Tag Archives: microbiome

Unknown's avatar lassesen 8:37 am on December 28, 2024
Tags: , , lactobacillus-probiotics, , microbiome, ,   

ME/CFS: The Evils of Lactobacillus Probiotics?

A reader wrote me today with the following question

I read your article on microbial involvement, can you explain in more detail why you recommended cutting out Lactobacillus? If I interpreted your analysis, you said lactobacillus was rare in ME/CFS, doesn’t that mean increasing it could be beneficial? “..lactobacillus shows up barely in only one result..”.Meaning lactobacillus is rare for ME/CFS patients?

I meant that there is no clear evidence of a lactobacillus deficiency with ME/CFS patients microbiomes. There are reasons to believe that it may be harmful and helps maintain ME/CFS state.

History

I am a facts/study based individual that have been reading studies, conference reports since 1990’s. Back in 1999, on eGroups CFSFM-Experimental, taking probiotics were often suggested. Why? Because probiotics has been promoted as a cure-all for all conditions. A influencer snake oil. Reported results on CFSFM-Experimental were disappointing.

My mind proceeded logically. So ask the US National Library of Medicine (PubMed), “Which probiotics have been helpful for ME/CFS? Given that there were 2400 studies on ME/CFS then, I expected to find a few dozen by then — after all, it would likely be one of the first choices by naturopaths who would rush to publish their results!! There were none that used lactobacillus probiotics. Even today, we have just 32 studies mentioning “chronic fatigue syndrome” probiotics in the 8500 studies posted. [Sarcasm] “Surely, there would have been a rush with all of the ME/CFS specialists to use lactobacillus probiotics given all of this evidence”.

Being a scientist, I know that what gets published are positive results — not no result nor negative results.

Reading conference papers presented by specialist on ME Research UK, I came across a report of a conference panel by active practitioners where the consensus was no benefit. I have worked as a professional technical writer and very “phrasing aware”, I read the wording to indicate that probiotics likely did harm in some of their patients. Slamming probiotics tend to be view as a heresy with many health influencers.

There Appears No Significant Objective Evidence that lactobacillus helps!

Yes, you will find testimonials — but that is not objective evidence. They may have helped because the person did not have ME/CFS (self diagnosis) or a different condition. It is incomprehensible that there have not been dozens (or hundreds) of studies trying lactobacillus — studies that are unpublished because of unfavorable results.

Why may it be EVIL?

Again, conference papers from Australia’s Alison Hunter Memorial Foundation play an important role here. From the Way-Back machine I retrieved items no longer on their site and pasted it into 1998 Was a very good year…. The key finding was “The mean distribution of E.coli as percentage of the total aerobic microbial flora for the control subjects and CFS patients was 92.3% and 49% ” Not a little drop, but almost half the level!

NOTA BENA: The typical (cheap) 16s tests used for most modern microbiome studies effectively ignore E.Coli. Shotgun testing (much more expensive) finds E.Coli in almost every sample. Some 16s finds it in 1 in a thousand samples as shown by the table below. Modern studies not repeating these results is a direct consequence of their methodologies!!

This was the motivation for my trying Mutaflor Probiotics (E.Coli Nissle 1917) which I happen to have in the house because my wife has Crohn’s and it made a huge difference for her (with lots of studies reporting it too!!!). I had a severe Jarisch–Herxheimer reaction for two weeks and a rapid recovery from ME/CFS afterwards.

If you look at Odds Ratios for Metabolites and ME/CFS, you will see that E.Coli probiotics has the biggest impact on the metabolite imbalance with ME/CFS

Going over to the E.Coli page on Microbiome Prescription we see that Lactobacillus constantly reduces E.Coli. So we are moving from levels that are 50% of normal levels to even lower levels.

IMHO, for ME/CFS, Lactobacillus probiotics are EVIL

Yes there are a few lactobacillus that will help some symptoms (and likely make other symptoms worse). Unless you are very sure that it has the actual probiotic strain used in studies, don’t do it. See Probiotics — what is advertised may not be what you get.

IMHO, for brain fog, Lactobacillus probiotics are EVIL

Interesting study relative to ME/CFS and brain fog. Lactobacillus can trigger “thick blood”, decreasing oxygen delivery (hypo perfusion). The aggregation of human platelets by Lactobacillus species

This extends to a few other Conditions

Bottom line, checking for clinical studies if a probiotics clearly helps is recommended. This search engine may help.

Bifidobacterium also?

