A reader emailed me and asked some questions.

My good friend that also has CFS/Lyme said to me that he is about 80% better in all his symptoms after using Ivermectin that his Lyme doctor prescribed him. His was almost bedridden, had extreme brain fog with depersonalization, low motivation etc. He used Ivermectin 2x a week 3ml oral. After 2 months he is now adding Metronidazol with minocyclin and his state is extremely improving. 
I tried to find some info on your blog but I didn’t find anything. Do you maybe know what Ivermectin did?  I also saw that his skin/face is looking like a baby hahahah he looks 15 years younger. 

I have a site for non-prescription items and give the list of items here. This site also provides prescription items for professionals. I looked up on that list and found:

I checked on the other common member,doxycycline (antibiotic)s, and found that it did not have a good impact.

The other item: Ivermectin,(prescription)  did not have a good profile for ME/CFS – but it does impact a lot of different bacteria

Chronic Lyme Prediction

Again, the cyclines are there with zero bad impact.

With ivermectin,(prescription)  showing good and bad impact.

Bottom Line

This was done with a-priori model of the bacteria shifts, that is, we assume that this person matched the typical shift seen in many studies and ignore the amount of shift. We know that there is a great variation of microbiome from person to person with the same diagnosis.

My criteria is that the suggestions have better odds of helping than hurting. In this case we see 2 takes appear to have worked, and one avoid did not. That is 2/3 or 66% success rate (which is above 50% — thus my criteria is satisfied, we did better than with random picks).

This list (with live time updates as data is added) on Microbiome Prescription web site. All suggestions from this page should be reviewed by your medical professionals. These are based on modelling and not clinical studies. These are based on family and lower taxonomy ranks (genus,species,strains) reported in studies on US National Library of Medicine.

In general, people report improvements from at least half of the items on the top of the list. Many items listed have been reports in clinical studies to help a significant percentage of patients. Items of special interest are those that are low in bad impact and high in good impact (i.e. Whey, pomegranate, fish oil, trametes versicolor( mushroom))
Best prediction is done when using a 16s microbiome result for the patient

