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]

If you are dehydrated you will typically see a change of stools. Seeing hard pebbles and dry stools is a logical consequence of the body rationing water. Recently, we got a new smart scale ($30 on Amazon) that comes with a smart phone app and does multiple measures, including hydration. I have been running below the desired range, so I am busy hydrating with Gerolsteiner Mineral Water (from Traders Joe) etc.

Conceptually, the availability of water should impact the microbiome. So tonight I started to search out studies to confirm my speculation.

Effect of Increased Daily Water Intake and Hydration on Health in Japanese Adults, 2020

There were five out of the 108 types of intestinal bacterium at the genus level that showed significant differences within and between groups due to water supplementation, and 17 out of 564 species identified by the homology search of OTU representative sequences in the DDBJ 16S database showed the same behavior… Of these, a slight correlation was seen in the intervention group between changes in blood pressure and changes in the Psudoflavonifractor capillosus bacterial count (R = 0.42) Kineothrix sp. (R = 0.36), Feacalibacterium prausnitzii (R = 0.38), and Ruminococcaceae (R = 0.34) showed weak correlations between changes in body temperature and changes in bacterial count

Some related studies that implies impact on the microbiome but failed to do microbiome analysis with the study

• Mild dehydration affects mood in healthy young women, 2011
• Mild dehydration impairs cognitive performance and mood of men. [2011]
• Influence of progressive fluid restriction on mood and physiological markers of dehydration in women. [2013]
• The effect of the consumption of water on the memory and attention of children. [2009]

Dehydration is often reported as a contributor to various conditions

• Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Diagnosis and Management in Young People: A Primer [2017]

Bottom Line

Hydration is an often overlooked aspect of improving the microbiome. It has impacts on blood pressure, body temperature, mood and cognitive ability. While we have few studies on it’s microbiome impact, we can likely assume safely that improved hydration will improve the microbiome. It should not be left to a “I drink enough water, I do not feel dehydrated”, but with actual measurements. Improving it is actually a slow process — my goal is to shift from my current level below, to at least 55%.

I just pushed an update that included features requested by a reader. The main items are:

• Ability to enter symptoms when you do a test (“Pending Sample”)
• Ability to copy symptoms from one sample to another
• Ability to delete all symptoms for a sample with one click
• Generation of a short list of possible symptoms from your bacteria

All of these options are shown for each sample via the dropdown:

Entering Symptoms

This has had one minor change, a new choice appears, “Pending Sample”. It allows you to enter symptoms when you do the sample (instead of trying to remember them 4 weeks later). Also two buttons are added to make status easier. Remember to use the Search box to filter

Quick Symptoms Additions

This takes your forecast symptoms with sufficient significance, removes any symptoms already entered, then show symptoms to consider.

If you check a few and click [Add]

These items will disappear from this list.

Symptoms Management

This allows you to copy symptoms between samples (for example, the same sample may be processed by multiple labs). Just select the sample you wish to copy from and click [Copy]

If you realized that you made a mistake, you do not have to uncheck item by item. you can single click all of the items.

Addendum

The algorithm for predicting symptoms has been revised (hopefully improved). There may be a further change, have some complex modelling to add. Also the ability to change from sample to sample has been added