Month: October 2023

There is no normal nor reference microbiome!

On top of different labs interpreting samples in different manner which I have covered in the posts below, there is an additional issue to compound determining if a level of bacteria is normal or not!

I described it in my 2017 post, and updating information here.

One of the common misconception is that there is a “normal” microbiome that can be used as a reference.  Below is a chart from “Metagenomic sequencing of fecal DNA[2016]“. Diet and environment makes a major impact on the distribution and volume of the bacteria.

  • “In a study of gut bacteria of children in Burkina Faso (in Africa), Prevotella made up 53% of the gut bacteria, but were absent in age-matched European children.”[2010]

The chart below is for healthy individuals in 12 different countries.  In some cases neighboring very similar countries (Sweden [SE] and Denmark [DK]) have very different compositions.

world

This great variation means that testing the microbiome can only be done as group of individuals living in the same area with similar eating habits…. If you are a vegetarian living in Australia, the reference ranges provided by your Australian lab are very questionable for you to use.

An individual result without reference from people with the same eating habits and possibly ethnic background is very fuzzy to interpret. Yes, highlights may be common — like low E.Coli, Lactobacillus and Bifidobacteria….  but they likely apply to no more than 80-90%, the other CFS patients may have different shifts.

Then we also find that DNA also impacts the microbiome,

Host genetic variation drives phenotype variation, and this study solidifies the notion that our microbial phenotype is also influenced by our genetic state. We have shown that the host genetic effect varies across taxa and includes members of different phyla. The host alleles underlying the heritability of gut microbes, once identified, should allow us to understand the nature of our association with these health-associated bacteria, and eventually to exploit them to promote health.Human genetics shape the gut microbiome , 2014

People have asked me, “Did you get your microbiome done, what was it?” My honest answer was “No, such testing was not available when I last had CFS. I simply assumed that my pattern would be an appropriate match to that reported from the 1998 Australian studies”

Age changes the microbiome

” DNA of the Clostridium leptum group and pathogenic Enterobactericeae increase in the gut microbiome with age and can be detected in the same individual’s coronary plaques along with pathogenic Streptococcus spp., associating with more severe coronary atherosclerosis. ” [2019]

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The presence of the Bifidobacterium, Faecalibacterium, Bacteroides group, and Clostridium cluster XIVa decreased with age up to 66-80 years of age, with differences reaching statistical significance for the latter group. Interestingly, the levels of some of these microorganisms recovered in the very old age group (>80 years), with these older individuals presenting significantly higher counts of Akkermansia and Lactobacillus group than adults and the younger elderly.

Age-Associated Changes in Gut Microbiota and Dietary Components Related with the Immune System in Adulthood and Old Age: A Cross-Sectional Study. [2019]

Latitude changes the Microbiome

Latitude means the distance from the equator. This may be due to sunlight-vitamin D levels.

Geographical variation of human gut microbial composition , 2014

These changes in the microbiome, also impacts symptoms, for example The Association of Latitude and Altitude with COVID-19 Symptoms: A VIRUS: COVID-19 Registry Analysis. [2022]

If you exercised recently impacts the microbiome

Underlying these macro-level microbial alterations were demonstrable increases in select bacterial genera such as Veillonella (+14,229%) and Streptococcus (+438%) concomitant with reductions in Alloprevotella (-79%) and Subdolingranulum (-50%). To our knowledge, this case study shows the most rapid and pronounced shifts in human gut microbiome composition after acute exercise in the human literature. 

Rapid gut microbiome changes in a world-class ultramarathon runner. 2019

Season Changes Microbiome

Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population [2020]

Some Population Studies

“We analyzed the combined microbiome data from five previous studies with samples across five continents. We clearly demonstrate that there are no consistent bacterial taxa associated with either Bacteroides– or Prevotella-dominated communities across the studies. By increasing the number and diversity of samples, we found gradients of both Bacteroides and Prevotella and a lack of the distinct clusters in the principal coordinate plots originally proposed in the “enterotypes” hypothesis. The apparent segregation of the samples seen in many ordination plots is due to the differences in the samples’ Prevotella and Bacteroides abundances and does not represent consistent microbial communities within the “enterotypes” and is not associated with other taxa across studies.” [2016]

” All Egyptian gut microbial communities belonged to the Prevotella enterotype, whereas all but one of the U.S. samples were of the Bacteroides enterotype.