Net	Substance	Good Impact	Bad Impact
24	bacillus subtilis (probiotics)	34	10
21	lactobacillus casei (probiotics)	30	9
20	pomegranate	27	7
19	resistant starch	34	15
19	whey	22	3
19	bifidobacterium longum (probiotics)	22	3
18	pediococcus acidilactic (probiotic)	21	3
17	brown rice	23	6
17	wheat	24	7
17	oregano (origanum vulgare, oil) |	24	7
16	almonds/ almond skins	18	2
15	soy	25	10
15	vitamin d	29	14
14	walnuts	27	13
14	whole-grain barley	22	8
14	pectin	22	8
14	wheat bran	24	10
14	Cacao	21	7
14	dietary fiber	14	0
14	lactobacillus plantarum,xylooligosaccharides,(prebiotic) (probiotics)	16	2
14	lactobacillus reuteri (probiotics)	27	13
14	fish oil	17	3
14	proline (amino acid)	19	5
14	bifidobacterium bifidum (probiotics)	25	11
13	lactobacillus paracasei (probiotics)	22	9
13	lactobacillus acidophilus (probiotics)	22	9
13	Human milk oligosaccharides (prebiotic, Holigos, Stachyose)	28	15
12	raffinose(sugar beet)	16	4
12	lauric acid(fatty acid in coconut oil,in palm kernel oil,)	17	5
12	high fiber diet	20	8
12	rosmarinus officinalis (rosemary)	25	13
12	Conjugated Linoleic Acid	14	2
12	Alpha-Ketoglutarate	18	6
12	Burdock Root	16	4
11	glycine	17	6
11	Glucomannan	11	0
11	pea (fiber, protein)	16	5
11	fructo-oligosaccharides (prebiotic)	26	15
11	lactobacillus rhamnosus (probiotics)	23	12
11	lactobacillus rhamnosus gg (probiotics)	19	8
11	lactobacillus casei shirota (probiotics)	13	2
11	fat	20	9
11	bifidobacterium pseudocatenulatum,(probiotics)	15	4
11	bifidobacterium infantis,(probiotics)	17	6
11	polyphenols	14	3
11	saccharomyces boulardii (probiotics)	20	9
11	oligofructose (prebiotic)	12	1
11	apple	21	10
11	whole grain,bran	11	0
10	vsl#3 (probiotics)	14	4
10	naringenin(grapefruit) (Flavonoid)	13	3
10	lupin seeds (anaphylaxis risk, toxic if not prepared properly)	20	10
10	magnesium	12	2
10	red wine	23	13
10	broad beans	20	10
10	fasting	16	6
10	lactobacillus plantarum (probiotics)	28	18
10	inulin (prebiotic)	26	16
10	enterococcus faecium (probiotic)	15	5
10	hou-po-da-huang-tang	11	1
9	Goji (berry,juice)	15	6
9	fruit/legume fibre	16	7
9	oligosaccharides (prebiotic)	12	3
9	banana	10	1
9	bifidobacterium adolescentis,(probiotics)	12	3
9	bifidobacterium animalis lactis (probiotics)	16	7
9	anise	13	4
9	triphala	34	25
9	zinc	27	18
9	vitamin a	23	14
8	trametes versicolor( mushroom)	10	2
8	red chiles (Capsicum)	8	0
8	xylooligosaccharide (prebiotic)	9	1
8	thyme	15	7
8	trametes versicolor(Turkey tail mushroom)	10	2
8	peppermint	13	5
8	persimmon tannin	9	1
8	resistant maltodextrin	16	8
8	selenium	9	1
8	mediterranean diet	21	13
8	omega-3 fatty acids	14	6
8	palm kernel meal	12	4
8	bifidobacterium catenulatum,(probiotics)	10	2
8	bacillus subtilis natto (probiotics)	9	1
8	cinnamon (oil. spice)	21	13
8	high resistant starch	12	4
8	green tea	14	6
8	jerusalem artichoke (prebiotic)	11	3
8	ketogenic diet	18	10
8	noni	12	4
8	Acacia Gum	9	1
8	bacillus,lactobacillus,streptococcus,saccharomyces probiotic	8	0
8	yogurt	8	0
8	sarcodiotheca gaudichaudii (red sea weed)	11	3
8	brown algae	11	3
8	Soymilk	8	0
7	plantago asiatica l.	12	5
7	lactose	11	4
7	Codonopsis pilosula	7	0
