A reader in Europe asked about this. I know it is a popular topic. So, I searched PubMed for the known biofilm forming bacteria and will be adding percentile ranking by labs in the coming days.
Raw Count Chart
As you can see below — a lot of people have ZERO of these bacteria. Other people may have 25% of their microbiome containing them. IMHO, influencers have seized on this concept as a “boogey man” for every one; it is not.
Transforming the data to get a Kaltoft-Møldrup estimator of the point of concern, we get a count of 565/million or 0.0565% being the threshold that action is strongly suggested. That is, with 85% of samples, it does not appear to be a significant issue. For 15%, it is
Stay tune. It will be added to the health analysis page with suggestions annotated with possible biofilm breakers for people exceeding 80%ile.
I have a longstanding history with ME/CFS from 2006 – diagnosed with EBV at the time
The primary concerns are: fatigue, PEM, brain fog, exacerbation of symptoms prior to menstrual cycle (PMDD), ADHD, POTS (improving), anxiety, PCOS. The fatigue and PEM is the main concern. Many other symptoms recently improved.
I’m currently taking L. rhamnosus, D-ribose, methylated B-complex, berberine, maitake, magnesium citrate, copper niacin and started myo-inositol after submitting the sample. I was also taking saccharomyces boulardii for weeks leading up to the sample collection. I’ve discontinued it since then. I would like to change my diet in general, but first want to see what’s recommended. Also particularly unsure about oxalates and whether or not to continue the maitake mushroom. I’m also curious to try oxaloacetate,
Interestingly enough, I had rather extreme vaginal discharge and discomfort for many months, which completely went away within a couple of weeks of using a probiotic mix. I stopped this probiotic (it had 7 strains, I believe) and the discharge has not returned, although fatigue is worse (but other things also changed).
Analysis
The graphic overview is shown below. There are clearly a group of bacteria that are overgrown (70-89%ile) and other bacteria that rarely have token representations (0 -29%ile). This does not identify the bacteria but identifies misrepresentations (thus dysbiosis)
Looking at General Health Predictors, we see 12 items of concern, higher than seen in most reviews. Both Oxalate degrading and Oxalate producing at below 1%ile. Dr. Jason Hawrelak criteria came in at 78%ile
We have quite a number of bacteria strongly statistically associated symptoms and others associated with with health risks.
Going Forward
Where there are many issues wrong, I do not attempt to work bacteria by bacteria — instead, I trust the expert system to consider and balance all of the factors in a consistent and logical method. This is especially with the revised algorithm (see Algorithm for “Just Give Me Suggestions” with symptoms) . It inherited included items that in the past I have done as extra suggestions.
I have recently added new option to make the analysis simpler.
Items to Take
Today, I am working on several other posts from ME/CFS and the suggestions here are very similar to those suggestions (just different orders). Spices and herbs can be done as capsules, teas, oils or just putting on food.
Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.
By old school, I mean what was reported to help most people on the ancient egroup list CFSFMExperimental. Namely:
Whey (non-denatured was thought the best)
B-Vitamins
Bidifobacteria probiotics (little Lactobacillus)
For all items, I would suggest checking for sufficient therapeutic dosages here. The dosages on bottoms usually are maintenance and insufficient to be therapeutic. Example: Neem at 120mg/day which is 3 “00” capsules per day (just measured it!). Garlic is 4 grams per day – typically 4 commercial 1000mg capsules per day (double or more of the dosages on bottles). As you can see below, recommended dosages may be just 1/3 of that.
My general rule of thumb is 1 “00” capsule with each meal for most herbs. We make our own capsules using organic powders without fillers. Cheaper and better quality than commercial pills.
Remember, with herbs and probiotics you do not want to take the same one continuously. Take each set for 1-2 weeks and then rotate to another. For example
You should check each to see if they have adverse effect on whatever probiotics you may take concurrently. For example Shen Ling Bai Zhu San and rosa rugosa both are reported to increase Bifidobacterium — so taking Bifidobacterium with them is fine.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
There’s one thing I which caused some bewilderment though, I put the screenshots from the recommendations from Biomesight here below, and I don’t understand why they seem quite divergent to what you are suggesting. I don’t know if it’s just my amateur eyes and then not so divergent after all, but to me they do seem quite different (apart from the lactobacilli). Shall I just ignore their suggestions ( also food wise) or would you say by and large it goes into the right direction?