In Visual Exploration of Odds Ratios, we see that ME/CFS people have higher then general population amounts of Bifidobacterium. On the flip side, the average amount is reported lower on several studies. This compounds issues with several things that needs to be investigated.

  • Did the lower bifidobacterium count not found in their average as zero? We use the values only when detected. Looking at the dots, we see that the dots are sparse/rare for lower values suggesting a lower detection rate. This suggests a threshold behavior of bifidobacterium.

Looking at impact on E.Coli, we see most studies say that it decreases E.Coli

There is not enough data to come to a safe conclusion.

Unknown's avatar lassesen 12:18 pm on December 23, 2024
Tags: , , microbiome, ,   

Microbial involvement in myalgic encephalomyelitis/chronic fatigue syndrome pathophysiology

This is the title of a new publication in Microbes & Immunity, available here.

Microbiome fluctuations or metabolic endotoxemia are proposed as possible disorder biomarkers. Based on the fact that gut microbiota dysbiosis reverts to a state of eubiosis in long-term patients with this condition, it may be hypothesized that disease progression begins with the loss of beneficial gut microorganisms, particularly short-chain fatty acid producers, leading to more widespread gastrointestinal phenotypes that are subsequently reflected in plasma metabolite levels. These alterations, specific of each individual, thereby result in metabolic and phenotypic shifts and in ME/CFS.

Microbial involvement in myalgic encephalomyelitis/chronic fatigue syndrome pathophysiology 6 Sep 2024

This has been my primary hypothesis for many years and lead to my writing Microbiome Prescription to normalize the dysbiosis. The bacteria shifts will be reported differently from different labs because of a lack of standardization of microbiome tests (See The taxonomy nightmare before Christmas… ).

Recently, I implemented an Odds Ratio analysis of the 5000+ sample microbiomes that have been upload to Microbiome Prescription. A quick overview is here: Bacteria Associated with General Fatigue.

Below I have pulled the lab specific dysbiosis shifts for ME/CFS at thhe genus level.

Biomesight Tests

The number are the percentile ranking for the bacteria listed. Each match increases the odds of ME/CFS by 1.5.

  • Methylonatrum >= 99
  • Planifilum >= 98.9
  • Thiohalorhabdus >= 98.9
  • Granulicatella >= 98.7
  • Amedibacillus >= 98.6
  • Enterococcus >= 98
  • Methylobacillus >= 98
  • Emticicia >= 97.7
  • Candidatus Tammella >= 97.7
  • Dokdonella >= 97.6
  • Runella >= 97.4
  • Collinsella <= 18
  • Pseudobutyrivibrio <= 16.4
  • Calothrix <= 13.8
  • Lachnospira <= 11.4
  • Veillonella <= 10.8
  • Shuttleworthia <= 8.5
  • Parabacteroides <= 8.4
  • Bifidobacterium <= 8.4
  • Faecalibacterium <= 7.5
  • Actinobacillus <= 7.5
  • Pedobacter <= 7.2
  • Coprococcus <= 4.6
  • Moorella <= 3.5
  • Natronincola <= 2.9
  • Mediterraneibacter <= 2.5
  • Oscillospira <= 1.8
  • Anaerovibrio <= 1.7
  • Sphingobacterium <= 1.6

Thryve

  • Collinsella <= 44.2
  • Bifidobacterium <= 41.1
  • Gemmiger <= 23
  • Dorea <= 19
  • Butyrivibrio <= 8
  • Fusicatenibacter <= 5.7
  • Lachnoclostridium <= 5.2
  • Gordonibacter <= 5.1
  • Eubacterium <= 4.8
  • Prevotella <= 4
  • Brassicibacter <= 3.9
  • Sporobacter <= 3.5
  • Johnsonella <= 3.5
  • Phascolarctobacterium <= 3.4
  • Dialister <= 3.4
  • Agathobacter <= 3.3
  • Lactonifactor <= 3.2
  • Murimonas <= 3.2
  • Moryella <= 3.1
  • Niabella <= 3.1
  • Ruminococcus <= 3
  • Hungatella <= 3
  • Anaerotruncus <= 2.8
  • Odoribacter <= 2.7
  • Lactobacillus <= 2.4
  • Eggerthella <= 2.3
  • Cellulosilyticum <= 2.1
  • Haemophilus <= 2
  • Holdemania <= 2
  • Terrisporobacter <= 2
  • Anaerobutyricum <= 1.9
  • Howardella <= 1.8
  • Hydrogenoanaerobacterium <= 1.8
  • Lachnobacterium <= 1.8
  • Hespellia <= 1.7
  • Agathobaculum <= 1.6
  • Pseudoflavonifractor <= 1.6
  • Desulfotomaculum <= 1.6
  • Intestinibacter <= 1.6
  • Barnesiella <= 1.5
  • Eisenbergiella <= 1.5
  • Facklamia <= 1.5
  • Acetatifactor <= 1.5
  • Ruminiclostridium <= 1.5
  • Natranaerovirga <= 1.5
  • Enterocloster <= 1.4
  • Caloramator <= 1.4
  • Thomasclavelia <= 1.4
  • Desulfovibrio <= 1.4
  • Parabacteroides <= 1.4
  • Shuttleworthia <= 1.3
  • Peptoniphilus <= 1.3
  • Akkermansia <= 1.3
  • Alistipes <= 1.3
  • Marvinbryantia <= 1.3
  • Acetivibrio <= 1.2
  • Paraprevotella <= 1.2
  • Veillonella <= 1.2
  • Bacteroides <= 1.2
  • Butyricimonas <= 1.2
  • Romboutsia <= 1.2
  • Ethanoligenens <= 1.2
  • Phocaeicola <= 1.2
  • Anaerocolumna <= 1.2
  • Blautia <= 1.1
  • Coprococcus <= 1
  • Lachnospira <= 1