7	rosa rugosa	11	4
7	dietary phytoestrogens (isoflavones)	12	5
7	chicken	7	0
7	sialyllactose (oligosaccharide ) (prebiotic)	11	4
7	polygonatum kingianum(Orange Flower Solomon’s Seal.)	7	0
7	arabinoxylan oligosaccharides (prebiotic)	20	13
7	bacillus pumilus	9	2
7	lactobacillus gasseri (probiotics)	16	9
7	glutamate	7	0
7	foeniculum vulgare (Fennel)	12	5
7	dates	9	2
7	black raspberries	12	5
7	arabinogalactan (prebiotic)	8	1
7	garlic (allium sativum)	20	13
7	neem	13	6
7	methyl gallate	10	3
7	polysorbate 80	11	4
7	Vitamin B-12 (Cyanocobalamin)	7	0
7	blueberry	12	5
6	buckwheat	8	2
6	vitamin b2(Riboflavin)	7	1
6	germinated barley food-stuff	6	0
6	schinus molle (herb)	7	1
6	raw potato starch	10	4
6	sesame cake/meal	7	1
6	safflower oil	7	1
6	barley	25	19
6	chicory (prebiotic)	8	2
6	chrysanthemum morifolium	12	6
6	fibre-rich macrobiotic ma-pi 2 diet	13	7
6	daesiho-tang	6	0
6	lactobacillus salivarius (probiotics)	16	10
6	lactobacillus brevis (probiotics)	9	3
6	Lactobacillus Johnsonii (probiotic)	12	6
6	Oyster Mushroom	7	1
6	corn	6	0
6	sesame	7	1
6	rye	7	1
6	grape fiber	6	0
6	chondrus crispus (red sea weed)	9	3
5	xylaria hypoxylon (fungi)	7	2
5	lactobacillus sakei (probiotics)	5	0
5	purple sweet potatoes	9	4
5	d-ribose	5	0
5	Whole Milk	6	1
5	brassica juncea	9	4
5	galla rhois	8	3
5	Kiwifruit	7	2
5	lactobacillus acidophilus,cellobiose (probiotics)	6	1
5	gum arabic (prebiotic)	6	1
5	chamomile (chamaemelum nobile)	8	3
5	cabbage	5	0
5	barley,oat	15	10
5	basil	6	1
5	bacillus (probiotics)	5	0
5	rhubarb	14	9
5	navy bean	15	10
5	n-acetyl-d-glucosamine	5	0
5	oats	7	2
5	bifidobacterium lactis bb12 (probiotics)	10	5
5	green-lipped mussel	11	6
5	genistein	8	3
5	salt (sodium chloride)	8	3
4	saccharomyces cerevisiae (probiotics)	9	5
4	sesuvium portulacastrum herb	5	1
4	tulsi	5	1
4	vegetable	4	0
4	resveratrol (grape seed/polyphenols/red wine)	24	20
4	tannic acid	10	6
4	marijuana	6	2
4	pea protein	7	3
4	mutaflor escherichia coli nissle 1917 (probiotics)	5	1
4	moderate-protein moderate-carbohydrate	5	1
4	marjoram	5	1
4	rosa canina	4	0
4	plantain bananas	4	0
4	bifidobacterium longum bb536 (probiotics)	13	9
4	black beans	7	3
4	chitosan,(sugar)	20	16
4	glucose (sugar)	4	0
4	fruit	7	3
4	koji aspergillus oryzae	5	1
4	laminaria digitata(oarweed – seaweed)	9	5
4	Psyllium (Plantago Ovata Husk)	13	9
4	Beet	4	0
4	Bifidobacterium animalis	4	0
4	wasabi	4	0
4	fucoidan	5	1
4	punicic acid	4	0
4	asparagus	4	0
4	Vitamin E	4	0
4	Vitamin B	4	0
4	lemon	6	2
4	western diet	4	0
4	allium cepa	4	0
4	Opium poppy (Papaver somniferum)	4	0
4	Spearmint(mentha spicata)	4	0
4	Mango ginger(curcuma amada)	4	0
4	cinnamomum zeylanicum	4	0
4	cinnamomum tamala	4	0
4	Exercise	10	6
4	potatoes	10	6
4	bifidobacterium breve (probiotic)	6	2
4	spirulina(cyanobacteria)	4	0
4	low protein diet	12	8
4	papaya	4	0
4	bean	5	1
4	fenugreek	7	3
4	quercetin,resveratrol	13	9
4	rosehip tea	5	1
4	pomegranate blossom tea	5	1
4	grape polyphenols	13	9
4	hypericum scabrum herb	5	1
4	high amylose cornstarch	4	0
4	maize	4	0
4	mannitol	4	0
4	tabebuia impetiginosa (taheebo) bark	5	1
4	vitex negundo (herb)	4	0
