and Accountability Act of 1996 (HIPAA) or equivalent in different area of the world.
• Posts are done usually on a first come, first serve basis — usually within 2 weeks.
  • I do not do private consults. I am not licensed to provide medical advice. I am a statistician and Artificial Intelligence engineer.
• If you choose to share the post with your Medical Professional and they are interested in discussing the post with me on a zoom or equivalent call, I will make the time. My temperament is to teach and share knowledge.
• There is no cost. If the suggestions work, feel free to buy me a coffee as a thank you.

My preference is for people to do “self serve”, examples of other analysis: Analysis Posts on Long COVID and ME/CFS

Analysis

I am doing a more detail analysis first. While similar to other ME/CFS samples (i.e. over representation of bacteria in the 0-9%ile range), we do not have the under representation in the 90-99%ile range.

Percentile	Genus	Species
0 – 9	64	94
10 – 19	6	11
20 – 29	10	15
30 – 39	15	18
40 – 49	15	17
50 – 59	19	20
60 – 69	19	31
70 – 79	19	31
80 – 89	26	39
90 – 99	46	40

The Likely Key Bacteria Causing Above show two genus, both with relatively low importance (Usually there is at least one over 3.5).

Rank	Bacteria	Importance	Percentage of Microbiome
genus	Ruminococcus	2.8	15% (100 %ile)
genus	Oscillospira	2.5	10% (95%ile)

Going over to Bacteria deemed Unhealthy, we see a likely why for getting COVID eight times! Two bacteria have been associated with getting COVID from studies. This suggests that the chemicals produced (or consumed) by these bacteria creates a friendly environment for the virus

Name	Rank	Percentile	Count	Comment	More Info
Anaerotruncus colihominis	species	73	2000	Not Healthy Predictor	Citation
Collinsella	genus	94	8620	High COVID Risk	Citation
Dorea	genus	85	8350	Increased COVID risk	Citation
Prevotella copri	species	76	2160	Over 70%ile Indicator of mycotoxin present	Citation

Looking at Dr. Jason Hawrelak Recommendations, we are at 95.6%ile with almost the not ideal being too low (which is likely caused by Ruminococcus and Oscillospira taking excessive space in the microbiome).

Using US National Library of Medicine studies:

• for Long COVID   (64 %ile) 56 of 212 matches
• but for COVID-19 only (15 %ile) 22 of 107

Using Special Studies, we see (in decreasing order) that the signature is closest to Long COVID.

•  35 % match COVID19 (Long Hauler)
•  22 % match Bloating
•  21 % match Easily irritated
•  20 % match Cold Extremities

On your matching of signature to symptoms, it does seem to be spot on with the long covid, bloating, easily irritated and cold extremity symptoms.

Feedback from reader on 1st draft

Research Features for Special Studies v.2 had no matches – adding to my observations of those results being low usability.

I am going to do the ‘Just give me Suggestions!’ button (which does the three typical selections of bacteria, plus Likely Key Bacteria Causing Above.

The quick take away with strong evidence include:

• Melatonin, NAC, Quercetin, Arbutin (polyphenol), Guaiacol (polyphenol), Hesperidin, Luteolin, Polyphenols, Resveratrol
• doxycycline, azithromycin – if you have a willing MD
• Gluten Free Diet in general BUT Wheat germ, crude , high-protein diet (low-fat diets – eggs especially)
• Whey (non denatured), Flaxseed, broccoli, Far infrared Sauna
• Black Cumin, Cinnamon, Fennel, Ginger, Glycyrrhizin/Pure Licorice, Grape seed extract (mostly Resveratrol cited above), Milk Thistle seed, Olive leaf extract, Rosemary, Wormwood
• Racetams, Vinpocetine (Both are known to help cognitive issues)
• AVOID: inulin, jerusalem artichoke, Resistant starch
• Probiotics: Mutaflor e.coli probiotics (Germany), symbioflor 2 e.coli probiotics (Germany),  enterococcus faecium, lactobacillus casei [typically Yakult]. Avoid probiotic mixtures
• Vitamins: B1,B2,B6,B7,B12, C
• Minerals: Magnesium, Selenium, Zinc AVOID: iron supplements

The downloads of simplified and consensus is below.