uBiome

  • Veillonella <= 22.4
  • Hespellia <= 19
  • Bifidobacterium <= 15.1
  • Anaerosporobacter <= 7.2
  • Streptococcus <= 6.8
  • Eggerthella <= 6.4
  • Phascolarctobacterium <= 4.1
  • Eisenbergiella <= 3.9
  • Marvinbryantia <= 3.4
  • Holdemania <= 3.1
  • Dorea <= 3
  • Anaerostipes <= 3
  • Oscillibacter <= 2.7
  • Dialister <= 2.3
  • Kluyvera <= 2.1
  • Peptoclostridium <= 1.7
  • Erysipelatoclostridium <= 1.4
  • Intestinimonas <= 1.3
  • Sarcina <= 1.3
  • Roseburia <= 1.3
  • Phocaeicola <= 1.2
  • Terrisporobacter <= 1.2
  • Bacteroides <= 1.1

Bottom Line

Bifidobacterium is common across all of these, and lactobacillus shows up barely in only one result. Since there can be some hostility between Bifidobacterium and Lactobacillus, I would suggest cutting out lactobacillus probiotics.

I repeated this for Bifidobacterium species and one species shone.

  • Bifidobacterium longum <= 9.9

My personal preference for a source is Maple Life Science which sells direct from factory resulting in very fresh and alive probiotics.

Some examples of analysis people with Long COVID and ME/CFS are there. I am working on building an algorithm to build suggestions based on odds ratio which should improve the suggestions more.

Unknown's avatar lassesen 12:56 pm on September 28, 2024
Tags: , , microbiome, ,   

ME/CFS Patient continues the trek to recovery

Prior Posts

Dealing with ME/CFS and many microbiome dysfunction is rarely a short journey

Recent Story

Some supplements that I have been taking since the last test:

  • Tetracycline 
  • Clove 
  • Holy basil (Neem)
  • Augmentin + Bromelain 
  • Grapefruit seed extract 
  • Monolaurin
  • Apple peel powder 
  • Thyme

My symptoms:

  • Still get the red nose (some form of rosacea). 
  • Still feel fatigued (both physically and mentally). But it is better than before.
  • Feeling stressed. But it is better than before.
  • Brain fog.
  • Bloated.
  • Lots of gas – I fart and burps a lot. 
  • Issues with allergies (itching eyes, stuffed nose and itchy skin)

Video

Analysis

We will start with the high-level comparison. Note that some numbers will change with time. There are no major changes. Since the latest sample reports 20% more bacteria, many counts are expected to be 20% higher – for example: Thorne Ranges: old: 230 + 20% = 276, with the seen count being 253 (so an apparent improvement although the number went up)

Criteria9/2/20241/22/20249/12/20232/22/20238/11/20223/25/202212/3/20218/31/2021
Lab Read Quality9.17.93.59.75.56.23.67.8
Outside Range from GanzImmun Diagostics1616161515171720
Outside Range from Lab Teletest2320 202424222225
Outside Range from Medivere1416161515151519
Outside Range from Metagenomics67799778
Outside Range from Microba Co-Biome32277111
Outside Range from MyBioma65 577778
Outside Range from Nirvana/CosmosId2120202323181821
Outside Range from Thorne (20/80%ile)253230198223223217217246
Outside Range from XenoGene3232 243232363639
Outside Lab Range (+/- 1.96SD)125 1510119914
Outside Box-Plot-Whiskers4852564236425942
Outside Kaltoft-Moldrup113123 70139567859140
Bacteria Reported By Lab600508399666478613456572
Bacteria Over 85%ile4852      
Bacteria Under 15%ile118157      
Pathogens2326 253023392430
Condition Est. Over 85%ile25      