Reader, May 23,2024
The answer depends on the logic each provider uses, which bacteria are in their microscope that needs changes, depth of their research and their skills in addressing contradictory results. I will look at three providers below:
Hovering over the item will show the bacteria believed to be impacted
Clicking on the name will show details. Note that the bacteria shown is correct. The link also shows “Galactooligosaccharides (GOS)” and notthe food suggested explicitly. The food selected contains GOS but none of the studies are explicitly for Beetroot. To MP, the beetroot contains multiple compounds, some may have overpowering negative effects — hence MP keeps to precisely what is cited in the study.
My inferred take-away from looking at the suggestions
Foods and substances are done by association and inference
This is from an early draft. They are using the database of Microbiome Prescription but with a set of proprietary rules, custom ranges, and algorithms. They restrict their scope to a few dozen genus. For the bacteria in their scope, MP has no contraindicated data and do not use inferences to parent or child taxa. That is, there is no need for balance algorithms. In short, it is a proprietary suggestion system designed.
Microbiome Prescription
For details on which bacteria are selected, see Algorithm for “Just Give Me Suggestions”. Typically we have an average of 65 bacteria under our microscope with 600 on some shotgun samples. Roughly 20-30% of the bacteria identified.
Now for every suggestion we make available the list of studies (137 for this probiotic suggestion). Note in the study names — that this probiotic is explicitly named.
We also include the negative effects
We have our own proprietary algorithm on how to evaluate this data. People can take this data and apply their own logic.
MP’s goal is to be the most comprehensive source with new studies adding every week. We have also been delighted that the startup (who I have been doing pro-bono consultation with) have set a team of their M.Sc. (or higher) staff on checking the citations. They have been finding a very low bad entry rate ( < 1%) but discarding 8% of studies for diverse reasons. The startup criteria (no contradictory results from different studies) often result in only 10% of available studies being used.
Bacteria Selected Determine Suggestions
Microbiome Prescription does NOT know what is the best method of picking bacteria to focus on. The Simple UI gives THREE different approaches.
Novice works on anything out of range – often including harmless bacteria in the calculation.
Beginner – Symptoms: Works off patterns of bacteria associated to user reported symptoms that are statistically significant
Beginner-Diagnosis: Bacteria shifts reported associated to diagnosis in published studies.
It is possible that the bacteria selected by each of these method will have no overlap. IMHO, Beginner – Symptoms is the most likely to be correct. THE BACTERIA SELECTED DETERMINE THE SUGGESTIONS.
For more advance users, there are a lot more (84x) methods of picking bacteria:
Regardless of method, if you go to Consensus Report
You will see PubMed with stacks of books under it. Just click on the books
This shows the studies used and the logic
Best practice is to always save the page as a PDF and the Consensus View as a CSV. Often people will come back later and see different suggestions because they selected a different method of picking bacteria. One other factor is that data is added weekly to the database which will cause shifts over time.
Bottom Line
What is the scope of their microbiome scope? IMHO: the bigger the scope, the better the results
Is the data based on explicit studies or on interference (A contain X and X helps — we’ll ignore B,C,D that is also in X)
BEWARE of sites that do not provide explicit studies – often they are working from hearsay.
Does the suggestion consider contraindicated information?
How big a database are they using? Have there been third party checking of the database?
Suggestions may be reasonable: a professional dietician would likely do the same logic in the case of BiomeSight suggestions.
Questions
Since Startup and Microbiome Prescription use the same database, will suggestions always agree?
No, for several reasons:
The bacteria in-scope-to-change are different. If MP picks one that Startup does not, then suggestions may shift for some substances. Startup computes its own definitions of what is high and low. They also look at a handful of genus only.
Startup hand select certain studies to be excluded or lessen in values. Studies may be on human, animals or a lab situation (petri dish) – they wanted to weight the value of each study different from MP.
What should I do if there are explicit disagreements?
The safest path is to do only things that there is agreement on.
If another item interests you, review the studies cited to make a decision.
I had no gut problems and only minor health niggles before Covid. I have been hypothyroid for 20 years.
After three rounds of covid (but no vaccines) I have burning and tingling parasthesias in my extremities, neuropathy in my face, plus gut pain, lots of hair loss, and I feel cold a lot and sleep poorly. Some fatigue and shortness of breath, but the other symptoms are much worse.