Questions from Reader

I usually send early and second drafts to readers to improve posts. Some of the questions sent are:

• I was incorrectly under the assumption that antibiotics and antivirals will always kill beneficial and detrimental bacteria, until I read your Antibiotics will kill everything — Not article. I have taken azithromycin injections on average 3x a year and 5 courses of 2 month long doxycycline cycles over the past 6 years.  My question is, can we infer from the data as to how long one should take antibiotics like doxycycline or azithromycin? My presumption is that regular microbiome samples should be taken 1/mo, ideally 1/week, until bacteria populations affected by these drugs are in optimal ranges. What are your thoughts?
  • Most antibiotics come from nature and usually from a bacteria that tries to reduce competitors. Usually they are discovered because it is effective against a troublesome bacteria (and ignore side-effects on anything else).
  • When to stop is a complex question. There are a variety of ways that a bacteria is “gone” but hibernating. My attitude is to take just one course if there is a specific infection. The goal is to knock the bacteria back sufficiently that your natural immune system can take over the fight. For changing a dysfunction microbiome where there could dozens of different bacteria in the cartel, I favor Cecile Jadin approach of alternating types of antibiotics with 7-10 days on and 20 days off between each course. It seems to be more effective against antibiotic resistance that often develops when the same antibiotic is regularly used. I have seen studies on sewerage treatment confirming this.
  • There is no “optimal range” IMHO, there are “typical ranges” with the problem that different folks will use different methods to determine those. I favor the Kaltoft-Moldrup ranges. See  The problem with “official” ranges from labs.
•  Do you have an article or any other info on the Cold Extremities symptoms caused by particular microbiome signatures? This issue has plagued me all my life and I’d really like to fix it if you have any suggestions on places to look.
  • I do not recall doing anything specific because there can be multiple paths to this symptoms. Some obvious ones:
    • Some forms of coagulation or vascular constriction issues that results in slow blood flow. Your saturated Oxygen Levels may be fine, just heat loss from taking too long to reach the extremities. This can also occur with inflammation.
      • This was the case for me. A genetic defect caused thick blood — my particular defect was easy to compensate for.
    • Hypothyroidism is another possibility
•  I am currently taking OMNi-BiOTIC(sold under AllergoSan USA) Stress Release pre and probiotics everyday, alongside a prebiotic called Omni Logic Plus. I saw that your report mentioned “Avoid Probiotic Mixtures”, so I will be reevaluating this strategy.
  – One scoop of the Omni Logic Plus prebiotic contains 1g of Fructo-Oligosaccharides and 1g of Galacto-Oligosaccharides, and causes me intense, painful symptoms of bloating for 24 hours. 
  -The Simple Suggestions sheet recommends 15gm FOS and 10gm GOS daily. Do you think I should be experiencing bloating alongside these prebiotics, and how should I work up to 15gm/10gm? What exactly is happening in the microbiome when this ramping of prebiotics occurs?
  • Remember these are suggestions only, many suggestions!! Since it causes painful bloating, I would not do.
  • The dosages are UPPER LIMITS that are deemed safe (has been used in clinical studies). The purpose is to show what may be therapeutic levels are. See this page. Often people dosages are closer to homeopathic than therapeutic. 🙁 . Then we hear on forums “I tried it and it did nothing”
  • You may wish to get the Oligosaccharides directly from food and not as supplements. This is always my preference.
•  Some of these suggestions counteract each other, such as Mutaflor e.coli probiotics (Germany), and doxycyline. Do you recommend prioritizing one or the other first?
  • See Suggestions Contradictions — Limits of Certainty for why contradictions occur. My usual preference is natural substances over prescription, second item is availability. If you can get a MD to prescribe an antibiotic while you wait for Mutaflor or Symbioflor to arrive — then the sequence resolves itself.
  • One thing to remember is this: We want to destabilize the bad microbiome. Doing everything at once will likely gain some ground initially but you then get stuck in trench warfare as the other side learns how to respond. I usually suggest breaking suggestions into 4-8 lists of 1-2 weeks duration and just rotate what you take. I refer to this as the resistance approach. It worked for the Americans against England in 1776, French Resistance against Nazi Germany, and Vietnamese (Viet Kong) against Americans in Vietnam, and Afghanistan against the British, Russia and the US. No great victory just constant small ones.
•  I noticed that you recommend high dose B1 Thiamine at 1.8gm/day and a high protein/low fat diet overall. I understand that there’s a variety of other dietary suggestions here, but would you recommend that a purely carnivore diet be tried? Have you noticed the carnivore diet having any permanent beneficial impact on the microbiome?
  • Short answer, B-vitamins are often nicknamed “Beef-Vitamins” because that is where most can be sourced from. On the flip side, getting the vitamins out of the beef, depends on stomach acid and what bacteria are there.
  • You can use the food site, to see how much B12 and B6 are in various foods. 100 grams of beef liver (3-4 oz) gives 0.13 mg of B-12. It is unlikely you will get therapeutic dosages from eating beef.

My usual advice is to do things for 4-8 weeks and then retest. You are sailing your microbiome to safer waters though an archipelago. The winds and the charts will often require many course corrections.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.