Bacteria are very very rarely bad or good

A reader messaged me this

hello I do not want to bother, I have a question in the laboratories of my country, in the microbiota tests they put veillonella as virulent, but in a recent publication of microbiome prescription I saw that it could be a solution, why do the laboratories attribute virulence to it?

My Answer

That is equivalent to saying “Italians are criminals”. Why would someone say that? “Some Italians belong to the Mafia”

Veillonella is a genus of gram-negative, anaerobic bacteria that are commonly found in the human oral cavity, gastrointestinal tract, and respiratory tract. While some strains of Veillonella can cause infections, particularly in individuals with compromised immune systems, the majority of strains are considered to be non-virulent or opportunistic pathogens. Some studies have suggested that Veillonella may play a role in certain disease states, such as periodontal disease, but more research is needed to fully understand the potential pathogenic mechanisms of this genus.


For a lab to creditably state that, the lab would need to identify the specific strain. Veillonella is a genus, composed of many species, each species is composed of many strains. In terms of our Italian allergy, Italians come from many regions of Italy (species), within each regions are many families (strains). There may be some of these families that tend to being Mafia, others may tend to be priests (and eventually Popes).


My attitude is that Yin and yang is a better way of viewing bacteria. Bacteria are out of balance. Too many poor people results in high crime rates (out of desperation), Too many rich people results in low class mobility (the only people that get ahead are their friends, “old school ties”). The “right balance” for a well functioning society varies by country — for example, Iceland versus Haiti. Similarly, your DNA and diet influences what the right balance should be.

This family’s favorite and most effective probiotic is Mutaflor, an Escherichia coli probiotic. All E.Coli is not bad, trying to eliminate all E.Coli is likely a very dumb choice.

Interesting Successful Clinical Trial for Long COVID and ?ME/CFS ?

A reader forwarded me this link,

A Randomized Controlled Trial of the Efficacy of Systemic Enzymes and Probiotics in the Resolution of Post-COVID Fatigue

The study concludes:

This study demonstrates that a 14 days supplementation of ImmunoSEB + ProbioSEB CSC3 resolves post-COVID-19 fatigue. The proposed supplement regimen significantly reduces the burden of both, physical and mental fatigue and is effective as an early intervention in the recovery of COVID-19 patients, many of whom continue to experience severe fatigue including muscle weakness and “brain fog” several months after initial infection. 

The substances used are very familiar to readers of my CFS Remission blog. They are:

  • Bacillus coagulans LBSC (DSM 17654)
  • Bacillus subtilis PLSSC (ATCC SD 7280)
  • Bacillus clausii 088AE (MCC 0538)
  • Serratiopeptidase,
  • Bromelain,
  • Amylase,
  • Lysozyme,
  • Peptidase,
  • Catalase,
  • Papain,
  • Glucoamylase
  • Lactoferrin

Some quick notes with citations for new readers:

This points back to the research and demonstration done by Dave Berg at Hemex Labs . “Berg and Joseph Brewer studied coagulation in CFS patients and concluded that approximately 85% of chronic fatigue syndrome patients had hypercoagulation, “[src].

My personal experience with the Hemex approach is good and put me into remission in 2000. Objective measurements showed coagulation in some parts of the coagulation cascade with piracetam and heparin being my favorite cocktail (both taken sublingual).


The study ended at two weeks with no ongoing tracking of patients. My observations of ME/CFS people over several decades has been that short term remission is common with a slow regression back to fatigue. An excellent examples are ME/CFS in Australia doing Fecal Matter Transplants with remission within 48 hours and relapse in 4-8 weeks. Just as some bacteria (bacillus cited above) reduces coagulation, other bacteria triggers coagulation. If those triggering bacteria are not adequately suppressed then the fatigue and brain fog will return over time. Think of a leaking dike, you bring in the pumps and remove the water behind the dike, 3 weeks later the water is back — you need to fix the leak in the dike also.

A reader pointed out that the product is available on Amazon US for $40. So a cheap experiment to try! If you do try it– please add your experience as a comment on this post.

Samples over time of ME/CFS Spouse

This is the spouse of someone with significant ME/CFS. It is well known that bacteria is transferred between people in the same household unit.