Trying to increase my bifido and lactobacillus via suggestions on biomesight has barely moved the needle.
All my blood tests work has been normal from a year ago, although now I have a weakly postiive ANA test result.
Analysis
We have 2 samples: 2023-11-20 and 2024-04-26. Both samples are very similar.
High Level Overview
“Leaked” from Oral Cavity: By volume 77%ile, prior 70%ile
General Health Predictors: 10 out of range, prior 11 out of range.
Looking at the “smoking gun”, Pedobacter, we found no known factors to reduce it 🙁
Quick Summary; Past action plan has “barely moved the needle.”
Going Forward
The usual “just give me suggestions” with one addition Bifido and lactobacillus are her primary concern, so I will hand picked those on both samples. and get an emphasis for thoses. We see that one went up and one went down.
I looked at the interaction charts, the first one is for Lactobacillus and noticed high (99%ile) for Rickettsia and for Heliobacter (61%ile). The last one suggests testing for Helicobacter pylori should be discussed with their MD.
The chart for bifidobacterium shows many of the same bacteria that will surpress bifidobacterium. Note that lactobacillus (top right) is indicated as surpressing bifidobacterium; this agrees with the above numbers.
This appears to illustrate that being focused on just one or two bacteria may not be the best path. A holistic approach (looking at what changes all of the bacteria above may be a critical step of improving things).
Antibiotic path
Long COVID is very similar to ME/CFS. Looking at antibiotics suggestions, about 60% of them are commonly use bt ME/CFS specialists. These areL
My personal preference would be one round of metronidazole, a three week break then minocycline, another break and then one of the other ones. This is following Dr. Jadin’s Current Protocol for ME/CFS using antibiotics
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
I’m at the end if my rope and need help. I’m at my wits end with:
mcas and
mcs.
I was hit by levaquin in 1/14/20. It killed off my microbiome 22 days later reactions started. I believe has Sibo since then but was confirmed 4/23 and 4/24: Methane and hydrogen
I started raw milk one year ago and was able to stop food and scent reactions I was 85% better until March when dryer sheets on someone I m home set me off then a true anaphylactic event on 4/1 needing epi pen. Since raw milk I developed sulphur intolerance
I’m miserable and like ready for assisted suicide… but not seriously. I can’t deal with it anymore the ecoli albertii is way high 97% higher than everyone who took Biomesight so is methanobacter smithii I can’t tolerate any of the sulphur products since raw milk over grew stuff making me sulphur sensitive to microbes releasing sulphur. I never had issues with sulphur before raw milk one year ago!!!! I used to soak in Epsom all the time and eat garlic and broccoli like crazy that all stopped with this over growth!!!
My mast cell reactions and brain fog are once again bad. I do have mthfr do it’s hard to detox not sure that matters
Initial Analysis
As a start point, this has the lowest eubiosis that I have reviewed. Eubiosis is a computation on the chart below it. We see a lot of different species at abnormally high levels. A balance gut would have all of the blue lines close to the red lines.
There are a number of these bacteria that are strongly associated statistically with different symptoms.
I added the symptoms cited and went over to the new “Symptoms associations to Taxon, Compounds and Enzymes” to give this new feature an actual data case.
Comorbid: Multiple Chemical Sensitivity
All 46 significant bacteria were high (over 95%)
36 Compounds were out of whack – some high and some low
I went to another person that used the same lab that I know with both of these conditions and we see something in common
The LLM comment stated: Metabolic Interactions: Some Veillonellaceae bacteria, including Dialister species, are known for their metabolic interactions with other bacteria in the microbiota. They can metabolize certain compounds produced by other bacteria…
The nasal microbiome in asthma [2018] Four species were differentially abundant based on asthma status after correction for multiple comparisons: Dialister invisus …
Going Forward
I am going to do “Just give me Suggestions include Symptoms” with the revised algorithm (see Algorithm for “Just Give Me Suggestions”) . I could have hand picked each bacteria associated with symptoms, but given the number of very high, this would likely produce similar effect with less effort.
This results in the Consensus having 7 sets of suggestions
Suggestions To Take
The top, non-prescription items are below. It is full of spices and herbs with just one vitamin and one probiotic.
Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.
The top items are below. In relationship to the take, it seems clear that spices and herbs may be critical — increasing vegetables may have limited benefit. Spices and herbs can be done as capsules, teas, oils or just putting on food.
The question of milk came up. AVOID . If you need a milk like substance, use Soy milk only – other milks will contain milk sugar.
Cow milk 4mg per 100ml
Goat milk 0.6mg per 100ml
Soy milk 0mg per 100ml
Bottom Line
This is an interesting sample, the very high number of high percentile bacteria (with corresponding low Eubiosis) present some challenges. The interesting thing is that just targeting the high percentile ones produce a similar set of suggestions as the “Just Give Me Suggestions”. The item that is interesting is the massive number of different herbs at the top of the list. With the Oral Bacteria leakage issue, strive to take them as teas.Caffeine is a weak to be avoided, so it looks like herb teas (without caffeine — i.e. not black teas with herbs, just pure herbs) will be the regular beverage.
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
This person is a long time ME/CFSer. I should start by pointing out that the Eubiosis measure is easy to misinterpret. This person has a good 90.2% eubiosis. This indicates that things are more even (balance is likely a poor choice of word, too many meanings attached) — this is not a health measure as such. It’s a statistical measure whether the microbiome is matching the ideal pattern (not health specific).
Health Analysis is health orientated. Looking at those values we see a loss of health indicators while the evenness has improved.
“Leaked” from Oral Cavity
By Taxa is 70%ile, was 48%ile (7/2023), 70% (09/2022)
By Volume 49%ile, was 19% (7/2023) , 38.5 (09/2022)
Jason Criteria: 17%ile was 17%ile the same
Key Symptoms bacteria went to 18 was 12
The Oral Cavity stands out as a concerning factor for this person.
Analysis
We have a historic trend of 6 samples. We need to be careful of our interpretation because of differences in Lab Read Quality. The Lab Read Quality bounces around, and with that, other values may echo these shifts (i.e. up to 20% shifts for some measures). A low read quality means less bacteria are reported, for example, when it was low, the Outside Kaltoft-Møldrup has low, when it was high, the value became high.
Another way to view it is this: If 10% are out of range and 850 are reported then we have 85. If we have 500 in another report then we would expect 50. This could be misread as a 85/50 or a 70% increase in out of range bacteria. Technically, it is more complicated but that should explain the problem.
We have only one item 🙂 that is a clear improvement and one item suggesting a loss :-(.
Criteria
1/5/2024
7/3/2023
9/26/2022
1/9/2022
3/8/2021
7/26/2020
Eubiosis
91.5
68.8
41.1
65.6
31.5
43.5
Lab Read Quality
7.9
4.4
11
3.3
3.6
3
Outside Range from GanzImmun Diagostics
15
15
19
19
13
13
Outside Range from JasonH
4
4
5
5
6
6
Outside Range from Lab Teletest
21
21
18
18
27
27
Outside Range from Medivere
16
16
17
17
13
13
Outside Range from Metagenomics
5
5
7
7
8
8
Outside Range from Microba Co-Biome
2
2
2
2
2
2
Outside Range from MyBioma
10
10
3
3
9
9
Outside Range from Nirvana/CosmosId
22
22
18
18
20
20
Outside Range from Thorne (20/80%ile)
215
215
224
224
228
228
Outside Range from XenoGene
36
36
35
35
37
37
Outside Lab Range (+/- 1.96SD)
7
14
2
10
11
26
Outside Box-Plot-Whiskers
55
49
46
73
92
103
Outside Kaltoft-Møldrup
114 🙁
72
84
47
38
86
Bacteria Reported By Lab
749
545
838
495
660
483
Bacteria Over 90%ile
23 🙂
47
34
66
69
100
Bacteria Under 10%ile
49
28
21
11
2
44
Shannon Diversity Index
1.958
1.172
1.595
1.491
1.97
0.933
Simpson Diversity Index
0.041
0.234
0.075
0.128
0.045
0.012
Chao1 Index
16554
7002
18614
6127
11112
7513
Pathogens
32
25
34
29
28
23
Condition Est. Over 90%ile
0
0
0
0
0
0
Actual Symptoms in top 10 Forecasted
n/a
5
n/a
3
5
8
We have a good number of bacteria strongly statistically associated with symptoms
The difference between the two symptom forecast methods is shown below. The newer method (genus only) appears to predict symptoms better
Going Forward
With the revised algorithm (see Algorithm for “Just Give Me Suggestions”with symptoms we get the following. Unlike many samples, there were few antibiotics at the top of the list.