3	nigella sativa seed (black cumin)	5	2
3	whole-grain wheat	5	2
3	sorghum	8	5
3	lactulose	14	11
3	bifidobacterium longum,lactobacillus helveticus (probiotics)	5	2
3	Curcumin	5	2
3	White-leaved Savory(micromeria fruticosa)	5	2
3	amaranth	8	5
3	Agavins (agave sugar)	7	4
3	avocado peel	4	1
3	Slippery Elm	30	27
3	Gallic acid	4	1
3	Ajwain (trachyspermum ammi)	6	3
3	Taxifolin	5	2
3	Ginseng	7	4
3	Lithium	9	6
3	Dendrobium officinale	7	4
3	lactobacillus fermentum (probiotics)	10	7
3	low animal protein diet	4	1
3	l-sorbose	4	1
3	fraxinus angustifolia (narrow-leafed ash)	3	0
3	capsaicin (hot pepper)	4	1
3	coriander oil	7	4
3	enterococcus durans (probiotics)	4	1
3	aspartame (sweetner)	9	6
3	animal-based diet	14	11
3	polymannuronic acid	17	14
3	momordia charantia(bitter melon, karela, balsam pear, or bitter gourd)	5	2
3	low processed foods diet	4	1
3	lychee fruit (nephelium longan)	3	0
3	xylan (prebiotic)	13	10
3	xylitol	7	4
3	sunflower oil	4	1
3	syzygium aromaticum (clove)	7	4
3	galacto-oligosaccharides (prebiotic)	19	16
2	oolong tea polyphenols	3	1
2	oolong teas	3	1
2	tomato powder	3	1
2	tea	18	16
2	vitamim e	2	0
2	oligofructose-enriched inulin (prebiotic)	11	9
2	oregano essential oil	3	1
2	paenibacillus polymyxa (prescript assist) (probiotics)	3	1
2	olea europaea (olive leaf)	5	3
2	mint	2	0
2	satureia montana(Winter savory)	3	1
2	(+)-catechin	4	2
2	abies alba mill. (silver fir)	3	1
2	bioflorin,enterococcus faecium sf 68,(probiotics)	3	1
2	bacopa monnieri	2	0
2	carum carvi (Caraway)	3	1
2	catechol	3	1
2	choline deficiency	2	0
2	chitooligosaccharides (prebiotic)	14	12
2	chaga (mushroom)	2	0
2	grapes	4	2
2	l-phenylalanine	2	0
2	l-arginine	2	0
2	lemon oil	2	0
2	lemongrass oil	5	3
2	lactobacillus helveticus,lactobacillus rhamnosus (probiotics)	2	0
2	Pork	8	6
2	camellia	2	0
2	rice bran	6	4
2	Tryptophan	6	4
2	nobiletin	2	0
2	Konjaku flour	6	4
2	lactobacillus helveticus	2	0
2	bacillus laterosporus (probiotic)	6	4
2	Immortelle(helichrysum italicum)	3	1
2	milk thistle(silybum marianum)	2	0
2	bandicoot berry(leea indica)	2	0
2	Bacillus clausii (Probiotics)	4	2
2	bifidobacterium (probiotics)	6	4
2	xylopia aethiopica (herb)	2	0
2	cylicodiscus gabunensis (mimosaceae)	2	0
2	d-fructose (sugar)	2	0
2	lactobacillus paracasei,lactobacillus acidophilus,bifidobacterium animalis (probiotics)	3	1
1	galactose (milk sugar)	12	11
1	hydrogenated palm oil	1	0
1	bifidobacterium lactis,streptococcus thermophilus probiotic	8	7
1	galla chinensis (herb)	10	9
1	Sijunzi decoction	4	3
1	Baking Soda (Sodium Bicarbonate)	7	6
1	strawberry	4	3
1	Fiber, total dietary	3	2
1	Haritaki	1	0
1	quinoa	2	1
1	Cacoa flavonoids	1	0
1	lactobacillus kefiri (NOT KEFIR)	11	10
1	grape seed extract	8	7
1	fumarate	1	0
1	ginger	10	9
1	doenjang (fermented bean paste)	2	1
1	aloe vera	2	1
1	ashwagandha (withania somnifera)	3	2
1	bacillus licheniformis,(probiotics)	10	9
1	ß-glucan	17	16
1	salvia officinalis (sage)	1	0
1	plant-rich diet	1	0
1	peppermint (spice, oil)	5	4
1	moderate-carbohydrate diet	1	0
1	magnolia bark	2	1
1	peganum harmala (rue)	2	1
1	thyme oil	1	0
1	thyme (thymol, thyme oil)	8	7

