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.
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]
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.
Using BiomeSight algorithm on FASTQ fileUsing Ombre algorithm on FASTQ file
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,
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.
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.
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
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
using SearchClicking [Show All Items]
Clicking [Show Picked Items]
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
A reader mentioned getting scheduled for one. Coincidentally, a week ago, I had a natural clearing out of the bowels (source unknown). I suspect that both scenario may produce the same opportunity to do some restructuring.
The first item to be aware of, gravity, bacteria further up the flow will repopulate (for better or worst). For myself, once it became clear that the bowels were being deeply emptied, I loaded up on herbs that impact many of the bad bacteria for a day (several capsules of each, several times a day).
The rationale was to thin out the bacteria that are up-channel.
I then started to repopulate, the first item, an E.Coli probiotic, symbioflor 2 e.coli probiotics, stopped the natural clearing within 2 hrs (not surprising given what made Mutaflor, the alternative E.Coli probiotic, famous back in 1918). I then proceeded to load up on only probiotics that are known to persist (see thus post, Studies on Probiotic Persistence). For myself, I noticed some improvements (but really I do not have much wrong to improve).
Long ago we changed over to making our own pills/capsules using Organic Bulk Purchases. It has the following benefits:
Much lower cost per capsules
It is organic ingredients
Often you can also make tea from it (depends if it is powdered or not)
No fillers or creative mixology from brands.
A few examples
454 g for $16, versus 41 g for $15 as retail capsules220 g for $7 versus 90 g for $19.00 as prepared capsules
One Readers Feedback
The experiment was an abject failure, unfortunately. I cleared the bowels and took no action the day of colonoscopy (Monday), other than to eat a dinner that included some fermentable fiber veggies. The next day (Tuesday) I took the baby scoop of Custom Probiotics D Lactate Free, which includes l rhamnosus. Continued eating meats and fermentable fiber veggies, introducing some shitaakes. SIBO symptoms roared back with a vengeance that seemed almost too fast to be possible. By Tuesday night I had gross SIBO burps and an upset tummy. Wednesday I took a heaping baby spoonful of d-lactate free probiotics and suffered even more upset. By Thursday I forewent the probiotics but continued eating fermentable fibers, with a violent, burning, smelly bowel clearing that evening. I also became uncharacteristically emotionally reactive.
Felt better Friday and switched to non-fermentable fibers. I had an mHBOT session that typically “resets” me, but after a low-fermentable fiber dinner, I got hit with a wave of brain fog I haven’t had for some time since doing rifaximin in Sept, continuing HBOT, and taking continued boswellia and Atrantil. I fogged out again after my morning Americano today, which is usually fine. Having unhappy poops again. A bit frustrated—I seem to have sent myself in the wrong direction and don’t totally understand why. I’ll add theanine for mast-cell control and start neem. Considering a rifaximin round. One theory—I have high mycophenolic acid in urine, and noted rats without microbiome do better when inundated with mycophenolic acid. Wonder if this is an angle to explore. Anyway! I thought you may be interested in the results—hope this wasn’t an overshare! I figure we’re all learning together.
My comment: It is clear that the clearing set things up for a change – unfortunately, it went in the wrong direction. One of the items that I cited, “load up on only probiotics that are known to persist (see thus post, Studies on Probiotic Persistence).” was not done — Custom Probiotics D Lactate Free is not known to persist.
These are often asked for with people often running off old research. Often the research is based on seeing an increase of one of these when a specific bacteria increase… hence. this bacteria must be producing it! This was the best that we could do from old, last millennium technology and lab tests. We have enter a new world that is summarized on Kyoto Encyclopedia of Genes and Genomes. Instead of measuring substances (never with a pure culture of a specific bacteria), we can look at the gene in each bacteria and what they produce. In other words, we can get more accurate information that is truly bacteria specific.
https://www.kegg.jp/entry/C00388
These pages list the enzymes that produces it, for example 1.4.3.222.1.1.8 2.3.1.- 4.1.1.22 6.3.2.18. We can then look to see if the enzyme consumes (substrate) or produces it.
https://www.kegg.jp/entry/2.1.1.8 This CONSUMES histaminehttps://www.kegg.jp/entry/4.1.1.22 this PRODUCES histamine
Then it is just a matter of looking up which bacteria has these enzymes!
Unfortunately, no lab detects all of these strains and often report “unknown Species in Some Genus“. I have seen that being as high as 45% not being identified in some samples. A work around is to look at the genus numbers — which are usually pretty complete for most labs. This is a two sided coin, because some members of a genus may be a producer and some may not be. We do not know the ratio for a genus between these two. This approach will identify potential candidates, but not definite candidates… more fuzzy logic.