To Take
Spices and herbs can be done as capsules, teas, oils or just putting on food, but given the Oral leakage — as teas should be considered.
Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.
This may be a likely contributor to ongoing issues. Why? the sinus and oral cavity repopulates the gut and undo prior improvements. My best suggestions are to address this are:
When possible, drink teas with the any of the suggested herbs.
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
A reader forward this image from BiomeSight to me:
Apart from wording being questionable (former technical writer speaking) because many people will read it as needing to be increased whereas the chart on the right clearly shows that it needs to be decreased.
Same sample on MP reports:
D-Lactic Acid 18%ile. Thus much lower than the mid point! A Contradiction! D-Lactic acid is the bad form of lactic acid. L-Lactic acid is the very good form!
A brief discussion of how metabolites are estimated. There are several approaches used by retail providers:
Based on clinical studies reporting that a certain bacteria produces this compound.
Then just total up the count of all such bacteria
Based on clinical studies reporting that a certain bacteria produces this compound AND the amount that each produces.
Then just total up the count times the amount of all such bacteria
Then just total up the count times the amount of all such bacteria
This is the method that Microbiome Prescription [MP] uses.
There are additional methods but most are significantly more expensive. Working from clinical studies always have the issue of some bacteria not being studies – hence estimates may be off.
Example of one metabolite (Reuterin) showing different amounts per bacteria according to strains
There is no “right” answer. You should ask the provider of the estimates exactly how are metabolites computed (and data sources). In the case of MP, the source and method are clearly identified above. Additionally, the site should provide some education on the significance of each. Often metabolites are requested by customers and the provider does an “economical” analysis and implementation to satisfy the customer request; the results may be less than ideal or complete.
Often education is needed. The reader that emailed me, asked “should I not stop all lactate/lactic acid producing probiotics“. NO…. because L-Lactic acid is good and inhibits bad bacteria. So I checked L-Lactate (commonly just called Lactate) – see below.
Description on MP of this Metabolite
D-Lactic Acidosis: Elevated levels of D-lactic acid in the blood can lead to a condition known as D-lactic acidosis. This occurs when the body’s ability to metabolize D-lactic acid is impaired or overwhelmed. It’s often associated with specific conditions such as short bowel syndrome (SBS) or other gastrointestinal disorders where there’s an increase in the production and absorption of D-lactic acid.
Neurological Symptoms: D-lactic acidosis can lead to neurological symptoms, including confusion, impaired cognitive function, difficulty concentrating, and altered mental status. Severe cases may even lead to coma.
Gastrointestinal Symptoms: Symptoms such as abdominal pain, diarrhea, and bloating can occur in individuals with D-lactic acidosis. These gastrointestinal symptoms are often related to the underlying conditions causing D-lactic acid accumulation.
Metabolic Acidosis: Elevated D-lactic acid levels can contribute to metabolic acidosis, an imbalance in the body’s acid-base equilibrium, leading to a decrease in blood pH. This can have systemic effects and affect various organs and bodily functions.
Impaired Energy Production: D-lactic acid can interfere with cellular metabolism and energy production, potentially contributing to fatigue and weakness.
Looking up Lactate Value
Clicking on this tab button shows the thousands of metabolites that can be estimated on MP from KEGG data which we can search over.
and we find Lactate (C3H6O3) listed at 27%. IMHO that is low and you want to increase it. The description provided on this is below.
Energy Production: Lactate is produced as a result of the breakdown of glucose during anaerobic metabolism when the body’s demand for energy exceeds its oxygen supply. It serves as an alternative fuel source, particularly for muscles and red blood cells, and can be converted back into glucose (gluconeogenesis) in the liver.
Exercise and Muscle Function: During intense physical activity, the body produces lactate as muscles work vigorously, leading to temporary increases in blood lactate levels. Contrary to earlier beliefs associating lactate with muscle fatigue and soreness, lactate is not the primary cause of muscle fatigue but is rather utilized as a fuel by muscles and other tissues.
