Another Long COVID Microbiome

While working on the last long COVID post, another Long COVID person contacted me. He was definitely frustrated (in the same way that I have seen people with ME/CFS be frustrated over the last decades).

 I’ve literally consulted with over 7 doctors (internist, hematologist, endocrinologist, ENT, GI specialist, cardiologist, & neurologist) over 3 weeks period and still have 4 consultations to go! All those doctors did is to request for more bloodwork and scans and then tell me that it’s all in my head (using smooth words) and send me home! 

Long Haul Covid Patient

Recap on the Literature

The Microbiome and COVID have strong relationships. The microbiome prior to COVID impacts the severity. The severity of the symptoms correlates with the microbiome changes. This leads naturally to Long COVID being a continuation of this theme.

 One study suggests that a core microbiota could predict COVID-19 severity in healthy subjects.27 Another study shows that the composition of the intestinal microbiota in the Chinese cohort is different between COVID-19 infected and un-infected controls, with symptom severity correlating with specific bacterial taxa.2The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort [2021]

A new study used fecal samples were collected at least 38 days following diagnosis. By common belief, the patients are fully recovered — except their microbiome are not!  What is the difference? It depends on where COVID presentation.

  • positive detection of SARS-COV-2 RNA from the respiratory tract, defined as respiratory positive (RP) 
  • failure to detect in the respiratory tract, but had covid, is negative

They found changes in “13 phyla, 18 classes, 44 orders, 88 families, 234 genera, 1 phylum, 1 class, and 1 order were significant”. To put it simply, look at the changes below — they are NOT minor but major shifts!

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Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study [2021]

Our Long COVID Patient

My ongoing long haul symptoms:
– Vertigo/lightheadedness. Can’t maintain proper balance and head feels heavy 🙁 I was walking into furniture in my home! It’s difficult to drive a car or even fast walk or go down the stairs. I feel as if my head is heavy and will fall.
– Mood swings/anhedonia. No more feeling of happiness or pleasure. Low serotonin? Low dopamine?
– Brain fog/memory loss/loss of concentration. I’m back to work and it has been extremely difficult to get tasks done.
– Occasional blood in stool. Ulcers? Never had GI bleeding in my life!
– Early evening fatigue. Feel extremely tired past 8pm. I also wake up super early (5-6am) and can’t go back to sleep.
– Blurry vision during night.
– Slight shakiness/tremors in hands and legs. Low iron? Low dopamine?
– Low libido/sex drive despite getting morning erections.

In his own words

Pro Forma Analysis

I am going to do the same process as with the other Long COVID person. First, we have two lists of bacteria available, the number of studies are few but slowly increasing.

Bacteria Out of Range

The earlier sample had just 7 out of range, the latest sample increased to 16, implying the microbiome is drifting further away from normal. Comparing samples, we found the following concerningly high on both samples:

The following high level taxonomy items went out of range in the latest sample:

End Product Out of Range

Three items were out of range, one in common with the other Long COVID but in the opposite direction a-Galactosidase was high, and the other was low.

KEGG Bacteria Products Out of Range

The earlier sample had 9 out of range, the latest sample has 145!! Another indication of shifting further away from normal 🙁

KEGG Modules Out of Range

Just one in each sample, nothing in common.

KEGG Enzymes Out of Range

The earlier sample had 8 out of range, the latest sample has 139!! Another indication of shifting further away from normal 🙁

Kegg Suggestions

Where there are so many items with issues, I usually do not bother looking at them individually. Instead, I look at what can be computed to address them. Because every item is low, we do not need to look at trying to reduce anything — just add,

KEGG Suggested Probiotics

This is done by seeking out probiotic bacteria producing enzymes etc that are not being produced enough by existing bacteria. These can be viewed as a biological supplement producing items not available as regular supplements. The retail probiotics Sun Wave Pharma/Bio Sun Instant and Prescription Assist appear to be good choices (if available).

These are the same ones as with the other Long COVID person. What surprised me was that the earlier sample had a higher value list than the latest sample. This implies that the new overgrowth are providing the material to stablize the microbiome (unfortunately, in the current state of dysfunction)

A common mistake is to slip into a homeopathic thinking, “oh, I am taking some — that is enough”. In general I recommend starting low and increasing to the maximum dosages used in clinical studies. See this page for amounts used and links to the study or clinical trial.

KEGG Suggested Supplements

I tossed in the prior review for reference, two supplements are in common with all three samples.

Earlier SampleLatest SampleOther Person
Vitamin B-12
Phytase (Enzyme)

We similarly identify supplements that are available retail (defined as being available on


Using the last Long COVID post as a model, I jump directly to suggestions using the latest results. EXCEPT – I selected everything — including antibiotics and antivirals. No antibiotic made it high on either list.

12%ile and COVID-19

Remember, we are restricting to only those reported for active COVID and with the same direction of shift

12%ile and Long COVID

We have a much longer list of bacteria selected — which likely reflect that it is long COVID.

Quick Kaltoft-Moldrup suggestions

A very short list – this happen because we do not have studies reporting what modifies many of these bacteria.

The earlier sample had just a half dozen bacteria picked. The latest had more
Earlier had only a few (not even 20 Add Suggectios)

Reminder – The WHY for suggestions

On the suggestion line, you may see a 📚. Clicking it will show the source of the recommendation and why. Remember the more positive impact (by number of studies reporting the same), the greater the confidence shown. It is the confidence that it will shift in the desired direction. It is not which works better.

