• If we review genus as an ethnic groups, we find over 3,365+ groups – each distinctive
  • Species are the equivalent of small business, community groups – we have 10,567+
  • Strains could be viewed as the individuals.
  • Some strains (people) are criminals and some community leaders
• To understand what is happening in the cities, we need to get data / characteristics
  • What foods are sent to the city
  • What products are exported from the city
  • What are the sources of energy for the city
  • How may people come in or leave by ethnic groups
  • What type of waste is produced by the city
  • What types of crimes happen in the city

From this information, we may gain insight into how to administer and change the city.

All of the above, except for End Products(Obsolete). This information is obtained from lab studies cultivating bacteria. Data is really hit and miss.

All of the other statistics is done using gene data from KEGG: Kyoto Encyclopedia of Genes and Genomes. Once the bacteria has been sequenced, all of this information can be computed. This works for both bacteria that can be cultured and those (most) that cannot be cultured in a lab.

Where do you find this data on Microbiome Prescription?

Seeing changes between Samples

When you have multiple samples, this line will appear. Multiple Samples Comparison is the button

These reports are the same as above – except you have numbers from different samples side by side

What is the difference between Outliers and Full Report?

Outliers ( AKA out of range) gives you the ability to filter by percentile OR use the Kaltoft-Moldrup Limits

The full range gives a much larger list (often hundreds) with filtering limited to the Search box on the page.

Above is for an individual sample — so you are given a list of your samples and the page will automatically update when you change samples.

For the multiple sample compare, you have already selected the samples and cannot change them from the page. You can go back to the selection page and pick different samples.

For multiple sample outliers — if one sample has an outlier, then the values of other samples will also be shown. The outliers are color coded:

VIDEOS COMING

The reader provide the following history (shortened)

Person’s Narrative

Sample BiomeSight:2021-02-24 In addition to my usual CFS symptoms I had a lot of trouble with gastritis. I was taking Slippery Elm, Marshmallow root, DGL, melatonin, magnesium, probiotic Bio.me Femme UT. I mostly avoided other supplements due to gastric issues. When the results came back I was only able to eat a few foods, so I couldn’t really follow the suggestions. I decided to wait until my stomach got better and retest.

Sample BiomeSight:2021-08-23 Taken after I’ve been on PPIs for 3 months. I haven’t been eating dairy for months which decreased B. Wadsworthia somewhat. I ate a lot of soy milk and soy yogurt. Mostly gluten-free, but eating lots of oatmeal. The combination of PPIs and yogurt made Streptococcus Thermophilus very high. The supplements at the time were melatonin, magnesium, zinc carnosine, d3 & k2, vit A, Omega 3, probiotic Bio.me Femme UT, occasional Slippery Elm to calm the stomach.

After I got results back I started taking:
– Miyarisan (Kegg AI Computed Probiotics),
– glycine (Kegg AI Computed Supplements),
– inulin, burdock root, L. Rhamnosus, L.Reuterii, almonds, oregano tea (suggestions from Targeted bacteria based on symptom Impaired memory & concentration).
I alternated modifiers so I wasn’t taking all of them all of the time.

I stopped:
– vit A and Slippery Elm (suggestions from Targeted bacteria based on symptom Impaired memory & concentration)
– yogurt (high S. Thermophilus)- oatmeal (it seemed to cause hypoglycemia. Replaced with tsampa – roasted barley flour)

Interestingly, Kegg AI Computed Supplements at level <15% reported Iron and 6 weeks later I was found to be anemic. That was an excellent prediction! I wish I would have gone and tested my iron status right away.

Sample BiomeSight:2021-11-28 Still on PPIs. Taken one month after I started taking prescription iron pills and lactulose to help with resulting constipation. Still eating soy milk daily, but no dairy, no yogurt. Taking more supplements at this point.

Analysis

Reading the history, my first question is to see if the predicted shifts from doing PPI (Proton Pump Inhibitors) is reflected between samples. Keep in mind that there are other microbiome compounders (i.e. other eating pattern changes). To this end, I’ve created a new page where you can pick a before, after and a modifier.

What is interesting to note is that the impact diminished overtime (80 -> 65). This agrees with my base model that rotation and re-testing is essential.