Lactate Threshold: The lactate threshold is the exercise intensity at which lactate begins to accumulate in the blood more rapidly than it can be cleared. Athletes often train to improve their lactate threshold, as it correlates with performance and endurance in certain sports.
Clinical Implications: Elevated lactate levels in the blood (lactic acidosis) can occur due to various conditions, such as sepsis, shock, hypoxia, liver disease, certain medications, or metabolic disorders. Severe lactic acidosis can lead to symptoms such as rapid breathing, nausea, abdominal pain, and, in severe cases, it can be life-threatening if left untreated.
Health Conditions: While lactate plays essential roles in energy metabolism, excessive accumulation due to underlying health conditions or imbalances can lead to health issues. Conditions associated with lactic acidosis require proper medical evaluation and treatment.
Diagnostic Tool: Blood lactate levels are sometimes measured in clinical settings to assess tissue oxygenation, especially in emergency and critical care situations, as elevated lactate levels can indicate tissue hypoperfusion and metabolic stress.
This is a follow up to this analysis ME/CFS after trying suggestions from Dr.A.I. from 2 years ago. The goal of MicrobiomePrescription is not to cure any condition — rather to generate suggestions that have a high probability of mitigate a person’s symptoms. Mitigate means reduce severity or eliminate. With some condition, it could result in a technical remission (i.e. no longer matches a diagnostic criteria). The term remission and not cure should be used always — because the microbiome could return to a dark place due to future events or inadequate ongoing care.
Update Story
I’ve been doing MUCH better for the last two years. I feel nowhere near the “normal” levels of energy that a 36 years old man should have and a lot of things are difficult, but I’ve been better and I’m able to work full time as a web developer, remotely. I know live with my significant other, and working + living with someone takes absolutely all of my energy, so I usually have no resources left to meet friends or do extra activities, but the fact of being able to work full time is a huge improvement compared to two years ago. Most of the brain fog has lifted. It comes back on my bad days, but it’s really not as bad as it used to be.
I feel that my energy levels are going worse these days and it’s getting harder to work full time though. That’s why I’ve done another microbiome analysis, and it seems to be even “worse” than 2 years ago, according to Biomesight’s score.
I still have trouble digesting things (even though it’s been a bit better the last two years, it has never been “normal” I think) and get diarrhea quite often. I usually have to go to the toilets 5-6 times a day. I’m still very skinny.
I take much less dietary supplements than I used to, but I’m still taking :
Acetyl L-Carnitine
Ubiquinole
R Lipoic Acid
B12
Vitamin D
Nattokinase
I’ve also done another round of “Spezzata”[Licorice] recently, but it definitely makes my blood pressure go up. I also eat a lot of dark chocolate and drink a lot of coffee.
My diet has changed a bit since I’ve started living with my Significant Other about a year ago. I eat a lot more rice than I used to now.
Analysis
The first thing that I noticed was the lab quality is down a lot. Lower quality means less bacteria types (793 dropped to 334) are identify and the estimated costs have greater uncertainty. On the plus side, all measures are the same or are significantly better.
Criteria
Current Sample 2024
Old Sample 2022
Lab Read Quality
2
5.4
Lab Quality Adjustment Percentage
85.9
100
Outside Range from GanzImmun Diagostics
19
19
Outside Range from Lab Teletest
25
25
Outside Range from Medivere
15
15
Outside Range from Metagenomics
9
9
Outside Range from Microba Co-Biome
6
6
Outside Range from MyBioma
8
8
Outside Range from Nirvana/CosmosId
21
21
Outside Range from Thorne (20/80%ile)
327
327
Outside Range from XenoGene
41
41
Outside Lab Range (+/- 1.96SD)
7
10
Outside Box-Plot-Whiskers
43
118
Outside Kaltoft-Møldrup
24
68
Bacteria Reported By Lab
334
793
Bacteria Over 90%ile
0
99
Bacteria Under 10%ile
0
31
Lab: BiomeSight
Pathogens
16
41
Condition Est. Over 90%ile
0
3
Standard Items
Looking at new features added. Note that the drop in number of bacteria reported impacts many of these values)
Measure
2024
2022
“Leaked” from Oral Cavity [LOW is better]
21.1%ile
65.7%ile
General Health Predictors [More is better]
6
17
Jason Hawrelak Ratio
10%ile
14%ile
Butyrate
9%ile
29%ile
Potential Medical Conditions Detected
0
3
Bacteria deemed Unhealthy
0
31
Eubiosis
8%
71.6%ile
The charts show similar patterns but with a group of bacteria dominating (80-90%ile) range
Conclusion: He is better than 2022 in many measures but is worse in a few (especially newer ones).