A reader wrote and a blog post was the easiest

Hi Ken,
tomorrow I have an appointment with a cardiologist, and I want to check for thick blood/coagulation if possible. What blood values would I need to test? Fibrinogen, Prothrombin Fragment 1+2, Thrombin/ AntiThrombin Complexes, Soluble Fibrin Monomer, and Platelet Activation. Is that right?

This has been part of my model of ME/CFS for a long time. It is a co-factor to things like the microbiome. A summary of the old treatment advice from Hemex and transcripts of talks with Dave Berg is here.

• Soluble Fibrin Monomer (SFM) – Normal Range 0-15mg/L
• Fibrinogen – Normal Range 200-300
• Prothrombin Fragment 1+2 test
• Antithrombin III (AT),
• Protein C,
• Protein S,
• APC Resistance
• Factor II level or the Prothrombin Gene Mutation
• Lp(a)
• PAI-1
• SED (Below 5 is a concern per Berg)

Example of the Family Reports from Hemex

This is from my ancient 2000’s CFS blog that is available here

The patient has done another sample and this continues the analysis. The original post, A German CFS Patient Experience and Analysis from July 2021. I am always interested in seeing changes that occur from the AI suggestions, they worked for me –I am as interested in them not working (to motivate improving algorithms).

What has changed?

There are a set of automatic comparison tools between samples, so I will check those first

I went to compare taxonomy outliers for the two samples and found just two items were on both. There was a lot of changes. We can ignore blues with no data besides – they were all likely what I term transitory bacteria that comes and goes. What we are interested

The two items of focus are VERY high on both:

• (species) Paraprevotella xylaniphila
• (species) Porphyromonas canis

Other component comparisons:

• End Product — most were unchanged except for Polyhydroxyalkanoic acids which jumped from none to 98%ile
• KEGG Bacteria Products nothing in common, on first sample we had only low values at risk, on latest sample only high values at risk
• KEGG Enzymes — the same thing, earlier sample has all risks being low samples, latest high values
• KEGG Modules — earlier sample had no risk items, latest had one high value
• Medical Condition (PubMed) — nothing for either sample

The overall impression is that things have changed significantly. This does not say that the person is better — only that the suggestions have changed the microbiome

Non-Automated Comparisons

Next I will look at various aspects and do side by side comparisons. First, using Dr. Jason Hawrelak Criteria, shown below. The worst shift was for Blautia, the best shifts was for Roseburia and Faecalibacterium prausnitzii

				Latest	Sample	Earlier	Sample
Taxonomy	Rank	Low	High	Your Value	Status	Your Value	Status
Bacteroidia	class	0	35	38.369	Not Ideal	33.945	Ideal
Akkermansia	genus	1	3	0.21	Not Ideal	0.017	Not Ideal
Bacteroides	genus	0	20	25.986	Not Ideal	25.266	Not Ideal
Bifidobacterium	genus	2.5	5	0.03	Not Ideal	0.021	Not Ideal
Blautia	genus	5	10	11.557	Not Ideal	6.174	Ideal
Desulfovibrio	genus	0	0.25	0.062	Ideal	0.091	Ideal
Eubacterium	genus	0	15	0.008	Ideal	0.004	Ideal
Lactobacillus	genus	0.01	1	0.012	Ideal	0.017	Ideal
Methanobrevibacter	genus	0.0001	0.02	0	Not Ideal	0.052	Not Ideal
Roseburia	genus	5	10	5.166	Ideal	0.624	Not Ideal
Ruminococcus	genus	0	15	2.848	Ideal	3.792	Ideal
Proteobacteria	phylum	0	4	11.225	Not Ideal	5.753	Not Ideal
Bilophila wadsworthia	species	0	0.25	0.598	Not Ideal	0.848	Not Ideal
Escherichia coli	species	0	0.01	0	Ideal	0.022	Not Ideal
Faecalibacterium prausnitzii	species	10	15	10.612	Ideal	3.415	Not Ideal

Health Status changes were a toss up, but appears marginally better

• Latest: 0 Healthy, 4 unhealthy
• Earlier: 2 Healthy, 6 unhealthy

KEGG Suggested Probiotics

• Earlier Sample had 11 probiotics listed with a maximum weight of 12 (most of the time I see much higher weights indicating greater dysfunction)
• Later Sample had 0 probiotics – this is actually a rare occurrence which hints at a better balance microbiome

KEGG Suggested Supplements

• Earlier sample has 3 items suggested (using default percentile)
• Later sample has 0 items suggested (using default percentile)

Pub Med CFS Profile

• Earlier sample had 5 low matches, 5 high matches
• Later sample has just 4 high matches

Citizen Science Models

• Early Sample: Total Matching Bacteria :26. Very Strong: 15, Strong: 8, Weak: 2, Very Weak: 1
• Later Sample: Total Matching Bacteria :24. Very Strong: 19, Strong: 4, Weak: 1, Very Weak: 0
• Less matching bacteria (means some have disappeared), while strong/very strong are the same, the weak association have dropped

From looking at all of the available objective measures:

• The microbiome has changed (our primary goal)
• Many measurements show indicate that the microbiome is moving towards normal, none has a suggestion of things getting worst.

Remember our goal is not to attempt a one-step cure

Our earlier post used this diagram, we appear to have successfully moved along the path to recovery. We need to see what our next step is.