All of this information is freely available on Kyoto Encyclopedia of Genes and Genomes, it just take diligence to extract and assemble it. If you see items on a labs reporting that is NOT on these lists, challenge the lab to produce evidence. I suspect most labs will produce studies with circumstantial evidence only, “because crime goes up when this ethnic group moves in — it must be that ethnic group” — ignoring that a different ethnic group may be behind it. An example of a drug problem in one city at one time. Most of the drug dealers were African-Americans, but the importers were Vietnamese. With KEGG, we are looking for the fingerprints on the gun or drug packages intercepted,
Back story-long history of gut issues/IBS.Terrible time post partum 22 years ago with sleep issues and mental health. I’ve been down the hell hole of modern medicine on all kinds of meds for years. Finally diagnosed with SIBO in 2019 and then no luck with treatment. More recently had bad reaction to high doses of Vitamin D-gut issues worse- total body pain, inflammation, food intolerances, terrible insomnia. I will add-horrific constipation not resolved unless I take herbal formulas [Microbe Formulas Bowel Mover and Dr. Christophers Lower Bowel Formula. I try to rotate. No specific order. I do think the garlic in the Microbe formulas does help.]
I am going to do layers of suggestion and see what evolves. We start with Dr. Jason Hawrelak criteria for a healthy gut. We find a lot of issues as shown below
The key suggestions computed by the AI are shown below. We will add more suggestions and end up with a consensus report joining all of these set of suggestions into a single report
A second approach is not to limit to a few key items, instead look for odd items across all bacteria. We use Kaltoft-Moltrup Ranges and get the following bacteria being identified:
Our third pass, is using US National Library of Medicine studies that identify certain bacteria associated with IBS. We will use IBS but widen the criteria used to extreme 6%. Some of the bacteria are cited above, and some are new.
Unfortunately the information we have for this is very limited.
Going back to US National Library of Medicine for SIBO, we get NO BACTERIA matches at all. My conclusion is that it may be atypical SIBO.
At this point, I want to check some specific items that she cited. There is a tool for that
For Vitamin D, we appear to have adverse effects
Categoric Sum:1
Categoric Average:0.1
Log(Count) Sum:-8.4
Log(Count) Avg:-0.6
For Garlic, we have a definite positive effect
Categoric Sum:3
Categoric Average:0.3
Log(Count) Sum:7.4
Log(Count) Avg:0.8
These predictions are solely from the microbiome and agree with what she has experienced.
Some Predictions
Above tested two substances that had been tried and the prediction appear to agreed with her experience. She asked about an items she was planning to take or recently started.
lactoferrin – which does not match any item, I selected iron and the results suggested that it will not improve matters. This looks at all undesired shifts.
Categoric Sum:0
Categoric Average:0
Log(Count) Sum:-10
Log(Count) Avg:-0.8
I also check the merge consensus report (see bottom) where we are selecting only the bacteria of concern. It is also an avoid
Consensus Report
Each of the above list of suggestions are stored on the server (for 24 hours) and we can see all of them together.
Our top suggestions (i.e. items that moves everything above in the right direction without exceptions)
Safest Takes
The complete list is below for the person to explore in more details. There are 400+ items that have good or bad impact.
As always, this is produced from a computer AI model and not clinical experience. Before any change is done, it should be discussed with your medical professional. Some items, like 1000 mg of niacin per day may require testing (see this summary on niacin from the National Institute of Health)
Mold and Lyme Markers
Lyme is always a fuzzy area –if the person had ever had EBV and their microbiome is off, then false positives are well reported in the literature.
Mold SensitivityLyme associated
The suggestions are shown below, there are a few matches with the above
I did a side by side comparison and found that there was a lot of disagreement between the sets of suggestions. That is not unexpected, because the bacteria selected determines the suggestions.
My gut feeling is that the IBS/SIBO is the preferred one — the citizen science did not have a single item auto checked, I had to go with the secondary items 💡 to get suggestions. This implies a weak match. Second, the IBS/SIBO included the gold standard bacteria identified from formal clinical studies. In short, likely better quality of information.
For those that are interested in how I created the above comparison, see this video — just change the URL to Source and enter a name in the column before pasting between sheets.
I am living with LongCOVID following infection in March / April 2020. I contracted COVID-19 in the workplace, employed as a pharmacist at an NHS hospital in South Wales, U.K.
I shared my story with WalesOnline at the latter stages of 2020 due to the lack of awareness around LongCOVID, and I share with you below for your interest.
Unfortunately, I am still troubled by GI symptoms and despite improving over the past few months, I’m still having difficulty with bowel urgency / diarrhoea and mild abdominal pain. I lost 10kg in 10 weeks between July – Sept. 2020 (72kg at my lowest); thankfully this has recovered and I have gained weight, albeit chubbiness, weighing 88kg last week. I was diagnosed at the start of 2021 with ‘post-viral IBS’ and ‘leaky gut syndrome’, but GI clinicians are at a loss of how to proceed with my symptoms, hence my purchase of the BiomeSight kit. I have tried numerous diets (FODMAP, dairy-, gluten-free), again, to no avail.