Let us look at some recent feature additions. First key bacteria — we see improvement we a lot of key bacteria dropping down below the threshold. (see Technical Note: Identifying Key Bacteria to Address for background)
As usual, I start with “Just give me Suggestions include Symptoms” with the new refactored algorithm (see Algorithm for “Just Give Me Suggestions”). The items were similar but with just a change of order.
First, let us look at what is currently being take. Microbiome changes over time. The highest for non-prescription items is 327 and lowest -516.
Acetyl L-Carnitine: 152
Ubiquinole: AKA COq 10, Not on current suggestions
None of the above is clearly a bad choice. The worst, vitamin D tend to be a slow acting supplement. This illustrates that doing a retest every 6 months to reset your course to recovery is likely good practice.
Some observations on suggestions:
60% of the top 5 items (all antibiotics) have [CFS], i.e. commonly used by ME/CFS specialists.
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
Hi Ken – I’m attempting to use MBP. I recall you linked (a long time ago) to a section that showed a list of probiotics useful in colitis, with each probiotic having the studies. How would I arrive to that page?
Where do I get the probiotics?
I prefer single species — and where I get mine?
Single species with (almost) no fillers. There are precisely three sources that I use:
Maple Life Science™: No strains yet, but shipments usually have manufactured date within 4 weeks of arrival (i.e. FRESH). Contains FOS
Bulk Probiotics: US based Newbie — but has some species not available at the other two sites. No other ingredients just the bacteria. Specifically, Lactobacillus Jensenii that has great potential for Crohn’s disease.
NOTE: none of these sell though retail outlets. This keeps their costs down and their product fresh.
There is a multiple step/layer approach that I would use. The sequence is below:
You will see the list of probiotics with the ones with the most studies listed first.
Below it are the links to the studies. You should read at least some of them – some may report “no effect”. The list is generated by a data gathering algorithm on the species and the condition and the condition may be mentioned in passing and not directly referenced or tested.
#2 Use Perplexity AI
Go to https://www.perplexity.ai and just ask “What is the most effective probiotic for…”. I use this AI because it provided links to data sources so I can verify the response
A typical response is below
#3 Probiotic Via Published Microbiome Shifts
In this case we are using the MP engine to generate suggestions. It is inferior in reliability to the above methods but is a reasonable fall back. Go to Medical Conditions with Microbiome Shifts from US National Library of Medicine ( https://microbiomeprescription.com/Library/PubMed ) and search for the condition
You can click the PDF download (which report TOP items only) or click Candidates (all items)
Surprise, surprise! #1 and #2 agree with Perplexity!!! vsl#3 is not listed because we do not have strain information for this mixture of probiotics. Remember – these are computed SOLELY from the microbiome shifts without reference to any studies on ulcerative colitis!
#4 Probiotic via Citizen Science
Goto Symptoms associated with conditions reported for Samples https://microbiomeprescription.com/Library/Symptoms Enter the name — in this case it was not found (not enough samples that people have annotated with ulcerative colitis). In that case, you may want to go over to symptoms you have; for example Diarrhea. This data is conditioned on the lab that the contributor was using and layered by taxa level.
I will be adding a suggestions icon to this page shortly, and you can then review those suggestions. Clicking on the bowl, produces suggestions that can be filtered to probiotics.
#1 and #2 above are #1 and #3 with the most studied one show in above!
Clicking on the symptom name takes you to the symptom page listing all of the bacteria
This will then use the expert system to generate suggestions which can be filtered to probiotics
This is ranked not by the number of studies published but by the ones with the greatest estimated impact by the expert system. We see Mutaflor, L. rhamnosus – and many familiar ones in the researched strain list.
Bottom Line
We have 4 ways of selecting probiotics. For the specific question asked, all 4 converge to the same items. In terms of clinical use, we see that the suggestions based solely on bacteria shifts going through the expert system appear to be cross-validated. IMHO, this explicit expert system works better than the typical MD would.
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