Symptoms Forecasts To Reported Symptoms

This reader was a good user and entered their symptoms – we have a 80% match rate. What is interesting is that one of the items not checked was a Keto Diet — this is interesting because a recent post dealt with a Keto diet resulting in Chronic Fatigue Like symptoms, with “Keto Flu” is some studies. A Keto diet is DEFINITELY NOT A SUGGESTION for this person, it will likely make things worst.

Updated Suggestions

For the earlier post, the consensus reports were not available. My intent is to run each of the matched predicted symptoms, the PubMed profile for ME/CFS and Citizen Science for ME/CFS – a total of 18 sets of suggestions will be merged. There are two ways of doing this:

• Only the Auto Checked (which picks a few best items)
• Auto Checked plus suggested one (marked with a light bulb).

This first pass is only with auto checked items (the most conservative approach) The bacteria selected are shown below, while there was some duplicates between symptoms, there was significant independence:

• Acidobacteria Too Low
• Anaerovibrio Too High
• Anaerovibrio lipolyticus Too High
• Bacteroides cellulosilyticus Too High
• Bacteroides finegoldii Too High
• Bacteroides salanitronis Too High
• Bifidobacteriaceae Too Low
• Bifidobacteriales Too Low
• Bilophila Too High
• Bilophila wadsworthia Too High
• Candidatus Phytoplasma Too High
• Clostridium malenominatum Too Low
• Deinococcaceae Too High
• Deinococcales Too High
• Deinococcus Too High
• Lelliottia Too Low
• Lelliottia amnigena Too Low
• Mitsuokella Too High
• Oscillospira Too High
• Parabacteroides johnsonii Too High
• Rhodocyclaceae Too Low
• Sphingobacterium bambusae Too High
• Sutterella stercoricanis Too Low

I noted that many are atypical bacteria that I do not see usually in pub med studies.

Safest Takes is full of items that I often have seen on my own (and other ME/CFS results).

On the Safer Take, we find a regular pattern of 3 takes and 1 oppose.

The avoid list is relatively short and most are from a single suggestion (which suggests that it may be ignored). high red meat is the greatest avoid, with saturated fats variation being right behind.

Done with Secondary Suggestions

Since I have just implemented this feature, I am curious about it’s impact. The number of bacteria almost doubled with a variety. A lot of bacteria appeared multiple time.

• Absiella Too Low
• Acidobacteria Too Low
• Acidobacteriaceae Too Low
• Acidobacteriales Too Low
• Acidobacteriia Too Low
• Adlercreutzia Too Low
• Adlercreutzia equolifaciens Too Low
• Anaerovibrio Too High
• Anaerovibrio Too High
• Anaerovibrio lipolyticus Too High
• Bacteroides cellulosilyticus Too High
• Bacteroides finegoldii Too High
• Bacteroides salanitronis Too High
• Bacteroides vulgatus Too High
• Bifidobacteriales Too Low
• Bifidobacterium Too Low
• Bilophila Too High
• Bilophila wadsworthia Too High
• Blautia hansenii Too High
• Butyricimonas Too High
• Candidatus Phytoplasma Too High
• Clostridium malenominatum Too Low
• Collinsella intestinalis Too Low
• Coriobacteriia Too Low
• Deinococcaceae Too High
• Deinococcales Too High
• Deinococcus Too High
• Eubacterium dolichum Too Low
• Eubacterium oxidoreducens Too Low
• Finegoldia magna Too Low
• Hymenobacter Too High
• Lelliottia Too Low
• Lelliottia amnigena Too Low
• Leptospira Too Low
• Leptospiraceae Too Low
• Leptospirales Too Low
• Megasphaera Too Low
• Mitsuokella Too High
• Oscillospira Too High
• Parabacteroides johnsonii Too High
• Peptococcaceae Too High
• Porphyromonas Too High
• Pseudanabaenaceae Too High
• Pseudonocardiaceae Too Low
• Rhodocyclaceae Too Low
• Rickettsiaceae Too Low
• Rickettsieae Too Low
• Selenomonas artemidis Too Low
• Slackia Too High
• Sphingobacterium bambusae Too High
• Streptococcus thermophilus Too High
• Sutterella stercoricanis Too Low
• Synechococcaceae Too High
• Synechococcales Too High
• Veillonellaceae Too High
• Veillonellales Too High