We can do combinations, for example PPI and melatonin between first and second sample. We lack studies on combinations and thus have to resort to this experiential approach to see how well predictions agree with actuals.

At the bottom of the pages, you get the details:

If a substance did not cause more improvements(Agrees versus Differs), then they are possible items to drop. Remember, the suggestions are theoretical prediction looking at many hundreds of bacteria. This allows you to objectively measure whether they worked well for you! They will not work for every one because of differences in DNA, diet, gender, age etc. I spot checked items like Slippery Elm (46.8 Agrees, 27 Differs), Miyarisan (KEGG Suggestion) (40.8 Agrees, 15 Differs) and was pleased with the results.

Looking at the next Step

Above, we (to my delight) verify that the suggestions are causing changes in the predicted direction for this person (based on their microbiome samples). Looking at predicting symptoms, we had 72% correct for the top 11 items ( So where do we go from here? Remember, the goal is to focus on the bacteria that likely contributed the most to the dysfunction (often high ones)

• From KEGG, the best probiotic is Sun Wave Pharma/Bio Sun Instant, if it is available. It has several species suggested in it.
• Looking at KEGG Products out of range — 7 were too low and 190 were too high. We are looking at an overproduction scenario.

I looked thru the predicted symptoms bacteria and there were a lot of secondary matches(shown with a # but very few direct matches. When we moved on to KM outliers, we had 25 items listed — 2 families and 5 genus with these items of considerable note — both for high percentile and high numbers:

• (family) Oscillospiraceae – 99.8%ile -18%
• (genus) Streptococcus – 98%ile – 4.2%
• (genus) Phocaeicola – 99%ile – 3.6%

So I did a hand picked with just these more extreme values. I tossed in everything we had. No prescription items showed up on the to take, but many (and a few b-vitamins) showed up on the to avoid list.

In terms of typical ME/CFS, we found only two matches, both two high:  Bacteroides ovatus and Streptococcus. In terms of this small subset — only one item was above 0.29 — Human milk oligosaccharides (prebiotic, Holigos, Stachyose) with iron and B-12 being on the to take list.

We also note that the Unhealth Bacteria page, was full of Streptococcus

I tossed all of these into our hand-picked list and ask for new suggestions — the suggestions did not change expect for minor shifts of confidence.

Bottom Line

Two probiotics:  lactobacillus plantarum (probiotics) and the mixture Sun Wave Pharma/Bio Sun Instant. I see the recommendation leads to the same type of breakfast that is regular for me: Barley/Oats with inulin and wheat bran. For all of the items, make sure you check the dosage links (where available)

The Microbiome is like a city full for billions of bacteria (people).

• Some items produced in the city are consumed in the city – for example, Bakery products
• Some items are imported into the city – for example, Wheat to make bread
• Some items are exported from the city – for example, factory goods

Similarly there are compounds / chemicals in the microbiome. Some imports may be coming from food or cells in the body, products out to be going to cells or into urine, some products are consumed by other bacteria

The intent of this new page is to attempt to get estimates of these flows. These are crude estimates because they depend on two things — the bacteria species identified by the lab (different labs detect different species) and whether the full genes of each species is in KEGG.

The flow is simple as illustrated below

1. The Stool sample is sent to a lab
2. The lab process it and produces a data file (“Fastq”)
3. The lab runs it thru software that produces a list of bacteria and their count
4. We then take all of the species reported that are found in KEGG and compute the count of enzymes. We assume one bacteria produces one enzyme.
5. From the totals of each enzymes, we go back to KEGG to find what is consumed (Substrate) by the enzyme, and what is produced by the enzymes. Again, we assume 1 unit of compound is produced for 1 unit of enzyme.
6. We total all of the compound being produced and consumed.
7. We then get the distribution over all samples and compute a percentile value for each.

Needless to say, that is a lot of calculations — a lot!

The New Page

The page is under Component Analysis as shown below

When the page for a sample loads, you may be missing the percentiles. This is done because of the amount of calculation involved, it is not done automatically.

At the top of the page is a button, just click it and wait a little while and the percentiles will appear

Use the search button to find items that you are interested in, For example, in how much of D-Lactic and L-Lactic acid is being produced and consumed. High D-Lactic acid is associated with brain fog. Remember that comparison must be done with the same lab software identifying.

Bottom Line

This is likely a useful tool for tracking changes between samples. Go to it and add comments when you find interesting things.