There is a new comparison table added that compares sets of symptoms bacteria for symptoms reported in either sample. This is a thought experiment on a different way of evaluating the microbiome, i.e. are symptom bacteria reducing. Remembering that we have 20% more bacteria reported, the improvement may be slightly under-reported.

Going Forward

My current preference is to use symptom associations suggestions with KEGG suggested suggestions. This assumes that the person has added their symptoms.

Using Entered symptoms

Since this person has access to antibiotics, I opted to include all classes of modifiers. We have 38 bacteria selected — a reasonable number

The suggests were a nice mixture for ME/CFS. Typically, I see the top being just antibiotics, in this case we have several probiotics there.

And suggested retail probiotics are:

Using Diagnosis and PubMed

Using a diagnosis provides less precise filtering compounded by different labs (with different identification of bacteria). If the person is using a lab that lacks a large number of annotated samples from that lab, then it is the best path.

The suggested path is to go down the list and pick the ones that has the highest value(s) that agrees with one or more of the diagnoses that you have.

In this case we have only 4 bacteria in the selection, so the suggestions will be likely more generic than specific.

There are no antibiotics in this list

The probiotic list is below. It has some similarities to the above list.

Using KEGG Derived Probiotics

This is an experimental approach that attempts to do a metagnòmia approach from the available data. We estimate which compounds are too high or too low. Then we match them to probiotics which produce or consumes them. Postbiotics can be used for items that are too low. There is no filtering of any type; we look at the entire microbiome.

The results are different — as to be expected. Why expected? The prior ways depended on studies being done what each probiotics bacterium does. Often there are no studies. This way uses the DNA/RNA sequences of everything and thus we do not need studies.

I usually focus on too low, with the assumption that a surplus will just be ignored or has less impact (i.e. starvation versus obesity) We can see where there is agreement between the lists.

  • aor / probiotic-3 is [30]
  • bioflorin (deu) / bioflorin is [25]
  • miyarisan (jp) / miyarisan is [22]
  • Microbiome Labs / MEGA Genesis is [27]
  • Bulk Probiotics / L. Reuteri Probiotic Powder is [27]

Consensus View?

You can build consensus views, a.k.a. Monte Carlo model, but IMHO that is likely done by those that want to “over work the problem”.

Summary of Suggestions

Remember these are suggestions, and NOT a protocol. What you actually do should be reviewed by a knowledgeable medical professional before starting.

My own proposal for discussion would be:

This can be made more complex by using consensus / Monte Carlo Model

Reader Plan

Microbiome Prescription produces suggestions, the weights/priorities are the odds of causing a change and not the amount of change (there is simply no objective data to compute the amount). This reader did their own evaluation of what they felt comfortable with (excellent idea).

I have also bought 2 more tests so I will do them with max 3 months apart as you said in the video.

I came up with this protocol by using the “Beginner-Symptoms: Select bacteria connected with symptoms”:

  • Week 1-2: Gum arabic
  • Week 3-4: Monolarin (lauric acid)
  • Week 5-6: Psyllium
  • Week 7-8: Rosemary 
  • Week 9-10: Parsley
  • Week 11-12: SymbioFlor-2

I found that I get best results from herbs, prebiotics and antibiotics. The only probiotic I’ve got good results from is Symbioflor 2 (an E.Coli probiotic) [Editor: E.Coli probiotics also worked best for me]

A lot of probiotics that I’ve tested I’ve got bad results from. 

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid.My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

  1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
  2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
  3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
  4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why
  5. My preferred provider for herbs etc is Maple Life Science™ – they are all organic, fresh, without fillers, and very reasonably priced.

Professional Medical Review Recommended

Individual health conditions may make some suggestions inappropriate. Mind Mood Microbes outlines some of what her consultation service considers:
A comprehensive medical assessment should consider:

  • Terrain-related data
  • Signs of low stomach acid, pancreatic function, bile production, etc.
  • Detailed health history
  • Specific symptom characteristics (e.g., type and location of bloating)
  • Potential underlying conditions (e.g., H-pylori, carbohydrate digestion issues)
  • Individual susceptibility to specific probiotics
  • Nature of symptoms (e.g., headache type – pressure, cluster, or migraine)
  • Possible histamine issues
  • Colon acidity levels
  • SCFA production and acidification needs

A knowledgeable medical professional can help tailor recommendations to your specific health needs and conditions.

