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).
Yin-Yang
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.
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:
“Serratiopeptidase is a proteolytic enzyme that has been used for reducing inflammation, it has antiedemic, analgesic, fibrinolytic and caesinolytic properties.” [2016]
Bromelain influences blood coagulation by increasing the serum fibrinolytic ability and by inhibiting the synthesis of fibrin, a protein involved in blood clotting [2012]
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).
Reservations
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.
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.
Criteria
6/8/2022
8/4/2022
9/6/2022
10/26/2022
Lab Read Quality
2.1
3.8
3.6
8.3
Bacteria Reported By Lab
534
774
721
775
Bacteria Over 99%ile
10
3
2
6
Bacteria Over 95%ile
58
27
24
22
Bacteria Over 90%ile
99
53
44
50
Bacteria Under 10%ile
25
68
48
127
Bacteria Under 5%ile
13
28
15
77
Bacteria Under 1%ile
5
3
1
16
Lab: Thryve
Rarely Seen 1%
8
14
9
12
Rarely Seen 5%
43
80
60
73
Pathogens
21
34
33
27
Outside Range from JasonH
5
5
7
7
Outside Range from Medivere
13
13
17
17
Outside Range from Metagenomics
9
9
9
9
Outside Range from MyBioma
7
7
8
8
Outside Range from Nirvana/CosmosId
23
23
19
19
Outside Range from XenoGene
44
44
49
49
Outside Lab Range (+/- 1.96SD)
38
39
26
22
Outside Box-Plot-Whiskers
177
202
153
118
Outside Kaltoft-Moldrup
206
257
203
292
Condition Est. Over 99%ile
0
0
0
0
Condition Est. Over 95%ile
0
0
0
0
Condition Est. Over 90%ile
0
0
0
0
Enzymes Over 99%ile
14
18
5
23
Enzymes Over 95%ile
115
105
59
112
Enzymes Over 90%ile
212
192
143
320
Enzymes Under 10%ile
63
106
93
266
Enzymes Under 5%ile
29
45
27
141
Enzymes Under 1%ile
2
2
0
8
Compounds Over 99%ile
37
36
31
119
Compounds Over 95%ile
289
288
275
281
Compounds Over 90%ile
372
381
361
385
Compounds Under 10%ile
288
255
235
298
Compounds Under 5%ile
192
159
136
216
Compounds Under 1%ile
37
14
4
31
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 IBS, Poor gut motility, Cold Extremities
8/4/2022 5-17%, top items: ME/CFS without IBS, Poor gut motility
9/6/2022 4- 18%, top items: ME/CFS without IBS, Easily irritated
10/26/2022 7 -22%, top items: General: Fatigue, ME/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):
Grapefruit seed extract (studies suggests that the preservative used is the active ingrediant)
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.
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.
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:
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.”
In discussion with readers, interest in non-drug treatment of mast cell and histamine issues is very high. Trying to get traction with the microbiome has not been successful.On how to use Half-Life, see Half-Life: Not the game but supplements!For Arginine and Glutamine, 100mg of each every hour is suggested.
Dosages: Are the maximum deemed safe by an authority, not recommended dosage
Most of the items above are modifiers on Microbiome Prescription. An interesting experiment is to see which bacteria/taxa are modified in common with the above. Below are the taxa that occurs 6 or 7 times for the above 7 items.
Taxa Name
Rank
Impact
Times Shared
Bacteroidaceae
family
Decreases
7
Lachnospiraceae
family
Major Decrease
6
Desulfovibrionaceae
family
Major Decrease
6
Clostridiaceae
family
Decreases
6
Bacteroides
genus
Decreases
7
Faecalibacterium
genus
Increases
6
Ruminococcus
genus
Decreases
6
Desulfovibrio
genus
Decreases
6
Roseburia
genus
Decreases
6
Eubacteriales
order
Decreases
6
Bacteroides xylanisolvens
species
Decreases
7
Bacteroides caccae
species
Decreases
7
Bacteroides ovatus
species
Decreases
7
Bacteroides uniformis
species
Decreases
7
Bacteroides thetaiotaomicron
species
Decreases
7
Phocaeicola vulgatus
species
Decreases
7
Items that are marked decreases, are likely bacteria you may want to reduce if you have mast cell issues. Faecalibacterium is the one bacteria that you want to increase.
Applying to your microbiome sample
On the [Research Feature] tab. Find this section and click #2
See Video above for the rest of the steps
As always, review your plan with your knowledgeable medical professional before starting. Some substances may be inappropriate for other medical constraints.
CFS Remission 