As expected, the suggests are similar

The risk items are similar with saturated fats dominating

Bottom Line

Earlier today, I updated this post Ketogenic diet did not help a health issue, it created one where the person ended up with a ME/CFS like scenario. Many of these suggestions were very similar. The main items suggested are:

• Fibre
  • Inulin like items (chicory, Jerusalem artichoke, inulin)
  • Fruit and legume fiber
  • Barley, Oats
• Cacao (usually I suggest working up to 85% cacao or higher chocolate bars)
• Apple
• clostridium butyricum (probiotics)
• rosmarinus officinalis (rosemary)
• B Vitamins (classic CFS MD recommended supplements)
• Vitamin D
• Soy
• Human milk oligosaccharides (prebiotic, Holigos, Stachyose)

In general, I favor “intact” fiber and herbs. I have seen several studies that the intact had a greater impact than the extract. Watch out for saturated fats — for example Pork is on the to avoid list

The excel file download (CSV) had only 291 items, less than other samples that I processed. I attached it as an example.

My usual advice is to take two weeks to sort out (and in some cases slowly move up to) the suggestions that are picked. It is helpful to check my Supplement Dosage page. That page is not numbers that I picked out of the air, but dosages used in various clinical trials (thus the dosages are likely safe, and more important, are sufficient to cause a change). Then at least 4 weeks for the microbiome to stabilize, then retest to find out the new status quo that will need to be adjusted.

For myself, I did notice a pendulum swing in my series of samples — an item was a take, then the next sample it was an avoid, then it became a take again and stayed as a take. The path is not always straight!

This post was kick-started by a post to a study on a Spanish ME/CFS site shown below

• Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS–CoV-2 in vitro.Oba M, Rongduo W, Saito A, Okabayashi T, Yokota T, Yasuoka J, Sato Y, Nishifuji K, Wake H, Nibu Y, Mizutani T.Biochem Biophys Res Commun. 2021 Sep 17;570:21-25. doi: 10.1016/j.bbrc.2021.07.034. Epub 2021 Jul 13.
  “our study suggests that the putative serine-protease(s) in natto may impair the infectious function of BHV-1 and SARS-CoV-2, probably through the proteolysis of its glycoprotein D and the spike protein, respectively.”

This is extra relevant because Nattokinase is one of my personal favorite tools for dealing with hypo-perfusion (low oxygen to the brain), something that I have experienced during ME/CFS flares. It is also the subject of my last post. I have cited Nattokinase in prior posts, some 9 years ago, and it seems time to update what we know.

• Nattokinase – 2nd choice for fibrinolytics 2012
• Histamines and Anticoagulants – a review 2014
• Potentiators: Often the difference between success and failure 2019

So what more has been added to our knowledge base. Nattokinase comes from Bacillus Subtilis Natto. This strain has been traditionally used in a Japanese dessert called “Natto” which you can buy is some Asian shops – it is a bit of an acquired taste (but I like it)