I approach my 20th month since first being infected and I am still quite a distance from where I was pre-COVID doing all I possibly can to recover, so I would be extremely grateful for your insight, not only to help myself, but others in a similar situation.
Approach #1
As we have two microbiome profiles for COVID from the US Nation Library of Medicine, I will apply each one using 6%ile filter (values in the top or bottom 6%ile) to get a feel for the ground work. Then I will apply the ME/CFS for a third one (because of the similarity of Long COVID and ME/CFS).
For those not familiar with selecting
We end up with a short lists of bacteria (the titles links to the bacteria and studies reporting these shifts)
Almost everything is too low. Rather than examining suggestions from each of them, I will go directly to the consensus report. We hit a surprising 108 items on the safest take (items that will not shift any of the above in the wrong direction). Most are recommended in each case (Take Count = 3)
Safest Take
A few quick notes: Apples are very rich in pectin (some studies used apples and other pectin — I always try to keep data as reported and not do ‘well it’s just like…’ simplification). Similar with inulin and chicory.
The Safer text (some pro and some con) list was short and a bit of a mixed bag. With 108 items on safest, I would tend to ignore these. No need to include them.
On the avoid list we have “magnesium deficient diet” — which usually translates to magnesium rich or supplements.
I attach the complete list below of 304 different items.
This person is a pharmacist and thus looking at off-label drugs may be interesting for him to review. There are no accepted drugs for Long COVID, however, for ME/CFS often the top off-label drugs have often been used (with good results) by ME/CFS specialist (often at risk of professional censure). I have also added in CFS/ME with IBS (only Bacteroides Low was a match), and IBS to the consensus report.
The Criteria Selection being tried
Bacteria selected from IBS
The number of drugs that could influence these bacteria (good or bad) was almost 1300. I included some non prescription items to serve as a reference point (i.e. do drugs do better than some alternatives). In the small list of antibiotics at the top, I see several of the works for ME/CFS antibiotics — especially, those used by Cecile Jadin, MD: Tetracyclines, macrolides. Jadin does antibiotic rotation: 10 days on and 20 days off, then change to the next antibiotic. I have seen a few PubMed studies finding rotation was superior.
Above we worked on diagnosis, we are now going to switch to symptoms. My experience is that symptom-to-bacteria associations are much stronger than diagnosis to bacteria. Mileage will vary.
Oh have I mentioned that the symptom prediction from bacteria matches my symptoms almost completely? I think it’s 17 out of 20. Pretty incredible.
From a user in Europe by email on 11/11/2021
Below are his reported symptoms against predicted symptoms. It is interesting that many several predicted symptoms are autism related (which he does not have). This approach uses the bacteria that citizen science has associated to the symptoms (instead of clinical studies to the diagnosis). In theory, it will often be more sensitive for identifying the bacteria of concern.
See the video for how we do this. The final suggestions in Excel/csv format is below
The intent of Microbiome Prescription site is to improve the odds of helping by working off studies on the US National Library of Medicines (at present, there are almost 6000 articles that we were able to harvest information from). We are very open on the where we get data, for example – for where we get the list of bacteria associated with a condition
From https://microbiomeprescription.com/citations/PubMedCitations?Code=LCV
And sources for how we know that something changes bacteria populations. In this case because of the high number of studies on inulin it will receive a high weight if certain bacteria are being targeted.
Example of what inulin impacts
We also try keeping faithful to the term used in the studies — apple contains large amounts of pectin, while some would just combined these to pectin (or apples), we attempt to keep the fine details. One related area that needs calling out is studies using items like luteolin (flavonoid). If you click on these, you will go to a summary page with a link to foods containing it
We have a list of foods and amounts that contain it. It’s an extra step, but since these foods were not cited in the study, we “keep religion” and only cite what was used.
I am not licensed medically, and thus there is no clinical experience (or bias) for the suggestions. It is an uber-logical model.
With that said, this person needs to sit down with his significant other, look thru the lists and decide which options they wish to try. Being a trained pharmacist means that he can also evaluate the prescription options for risk and in some cases, try to game the system… for example: Atorvastatin … he may want to test for the conditions where it would be prescribed, if he is a little high — he may wish to use that as a “standard of care” rationale for getting a prescription — it’s an off label use (like Viagra was not intended for what it is prescribed for today).
As always, any planned action should be reviewed by their knowledgeable medical professional before starting.
Before COVID, you had a unique microbiome, COVID “infection formed” it to suit its needs. These changes caused symptoms, made it easier for secondary infection and allow “alternative community of bacteria” to become established. How it changed depends on what it was like before and which variant of the virus. While the above suggestions are likely similar to what your suggestions could be, it is really important to get your own microbiome sample to work from. There will be large differences between people. With this approach, we can be single person specific for a treatment plan.
P.S. This sample was done via Biomesight, a UK based firm
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