This is similar to Kombucha, see my prior post from 2017 here. Every species (and strains) have different impacts and I prefer to reduce the risk of adverse outcomes.

“Similarly to milk-derived kefir, the exact microbial composition of kombucha cannot be given because it varies. “

 A Review on Kombucha Tea—Microbiology, Composition, Fermentation, Beneficial Effects, Toxicity, and Tea Fungus [2014]

Great good can come from Kefir, for example, the probiotic Lactobacillus Kefiri LKF01 (DSM 32079) LKEF. It was discovered after investigating dozens of different Kefirs. See this 2017 post on this probiotic.

Kefir can contain many different species and families — including [2008] [2021] [2015] [2011] [2006]

• Lactobacillus kefiri (occasionally)
• Lactobacillus  kefiranofaciens
• Leuconostoc mesenteroides 
• Lactococcus lactis 
• Liquorilactobacillus nagelii,
• Lentilactobacillus hilgardii/diolivorans
• Lacticaseibacillus casei/paracasei,
• Lactobacillus perolens,
• Lactobacillus parafarraginis,
• Lactobacillus diolivorans,
• Oenococcus oeni 
• Lactobacillus acidophilus,
• Streptococcus thermophilus, 
• Sphingobacterium

The grains used, the processes and environment, all contribute to variable outcomes.

Bottom Line

I have a strong bias in wanting to know precisely what bacteria are being taken. “Fermented drinks are good” is gospel for many…. for me, it is randomness… some people will do good and some will not – often dependent on the brand, or how it was fermented….. I am risk adverse…

Kefir grains could come salted with specific bacteria (to increase the odds) — but I would expect that the provider would provide information on the strains and links to the literature for each.

Comments

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 for other conditions. Many items listed have been reports in clinical studies to help a significant percentage of patients.

Items with a low bad impact and high good impact are likely the best to start with (i.e. Sumac(Rhus coriaria) , laminaria hyperborea( tangle/cuvie – seaweed)  thyme  (oil), coriander oil  , peppermint  oil). Many of these suggestions are similar to those for Chronic Fatigue Syndrome (Long COVID sibling). Suggestions for ME/CFS agreed with clinical studies results.

Reversion of Gut Microbiota during the Recovery Phase in Patients with Asymptomatic or Mild COVID-19: Longitudinal Study. Microorganisms (Microorganisms ) Vol: 9 Issue 6 Pages: Pub: 2021 Jun 7 Epub: 2021 Jun 7 Authors Kim HN , Joo EJ , Lee CW , Ahn KS , Kim HL , Park DI , Park SK , if(open==true){ } Summary Html Article Publication

The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort. Gut microbes (Gut Microbes ) Vol: 13 Issue 1 Pages: 1-15 Pub: 2021 Jan-Dec Epub: Authors Newsome RC , Gauthier J , Hernandez MC , Abraham GE , Robinson TO , Williams HB , Sloan M , Owings A , Laird H , Christian T , Pride Y , Wilson KJ , Hasan M , Parker A , Senitko M , Glover SC , Gharaibeh RZ , Jobin C , if(open==true){ } Summary Html Article Publication

Gut Microbiota May Not Be Fully Restored in Recovered COVID-19 Patients After 3-Month Recovery. Frontiers in nutrition (Front Nutr ) Vol: 8 Issue Pages: 638825 Pub: 2021 Epub: 2021 May 13 Authors Tian Y , Sun KY , Meng TQ , Ye Z , Guo SM , Li ZM , Xiong CL , Yin Y , Li HG , Zhou LQ , if(open==true){ } Summary Html Article Publication

Gut Microbiota Interplay With COVID-19 Reveals Links to Host Lipid Metabolism Among Middle Eastern Populations. Frontiers in microbiology (Front Microbiol ) Vol: 12 Issue Pages: 761067 Pub: 2021 Epub: 2021 Nov 5 Authors Al Bataineh MT , Henschel A , Mousa M , Daou M , Waasia F , Kannout H , Khalili M , Kayasseh MA , Alkhajeh A , Uddin M , Alkaabi N , Tay GK , Feng SF , Yousef AF , Alsafar HS , if(open==true){ } Summary Publication

Best prediction is done when using a 16s microbiome result for the patient

Net	Modifier2	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

The site also provide prescription suggestions with those below being the highest ranked.