This raises all sorts of questions — which I am not interested in exploring… “For better or worse, in sickness and in health”

My wink wink suggestion for microbiome issues has been “Snog a lot of pretty young healthy things as the best probiotic” — my wife does not agree…..

Comparison between Samples

The first step that I did was to verify that all samples used the same reference sticks. This means clicking this for each sample first.

This person has processed FASTQ data thru both BiomeSight and OmbreLabs. I am using OmbreLabs data below. Using reference tables uploaded in 2023.

Lab Read Quality2.
Bacteria Reported By Lab534774721775
Bacteria Over 99%ile10326
Bacteria Over 95%ile58272422
Bacteria Over 90%ile99534450
Bacteria Under 10%ile256848127
Bacteria Under 5%ile13281577
Bacteria Under 1%ile53116
Lab: Thryve
Rarely Seen 1%814912
Rarely Seen 5%43806073
Outside Range from JasonH5577
Outside Range from Medivere13131717
Outside Range from Metagenomics9999
Outside Range from MyBioma7788
Outside Range from Nirvana/CosmosId23231919
Outside Range from XenoGene44444949
Outside Lab Range (+/- 1.96SD)38392622
Outside Box-Plot-Whiskers177202153118
Outside Kaltoft-Moldrup206257203292
Condition Est. Over 99%ile0000
Condition Est. Over 95%ile0000
Condition Est. Over 90%ile0000
Enzymes Over 99%ile1418523
Enzymes Over 95%ile11510559112
Enzymes Over 90%ile212192143320
Enzymes Under 10%ile6310693266
Enzymes Under 5%ile294527141
Enzymes Under 1%ile2208
Compounds Over 99%ile373631119
Compounds Over 95%ile289288275281
Compounds Over 90%ile372381361385
Compounds Under 10%ile288255235298
Compounds Under 5%ile192159136216
Compounds Under 1%ile3714431

General Impression

  • After the first sample, the next two had improvements but the last one went the wrong way.
    • Too high and Too low reduce for 2 samples and then increased
    • Too high or too low for Enzymes were the highest for the last sample
  • Most of the third party ranges were constant for the first two samples and most got worst for the last two samples.
  • Compounds are much less indicative of issues.
  • Special Studies are sensitive to lab quality,
    • 6/8/2022 4-14%, top items: ME/CFS without IBSPoor gut motilityCold Extremities
    • 8/4/2022 5-17%, top items: ME/CFS without IBSPoor gut motility
    • 9/6/2022 4- 18%, top items:  ME/CFS without IBS,  Easily irritated
    • 10/26/2022 7 -22%, top items: General: FatigueME/CFS without IBS

ME/CFS without IBS is a consistent top item and we see that the percentage is increasing.

Proposed Approach

Unlike many samples, we see distinct deterioration in several 3rd party criteria. For many samples, there is no change between samples. We will include those in the consensus, namely:

  • JasonH
  • Medivere
  • MyBioma
  • Xenogene

It is interesting to note that one 3rd part criteria improved: Nirvana. To this, we do our usual:

  • Lab ranges
  • Box-Plot-Whiskers
  • Kaltoft-Moldrup

The net result will be more bias to those in the 3rd party criteria cited above. Another way of stating that, we will emphasis more that which everyone agrees are most concerning.

The top suggestions (easily obtained):

The top avoids are:

The downloads are attached:



Food Suggestions

We mostly eat pastured meats and vegetables. No cereals and little in the way of carbs or even fruit. I used to eat linseed crackers in the USA, but here I eat buckwheat instead. Here in Spain we switched from wild Alaskan salmon, to seasonal, local, small blue fish, like mackerel, sardines, etc. Added Rabbit and can eat a lot more quality raw cured pork, if we want to. I have always enjoyed natural wine and Spain has plenty of it. Fresh made coffee and 100% cocoa. Raw goat, sheep and cow’s milk are also available and I do enjoy them with some regularity.

I used the latest sample with the Kaltoft-Moltrup Normal Ranges. The top suggestions are each because of different nutrients that appear significant with Fiber, total dietary and Magnesium, Mg being a common theme.

On the avoid list we have at the bottom:

Remember, foods are filtered to the nutrients that are above typical levels for foods containing the same nutrients. The goal is to reduce the intake of nutrients that have been identified to shift things in the wrong direction.