• Fibrinolytic characteristics of Bacillus subtilis G8 isolated from natto.Pinontoan R, Elvina, Sanjaya A, Jo J.Biosci Microbiota Food Health. 2021;40(3):144-149. doi: 10.12938/bmfh.2020-071. Epub 2021 Feb 20.
  “Both nattokinase and B. subtilis G8 were able to dissolve both whole blood and euglobulin clots.” – important for COVID micro-clots.
• Data Recorded in Real Life Support the Safety of Nattokinase in Patients with Vascular Diseases.Gallelli G, Di Mizio G, Palleria C, Siniscalchi A, Rubino P, Muraca L, Cione E, Salerno M, De Sarro G, Gallelli L.Nutrients. 2021 Jun 13;13(6):2031. doi: 10.3390/nu13062031.
  “we can conclude that the use of nattokinase represents an efficient and safe treatment able to both prevent and treat patients with vascular diseases.”
• Breaking the vicious loop between inflammation, oxidative stress and coagulation, a novel anti-thrombus insight of nattokinase by inhibiting LPS-induced inflammation and oxidative stress.Wu H, Wang Y, Zhang Y, Xu F, Chen J, Duan L, Zhang T, Wang J, Zhang F.Redox Biol. 2020 May;32:101500. doi: 10.1016/j.redox.2020.101500. Epub 2020 Mar 11.
  “we extended the anti-thrombus mechanism of NK by demonstrating the anti-inflammatory and anti-oxidative stress effects of NK in ameliorating LPS-activated macrophage signaling and protecting against LPS-stimulated AKI as well as glomeruler thrombus … opening a comprehensive anti-thrombus strategy by breaking the vicious cycle between inflammation, oxidative stress and thrombosis.”
• The effects of nattokinase supplementation on collagen-epinephrine closure time, prothrombin time and activated partial thromboplastin time in nondiabetic and hypercholesterolemic subjects.Yoo HJ , Kim M , Kim M , Lee A , Jin C , Lee SP , Kim TS , Lee SH , Lee JH .Food Funct. 2019 May 22;10(5):2888-2893. doi: 10.1039/c8fo02324g.
• Nattokinase: A Promising Alternative in Prevention and Treatment of Cardiovascular Diseases.Chen H, McGowan EM, Ren N, Lal S, Nassif N, Shad-Kaneez F, Qu X, Lin Y.Biomark Insights. 2018 Jul 5;13:1177271918785130. doi: 10.1177/1177271918785130. eCollection 2018. – Note cardio issue arise in COVID and LONG COVID.
• [A clinical study on the effect of nattokinase on carotid artery atherosclerosis and hyperlipidaemia].Ren NN, Chen HJ, Li Y, Mcgowan GW, Lin YG.Zhonghua Yi Xue Za Zhi. 2017 Jul 11;97(26):2038-2042. doi: 10.3760/cma.j.issn.0376-2491.2017.26.005.
  “daily NK supplementation is an effective way to manage the progression of atherosclerosis and potentially may be a better alternative to statins which are commonly used to reduce atherosclerosis and further to prevent cardiovascular attack and stroke in patients.”
• Nattokinase: An Oral Antithrombotic Agent for the Prevention of Cardiovascular Disease.Weng Y, Yao J, Sparks S, Wang KY.Int J Mol Sci. 2017 Feb 28;18(3):523. doi: 10.3390/ijms18030523.
• Consumption of nattokinase is associated with reduced blood pressure and von Willebrand factor, a cardiovascular risk marker: results from a randomized, double-blind, placebo-controlled, multicenter North American clinical trial.Jensen GS, Lenninger M, Ero MP, Benson KF.Integr Blood Press Control. 2016 Oct 13;9:95-104. doi: 10.2147/IBPC.S99553. eCollection 2016.
• Antioxidation, angiotensin converting enzyme inhibition activity, nattokinase, and antihypertension of Bacillus subtilis (natto)-fermented pigeon pea.Lee BH, Lai YS, Wu SC.J Food Drug Anal. 2015 Dec;23(4):750-757. doi: 10.1016/j.jfda.2015.06.008. Epub 2015 Jul 29.
• A single-dose of oral nattokinase potentiates thrombolysis and anti-coagulation profiles.Kurosawa Y, Nirengi S, Homma T, Esaki K, Ohta M, Clark JF, Hamaoka T.Sci Rep. 2015 Jun 25;5:11601. doi: 10.1038/srep11601.
• Nattokinase improves blood flow by inhibiting platelet aggregation and thrombus formation.Jang JY, Kim TS, Cai J, Kim J, Kim Y, Shin K, Kim KS, Park SK, Lee SP, Choi EK, Rhee MH, Kim YB.Lab Anim Res. 2013 Dec;29(4):221-5. doi: 10.5625/lar.2013.29.4.221. Epub 2013 Dec 20.

Putting it together

Nattokinase seems to treat many conditions associated with western diet. The next question is simple, what are dosages used in studies?

• Oral nattokinase 2,000 fibrinolytic units daily [Nattokinase Atherothrombotic Prevention Study (NAPS)]
• nattokinase-mono formula (3500FU x 4 =14,000 FU) [Efficacy and Safety of Geneferm Nattokinase]
•  (100 mg) nattokinase/day [Effects of NSK-SD (Nattokinase) on Blood Pressure] [Nattokinase Supplementation and Hemostatic Factors]

Usually 100 mg = 2000 FU on most commercial products, so the range in trials is 1-7 100mg capsules per day.