This is a part of an ongoing series of posts that are intended for microbiome testing labs, or those interested in starting one. I am downstream from all of the microbiome labs and will gladly work with any of them — my main concern is making people better — not the financial bottom line.

This post looks at issues involved with selecting studies to use for giving suggestions to consumers of microbiome result. These are questions that I have looked at and have made my own choices (a.k.a. technically trade secrets).

Method of microbiome detection used

There are three main types, listed below. Do you restrict to only one? Do you give a weight to different methods, for example the values suggested after each below?

• Cultured Sample – Weight 0.1
• 16s Sample – Weight 0.8
• Metagenomics – Weight 1.0

For a discussion of the last two, see Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota [2021]

Life Form/non-form that the study was done on

We have a wide variety of “bacteria incubators” reported in studies, including

• Fish (Zebra fish especially)
• Animals – which ones? Horses, Dogs, Cats, Cows, Pigs etc
• Chemical Reactors simulating some living creature’s environment
• Humans
  • Which ethnic groups
  • Location that the study was done (a proxy for diet) — different results from Mexico and Japan!
  • Age — children, adults and the elderly have different responses
  • Medical conditions in the cohort

Do you do a binary include/exclude or do you apply a weight to each?

Quality of Study

The following are commonly used in evaluating studies:

• Read Beyond the Abstract – that means getting and reading the full study, including the appendix
• Determine Whether All Results Were Included
• Observational Study versus Randomized Controlled Trial
• Odds Ratios and Confidence Intervals
• Size of study

Do you give different weights based on the above? Some literature is below:

• Understanding and evaluating clinical trials
• A General Framework for the Evaluation of Clinical Trial Quality
• A Simple Method for Evaluating the Clinical Literature

Interpreting Studies

Different studies report things differently. For example some may report the % change of a bacteria average, others may provide the actual distribution, others may just report that the control or the cohort average was higher with (P < 0.5). It is like trying to buy gas – one person is offering it by the gallon in US$, another in litres in Euro, a third “sufficient fuel to drive 200 miles in a 1958 Land Rover” for 3 oz of silver.

Method of Aggregation

Some studies use the Hartung–Knapp–Sidik–Jonkman random effects model [2021] to combine results. Other studies use DerSimonian-Laird method (cited by Cochrane) or The generic inverse variance outcome type in RevMan.

Bottom Line

I have my own magic in combining a multitude of studies and resolving the many many issues cited above. I encourage labs to do their own resolutions and then let people compare results (if they are in agreement, everyone should be happy). The real test is whether the suggestions work. So far, for my own experience and for a reasonable number of people that have provided feedback – they have. The suggestions may not be perfect, but my goal is to give suggestions that are more likely to help.

The recent article Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome [2021] identifies upstream as a maintainer of SIBO. A response to this post was people asking what to do This is not news for me, I have written about this over the last 7 years.

• A mouth full – for better or worst [2014]
• Oral Probiotics [2015]
• Dealing with repopulation of bad bacteria [2016]
• Your mouth can trigger flares [2017]
• Probiotics for mouth, sinus and eyes [2019]
• Science based mouth wash for ME/CFS [2019]
• Beware of the additives applied to you mouth! [2019]

My short form would be to use Symbioflor-1 (to address sinus issues) and make sure that you rotate through different active ingredients in mouthwashes (and I would include my dad’s favorite: rinse your mouth with Scotch Whisky [or similar] – I will leave it to you if you spit out or not 🙂 ). I would suggest reading some of the above earlier posts.

A while back I built a bacteria to bacteria interaction model with rich results. With the addition of the anti-modifier page for professionals, my mind went over to finding probiotic interactions. This is based on the 2000+ microbiome samples uploaded. I have the basic results below

The more positive, the Impact number the more it helps the other species. A negative number indicates that it will reduce the other. Thus, you should not take Clostridium butyricum and Akkermansia muciniphila together. If you are trying to increase Bifidobacterium bifidum then take Arthrobacter (in Prescript-Assist®/SBO Probiotic) and/or Lactobacillus paracasei.

You may wish to check my retail probiotic page to find out which products contains different species.