Unknown's avatar lassesen 7:48 pm on February 20, 2024
Tags: , , , microbiome, wellness   

ME/CFS Books and MDs

In the family dealing with ME/CFS we were very fortunate in working with now retired folks, (links to MEPedia pages on them). It was 25 years ago.

Also we had significant interaction with

Many support groups provide lists of local MDs that are sympathetic to ME/CFS patients. Typically, they will attempt to do symptom relief, not remediate the underlying cause or do not test outside of their local standards of practice (i.e. testing for associated viral infection, Lyme or rickettsia infections) – independent of insurance coverage or the patient being will to pay.

For example:

The family was extremely fortunate to be covered by the old Microsoft Medical insurance that covered everything that the MD wanted with no deductibles; and we had a MD that was willing to learn and explore.

My recommendations for books are:

Other books can be found here:

Note that the better books are often difficult or impossible to understand due to brain fog (and sometime lack of sufficient education is specific areas)

Determine a Model and if possible, see if there is evidence that the model works

I went with two models for ME/CFS: A hypercoagulation condition (David Berg) and an “occult rickettsia like infection” (Cecile Jadin); today we could call it “post Infection Fatigue Syndrome”. Both were testable (by lab or by reaction to low risk drugs, i.e. an antibiotic often prescribed for Acne) and actionable.

Today, my thinking is that the simplest model is a persistent microbiome dysfunction. This is very testable with direct retail tests; and actionable (using Microbiome Prescription). Often the antibiotics suggestions from Microbiome Prescription mirrors the Jadin approach. The treatment plan works for her models and my microbiome model!

Going with a hypothesis that is not both testable and actionable is not recommended. Take action today incase it works! Leave speculations to researchers trying to get grant money for their special interests.

For examples using my model: see Analysis Posts on Long COVID and ME/CFS

Symptoms and Bacteria appears to be strongly related

It is typical that Microbiome Prediction correctly predicts 80-100% of a person’s dominant symptoms from their microbiome. This implies that the bacteria shifts are causing the symptoms; thus correcting the bacteria shifts may reduce or eliminate symptoms.

Suggested Questionnaire for Evaluating a MD

What testing would you like to do?

Are you going to just provide symptom relief or are you going to search for the underlying cause to eliminate it?

Unknown's avatar lassesen 7:40 am on December 15, 2023
Tags: , , , microbiome,   

Tool for getting suggestions for your specific ME/CFS Symptoms

After I posted List of Bacteria significant for ME/CFS from the shared samples uploaded to Microbiome Prescription, several readers asked “How do I use this”. This took me a few days to come up with, code and implement an answer.

I wanted this to go beyond just ME/CFS because there is a huge variety of symptoms and co-morbidity seen with ME/CFS. After testing and tuning the algorithm, I am pleased with the current results.

The process is show below.

The Steps

  1. First get a suitable microbiome test done (See this list of supported tests)
  2. Transfer or upload your results to Microbiome Prescription
  3. An email will be sent to you to login
  4. Login in.
  5. Enter your symptoms
  • Return to “My Profile”
  • A new button will appear

Clicking it will move to the page below. YOU MAY FIND THAT IT TAKES UP TO A MINUTE (We are doing a massive number of computation)

This will show a tree of the bacteria involved. The Species are under the genus they below to. In the example below we see the ENTIRE phylum that Bifidobacterium is in are low (none found) of 9 species whose presence would likely reduce your symptoms.


Elsewhere you may see highs with certain bacteria species desired to higher. Often the symptom key is at the species level.

At the bottom you will see a button to get suggestions

The next page shows the symptoms being targeted to and choices of what you want to consider.

Make any changes desired and click show suggestions

REMEMBER these are suggestions for ONE person using their Symptoms and their microbiome profile. It is intended for them only. Your own suggestions may be very different with many items exchanged between ADD and REMOVE.

Technical Methodology Details are described here Technical Note: Prevalence, Average and Not Reported.

Post-Script

This approach sidestep the proforma process often drilled into researchers (you must have a healthy control group and a verified, criteria matching target population). I kept to rigorous statistical analysis while ignoring these constraints which are philosophical in nature. We used the available data and set our significance level to P < 0.005; instead of the typical research level of P < 0.05. In other words, we are 10 times more certain about our results.