Putting Suggestions Together

With much bigger lists of bacteria, we also run the risk of more complexity and contrary suggestions [for example, bifidobacterium longum bb536 (probiotics) was a take, but  bifidobacterium longum (probiotics) was an avoid]. I find myself giving the 12%ile and Long COVID Suggestions the greatest credence. It has some interesting

What seems to be reoccurring – make sure you look up dosages where available. Start low and work up to the maximum dosages used in clinical trials (after consulting with your medical professional)

I also expanded the list to 50 pro and con and notice the following items of interest

Probiotic Advice

My read of the data is to avoid all Lactobacillus and Bifidobacterium probiotics. You have above the median amounts of both of them 85%ile and 66%ile respectively – you do not need more, in fact, they likely contribute to the dysfunction! Miyarisan, Prescript Assist (or Equilibrium), aor / probiotic-3 and Sun Wave Pharma/Bio Sun Instant appears to be the best retail candidates for probiotics.

This is a MODEL not a PROTOCOL

This is directed to people reading this post and saying “I will do what is described”. What is the difference? A Protocol comes from clinical experience and is a defined set of actions that are repeated for each patient. A model is a theoretical way to generate candidate actions that may help. This is not a model for Long COVID patients, it is a model for one person’s microbiome. Every Long COVID patient will have a different microbiome and thus different candidate actions. You can see this by looking at the next post on Long COVID microbiome.

An analogy, Long COVID can be compared to a headache. There are at least 17 types of headaches. You may need to see a dentist (tooth issues), or take a antihistamine (allergy) or take oxygen or …. Details drives the treatment.

For information on suitable 16s Microbiome Providers.

To help illustrate this, I have put the bacteria targeted from each of them below. You will note a lot is in common.

Female Prior Long COVIDMale This Post
This image has an empty alt attribute; its file name is image-63.pngThis image has an empty alt attribute; its file name is image-60.png

Logical Treatment Options based on test results

Above you read about this user’s frustrations with the medical professionals. The root problem is that profession runs on encyclopedic knowledge (often photographic memory) that looks for a match and retrieves it as treatment. I term this as cook-book medicine. If there are no matches, then we typically see “deer in the headlights“, a deer with a MD.

Microbiome Prescription builds predictive modelling with a wide variety of suggestion options. Most of the options do not require a prescription, the user is in primary control. There is a full chain-of-evidence to the basis of the suggestions for people to review (yes, some people may need to upgrade their reading skills). The core facts are your microbiome.

Improvements can be objectively measured (instead of a vague “do you feel better”). Feeling better is important, but it should not be the sole criteria.

Questions and Answers

For many of these questions I went to the “See Impact..” with the specific sample.

Q: I’m currently on bovine Colostrum, is it ok to keep taking it?

A: Bovine Colostrum is not the database, the closest match is whey. It has no known impact – so you can assume it is safe.

Q:  I’m eating boiled and cooled down potato every day as source of resistant starch. Is it ok?

A: Cooking an item with resistant starch can breakdown that starch.  see  Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review [2020]).
As above – potatoes– no known impact — so you can assume it is safe.
But : raw potato starch is a negative
Resistant starch is a NEGATIVE

Q: Is Mutaflor ok? Since my E coli appears low? I’m sorry if I’m not following I’m going through brain fog.

A: As above – no known impact — so you can assume it is safe.

Q: I see the suggestions recommend against inulin. However, I’ve recently included garlic, onion and ginger in my diet. Are they ok? 

  • Garlic – mild negative
  • Onion – no known impact — so you can assume it is safe.
  • Ginger – no known impact — so you can assume it is safe.

Q: ThryveInside also says I have zero bacteria for absorbing Vitamin K2 and refers to Bacillus. Is it ok to take Bacillus Subtilis from Natto?

A: You may wish to contact ThryveInside to find out exactly how they computed this. I show that you are at the 56%ile for vitamin K production.

  • You may wish to be explicitly tested for Vitamin K by your medical professional
  • Vitamin K2 0 As above – no known impact — so you can assume it is safe.
  • Bacillus Subtilis – it is a definite avoid, Use Vitamin K2 supplements
Bacillus Subtilis

Q: Which product do you recommend for HMOs? I found this on Amazon: this the one you are referring to?

A: Yes, That is actually the product that was used in most of the studies cited.

Q: Which nuts is best for my case (pistachio, hazelnut, cashew, brazillian nut, etc.)? I’ve been eating walnuts and almonds for several months.

A: I checked the types that we have data for:

  • Peanuts – no known impact — so you can assume it is safe.
  • Walnuts – positive impact
  • Generic nuts – no known impact — so you can assume it is safe.

Q: My vitamin D turned out high-normal. My 25-hydroxy vitamin D reading is 29.1 ng/ml & reference range (20 – 40). The suggestions included Vitamin D.

A: Vitamin D supplement are estimated to be a net negative benefit (same numbers as above). I looked at the citations used to make that decision and see a mixed impact on different items according to different studies. The results illustrates why suggestions may change from month to month. If new studies are added (which happens monthly) then the impact estimates change. My goal is deliver the best estimate from current studies – a moving target,

 Whatever happens, I just want you to know that you have helped me a lot even before getting Covid-19… One word, thank you Ken  💐

REMINDER: These are suggestions generated by an artificial intelligence program. Before implementing, they should be reviewed by your medical professional.

3 thoughts on “Another Long COVID Microbiome

    1. The issue is the salesmanship being done on these two bacteria PLUS which test you are using. Some tests reports only 44% of people have Lactobacillus (
      and 40% for Bifidobacterium (see ).

      Most labs report (and calculate) incorrect ranges, some have 60% of their reports having low levels.

      Look at the chart here.
      The average is at the 80%ile, that is 4/5 are below average and just 1/5 are above. If they calculate ranges using average +/- 2 std dev (the norm for most labs), you will have over half the population being very low

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