Take This	To Increase This
Akkermansia muciniphila	Clostridium butyricum	-6
Arthrobacter	Bifidobacterium bifidum	21
Arthrobacter	Bifidobacterium catenulatum	4
Bifidobacterium adolescentis	Bifidobacterium bifidum	3
Bifidobacterium adolescentis	Bifidobacterium breve	7
Bifidobacterium adolescentis	Lactobacillus fermentum	8
Bifidobacterium adolescentis	Lactobacillus rhamnosus	3
Bifidobacterium bifidum	Arthrobacter	20
Bifidobacterium bifidum	Bifidobacterium adolescentis	3
Bifidobacterium bifidum	Bifidobacterium catenulatum	7
Bifidobacterium bifidum	Lactobacillus fermentum	8
Bifidobacterium bifidum	Lactobacillus paracasei	13
Bifidobacterium bifidum	Lactobacillus salivarius	4
Bifidobacterium bifidum	Lactococcus lactis	5
Bifidobacterium breve	Bifidobacterium adolescentis	4
Bifidobacterium breve	Bifidobacterium longum	13
Bifidobacterium breve	Lactobacillus crispatus	9
Bifidobacterium breve	Lactobacillus rhamnosus	6
Bifidobacterium catenulatum	Arthrobacter	5
Bifidobacterium catenulatum	Bifidobacterium bifidum	7
Bifidobacterium longum	Bifidobacterium breve	18
Bifidobacterium longum	Lactobacillus fermentum	3
Clostridium butyricum	Akkermansia muciniphila	-6
Lactobacillus crispatus	Bifidobacterium breve	12
Lactobacillus crispatus	Lactobacillus rhamnosus	7
Lactobacillus crispatus	Pediococcus	6
Lactobacillus fermentum	Bifidobacterium adolescentis	9
Lactobacillus fermentum	Bifidobacterium bifidum	8
Lactobacillus fermentum	Bifidobacterium longum	3
Lactobacillus paracasei	Bifidobacterium bifidum	12
Lactobacillus paracasei	Lactobacillus plantarum	4
Lactobacillus plantarum	Lactobacillus paracasei	3
Lactobacillus plantarum	Lactobacillus rhamnosus	3
Lactobacillus plantarum	Pediococcus	3
Lactobacillus rhamnosus	Bifidobacterium adolescentis	4
Lactobacillus rhamnosus	Bifidobacterium breve	6
Lactobacillus rhamnosus	Lactobacillus crispatus	9
Lactobacillus rhamnosus	Lactobacillus plantarum	5
Lactobacillus salivarius	Bifidobacterium bifidum	4
Lactobacillus salivarius	Pediococcus	5
Lactococcus lactis	Bifidobacterium bifidum	4
Leuconostoc mesenteroides	Pediococcus	3
Pediococcus	Lactobacillus crispatus	8
Pediococcus	Lactobacillus plantarum	4
Pediococcus	Lactobacillus salivarius	5
Pediococcus	Leuconostoc mesenteroides	4

This is a personal observation post and not my traditional aggregation of studies. Your experience may differ.

Known Sources:

• In US (does not ship outside at last query): https://pendulumlife.com/products/pendulum-akkermansia-3?view=akkermansia
• Outside of US: https://www.desertcart.ae/products/401266402-akkermansia-muciniphila-25-billion-cfu-p

Akkermansia Probiotic

This is available exclusively as Pendulum Akkermansia. We signed up for the subscription plan when it was first announced, and they have kept shipping at their low introductory price every month. Within I week of getting the first shipment, I read a few posts that “it did not persist”. Excuse me, the typical turnaround time for a microbiome test is 3-4 weeks. I suspect that someone is gas-lighting. Or, they may have been taking a hostile probiotic at the same time.

We subscribed to only one bottle and we decided that the wife would take it for the first two months (we rotate probiotics). The results were her Akkermansia muciniphila went from 4,530 to 64,920 (91%ile) — so, it appears to have persisted (or helped the native ones to prosper by creating a friendlier environment). I should point out that that the fact that she has some to start with may be a significant factor for this awesome increase (that is, the environment was not totally hostile).

She noticed some significant changes, to her the most significant one was a major improvement in sleep.