For most people, if you say reduce folic acid in your diet — most people will not have a clue. The purpose of the food suggestions is to translate a precise item into common foods.

Note: If a food in your diet is not in the list then we deem it as neutral. For example: there are 24 variety of rabbit in the food database, only one shows up in the suggestions from the sample, Rabbit, meat, raw, Oryctolaguscuniculus, (Nyama ya kalulu), which suggests to keep eating rabbit. Similarly for milk, the two that shows up are Milk with Cow’s blood (from Africa) of 626 entries for milk.

The video below may help understand Food Suggestions better.

Antivirals and ME/CFS: Paxlovid, Tamiflu etc

A reader asked me to look at these and other antivirals for Myalgic encephalomyelitis/chronic fatigue syndrome :

“I hope your 2023 is off to a healthy start. I was wondering if you could look into how Paxlovid and similar protease inhibitor-style antivirals impact the microbiome.

I got Covid around Christmas and was prescribed Paxlovid. To my surprise, not only did I immediately feel better Covid symptom-wise, but there were many other positive changes.

My brain fog and fibromyalgia-like symptoms improved quickly and drastically. Unfortunately, these changes did not last very long after finishing my course of Paxlovid.

A similar thing also happened to me years ago when I got influenza A and was prescribed Tamiflu.

Also, anecdotally, from Twitter and Facebook groups around CFS, I know I’m not the only one to have this experience with Paxlovid.

There is also at least one trial underway testing the use of Paxlovid in Long covid patients.

Or perhaps it could also relate to the additional antiparasitic and/or anti-inflammatory actions of some antivirals?

Very curious to get your take and expertise on how this might be microbiome related.”

From a reader

Conceptual Model

It is well documented that virus changes the microbiome (see this list 20+ studies for COVID). A possible reason is that the virus wants to increase substances it needed to reproduce and decrease the substances that inhibits it. This is done by chemical signaling — the virus sends bogus messages to the microbiome.

By reflection, it is likely that antivirals also change the microbiome – possibly by reversing the changes done by the virus. Likely along the same mechanism.

” a viral infection usually results in substantial perturbations in the commensal microbiota, causing dysbiosis in the host, which may in turn further affect viral infectivity.” [2019]

HCV infection alters the gut microbiota, whereas intestinal dysbiosis induces an underlying inflammatory state.” [2023]

For some literature on this – note that this has only become of interest in research very recently:

Past Studies of Antivirals and ME/CFS

I have covered some in some past posts:

Valacyclovir has information available on the microbiome impact. For other antivirals I was not able to find new studies in the ME/CFS context

What was interesting is for a condition that is comorbid, Sjögren’s syndrome

Antiviral Impact on Microbiome

The use of antiretrovirals caused a significant impact on the individuals intestinal microbiota” [2007]

Bottom Line

Antivirals likely have antibiotics like effects on the microbiome. This is documented above. The problem is a lack of studies on which bacteria are impacted. This gives it uncertainty for being effective for any specific individuals.

My wish is that for any long term studies using these for Long COVID or ME/CFS is that microbiome samples be done before after and then 3 months after treatment stops. This would provide concrete information that can be applied at an individual.

My gut feeling is that a single course will not be sufficient for remission. I would suggest following the pattern of rotating and pulsing the antivirals which has helped. This could be combined with appropriate antibiotics. For those not familiar with this pattern:

  • Once a month take a course of antiviral or antibiotics (7-14 days) and then nothing for the rest of the month
  • Next month take a different one

There are several studies showing that this pattern is more effective than continuous. The conceptual model is that you disturb the bad bacteria and give a chance for the good bacteria to attempt a recovery. The survivors of the bad ones slowly regrow, changing antibiotics or antiviral will typically reduce these survivors because the new substance mechanism is different (so the antibiotic-resistance genes that the survivors had, may not work anymore).

More Coming…

“Thanks, Ken! Just saw the posted version. It won’t be perfect, but I do have a sample about a month before I got Covid and have one on the way, which will be sampled about two weeks after finishing Paxlovid. Not sure you’ll be able to glean anything from that specific test, but worth a shot.”