Kampo (Japanese Name)

This is also known as fang feng tong sheng san (Chinese: also may be named: Fang Feng Tong Sheng Pian (Fang Feng Tong Sheng Wan,  防风通圣片) – best names to use on Amazon) or Bofu-tsusho-san. A professional user of Microbiome Prescription reported a major increase of Akkermansia with his patients using this and forwarded two studies that illustrated this.

• Bofutsushosan improves gut barrier function with a bloom of Akkermansia muciniphila and improves glucose metabolism in mice with diet-induced obesity. [2020]
• Increase of Akkermansia muciniphila by a Diet Containing Japanese Traditional Medicine Bofutsushosan in a Mouse Model of Non-Alcoholic Fatty Liver Disease [2020]

So, what else does Kampo do?

• Bofutsushosan Significantly Ameliorated Betamethasone-Induced Cushing’s Syndrome [2018]
• Mechanisms for the anti-obesity actions of bofutsushosan in high-fat diet-fed obese mice. [2017]
• Effects of the oriental herbal medicine Bofu–tsusho–san in obesity hypertension: a multicenter, randomized, parallel-group controlled trial (ATH-D-14-01021.R2). [2015]

For additional studies, see pub-med.

Other Approaches

• Triggering Akkermansia with dietary polyphenols: A new weapon to combat the metabolic syndrome? [2016] cites:
  •  cranberry 
  • grapes (Reservatol)
• For additional items to help (or hurt) see this page (1400 items listed).

Current Experiment

As mentioned above, we rotate probiotics as a standard practice in our household. I am starting both the Akkermansia and Kampo and plan to do a new microbiome report in a month (so 2 months until this post gets updated). I expect a significant jump in my Akkermansia. At last test, it was 570 or 0.05% (via Biomesight), below the lower end of Dr. Jason Hawrelak Recommended ranges.

Results:

A 7 to 8 fold increase was seen after a month. The probiotic was stopped for a week before the sample was taken.

As an unintended side-effect, a lost of 7+ kilos over 7 weeks without changing diet (or dieting)!!! I have also taken high dosages of bifidobacterium infantis with it. It is known to encourage akkermansia too.

A user of my site that is active consulting on autism microbiome manipulation obtained permissions for me to do an analysis of one of his patients going through FMT. All of the microbiome testing was done via Biomesight (including the donor). This is specific type of data that I have been pleading to see if we can make predictive models of what could occur with FMT.

Measure	Prior	Donor	After
Taxonomy	374	406	550
Elusive	3	3	6
Rare	4	8	17
Sparse	12	15	33
Infrequent	28	37	68
Uncommon	66	89	145

I did analysis at the Species, Genus, Family, Order and Class level trying many many approaches. This summarize my key findings.

The second sample was done one month after the FMT. Patient was very good for a couple of days, then “the war started”. New more severe autism symptoms appeared.

Do NOT expect it to reduce overgrowths!

Looking at the lowest numbers of the recipient prior and the donor, we found that the post-FMT numbers had a clear pattern.

• At the Class level, 97% was higher than the lowest of the two, 58% was higher than the highest
• At the Order level, 96% was higher than the lowest of the two, 56% was higher than the highest
• At the Family level, 95% was higher than the lowest of the two, 61% was higher than the highest
• At the Genus level, 91% was higher than the lowest of the two, 51% was higher than the highest
• At the Species level, 94% was higher than the lowest of the two, 47% was higher than the highest

This was shocking — 50% of the bacteria will be higher than either the donor’s or recipient’s levels. Many people will assume that the levels will magically average the two levels. The reality seen here is that only 50% of the time will the new level be between these two levels and 50%of the time it will be higher than either. This is unlikely to be a preferred outcome.

Unexpected Disappearances

There were several items where both the recipient and the donor had bacteria, they were gone in the post-FMT sample! This was not expected, of special interest is that Lactobacillus was wiped out.

• Order: Puniceicoccales
• Family: Clostridiales Family XVI. Incertae Sedis
• Family: Lactobacillaceae
• Family: Puniceicoccaceae
• Genus: Alkalibacterium
• Genus: Butyricimonas
• Genus: Carboxydocella
• Genus: Catonella
• Genus: Lactobacillus
• Genus: Macrococcus
• Genus: Pelagicoccus
• Genus: Turicibacter
• Species: lingnae
• Species: Streptococcus oralis
• Species: Veillonella parvula
• Species: Streptococcus pseudopneumoniae
• Species: Carboxydocella ferrireducens
• Species: Sutterella wadsworthensis
• Species: Catonella morbi

Many New Kids showed up!

These are bacteria not seen in the recipient prior nor the donor sample

• Class Level: Acidobacteria, Calditrichae,Chitinophagia,Flavobacteriia,Ktedonobacteria,
• Order Level: Acidobacteriales, Calditrichales, Caulobacterales, Chitinophagales, Chroococcales, Desulfobacterales, Flavobacteriales, Kiloniellales, Nostocales, Oscillatoriales, Rhodocyclales, Rickettsiales, Streptosporangiales, Synechococcales, Syntrophobacterales, Thermogemmatisporales,
• Family Level: Acetobacteraceae, Acidobacteriaceae, Anaplasmataceae, Calditrichaceae, Caulobacteraceae, Chitinophagaceae, Chroococcaceae, Clostridiales Family XII. Incertae Sedis, Cyanobacteriaceae, Cytophagaceae, Desulfobacteraceae, Dysgonamonadaceae, Flavobacteriaceae, Fusobacteriaceae, Hymenobacteraceae, Kiloniellaceae, Listeriaceae, Nostocaceae, Oceanospirillaceae, Oscillatoriaceae, Oxalobacteraceae, Prevotellaceae, Pseudanabaenaceae, Rhodanobacteraceae, Rhodocyclaceae, Rickettsiaceae, Rivulariaceae, Streptosporangiaceae, Synechococcaceae, Syntrophobacteraceae, Thermogemmatisporaceae, Thiotrichaceae, Verrucomicrobiaceae,
• Genus Level: Acholeplasma, Acidaminobacter, Aminobacterium, Ammonifex, Anoxybacillus, Asticcacaulis, Bilophila, Caldithrix, Calothrix, Catenibacterium, Chroococcus, Cyanobacterium, Desulfofrigus, Desulfosporosinus, Dokdonella, Dysgonomonas, Edaphobacter, Ehrlichia, Emticicia, Escherichia, Fusibacter, Fusobacterium, Gillisia, Haemophilus, Insolitispirillum, Kushneria, Listeria, Luteibacter, Lysinibacillus, Marinospirillum, Microbacterium, Neisseria, Niastella, Novispirillum, Oleomonas, Olivibacter, Oscillatoria, Parapedobacter, Paraprevotella, Pelotomaculum, Pontibacter, Ralstonia, Rickettsia, Roseomonas, Sarcina, Sebaldella, Skermanella, Tepidanaerobacter, Tepidimicrobium, Thalassospira, Thermoanaerobacter, Thermogemmatispora, Thiothrix,
• I will skip the species level…

Bottom line is that the microbiome has become much more diverse

Recent FMT aspects

FMT destabilizes the microbiome, there are “strain riots” in the guts. We can see this with all of the “New Kids” showing up because the existing occupants are busy dealing with each other. This can be seen by the post microbiome having a lot more taxonomical items (550 vs 374 before – a 47% increase), The microbiome, over time, will downsize and stabilize with a new normal. During this period, you want to entrench your desired items by feeding it the right things and avoiding the wrong thing.

Personally, I would suggest a new sample every 6 weeks to monitor the stabilization.

Is FMT Worth the Risk?

FMT is effectively an organ transplant. Like organ transplants, there are significant risks of rejection and no way to undo it once it happens. From correspondence with many people who have tried it for ME/CFS, my feelings are that it is not a magic bullet. It is closer to playing Russian roulette, but with 5 of the 6 bullet chambers having bullets in the chambers.

I just spent 90 minutes zooming to the consultant involved with this autistic child. We both agreed that FMT for autistic children is not a wise course. The consultant is scratching their head on what to help this child recover from this situation.

Some prior posts on FMT

• Fecal Matter Transplant for ME/CFS – 2021
• A case study of a fecal transplant for CFS [2018]
• Current State of Fecal Matter Transplants [2018]
• uBiomes before and after a Fecal Microbiota Transplant [2017] (no donor microbiome available)
• Fecal Microbiota Transplantation (FMT) [2016]
• Fecal Transplants – not for the herx adverse! [2016]
• Review: The poop on Fecal Transplants [2014]