  • The intestinal environment of Egyptians was characterized by higher levels of short-chain fatty acids, a higher prevalence of microbial polysaccharide degradation-encoding genes, and a higher proportion of several polysaccharide-degrading genera.
  • Egyptian gut microbiota also appeared to be under heavier bacteriophage pressure.
  • In contrast, the gut environment of U.S. children was rich in amino acids and lipid metabolism-associated compounds; contained more microbial genes encoding protein degradation, vitamin biosynthesis, and iron acquisition pathways; and was enriched in several protein- and starch-degrading genera.
  • Levels of 1-methylhistamine, a biomarker of allergic response, were elevated in U.S. guts, as were the abundances of members of Faecalibacterium and Akkermansia, two genera with recognized anti-inflammatory effects.
  • The revealed corroborating differences in fecal microbiota structure and functions and metabolite profiles between Egyptian and U.S. teenagers are consistent with the nutrient variation between Mediterranean and Western diets.” [2017]

“This suggests that similarities between the Inuit diet and the Western diet (low fiber, high fat) may lead to a convergence of community structures and diversity. However, certain species and strains of microbes have significantly different levels of abundance and diversity in the Inuit, possibly driven by differences in diet.” [2017]

For a Worked Example Using Dr. Jason Hawrelak Recommendations, see The taxonomy nightmare before Christmas… Episode III

Bottom Line

There is no clear definitive benefit from doing an individual microbiome testing — there is no definitive reference ranges. This is an inconvenient truth about the microbiome testing – rarely talked about and typically ignore.

My training is in statistics and artificial intelligence where there is no concept of definitive, just probability and fuzzy data.

The path that I have walked down on my Microbiome Prescription site accepts this problem and use a wide variety of methods (familiar to some of those people who are very well practiced and experienced in probability, statistics and artificial intelligence) to maximize the odds that suggestions will improve a person’s health. Both the simplified logic of influencers and the naïve application of the “hottest new” artificial intelligence fad are ignored. Many people cannot get their minds wrapped around the nature of this problem, IMHO.

This latter issue persists even if you get lab test results to agree.

” This work supports that sex is a critical factor in colonic bacterial composition of an aged, genetically-heterogenous population. Moreover, this study establishes that the effectiveness of dietary interventions for health maintenance and disease prevention via direct or indirect manipulation of the gut microbiota is likely dependent on an individual’s sex, age, and genetic background. ” [2019]

Are probiotics 100% safe – No, Just 99.99% safe

This is an update of a post that I did back in 2018 [Original Post]. A reader had messaged me about the safety of soil based organisms probiotics. For hundreds of thousands of years, soil based organism was a part of our diet because of the absence of safe water, soil was often on the food consumed. I recall reading that the human gut bacteria has strong similarity to that seen around root vegetables. This is not surprising, pulling roots out of the ground (without washing!!!) was likely common for most of these thousands of years…

“But I read about someone getting sick from SBO!”

  • There are two types of sick to consider: bacteremia or endocarditis (BAD), and herxheimer reaction (usually a good sign — I was really sick when I first started Mutaflor, it ebbed and I was much better afterwards)

This recent event caused me to revisit this item: “FDA investigating baby’s death linked to probiotic given by hospital” with FDA Letter pointing out that it was not legal to sell it with the claims it made.

Some Counts of Adverse Probiotic Infections

The most dangerous probiotic (using report counts) are Lactobacillus.

There are similar risk from eating “safe” lactobacillus probiotics, cheese, yogurt, etc. Even deaths have been reported: “Lactobacillus-Cause of Death ” [2010]

” Lactobacillus has been used as a probiotic bacteria to treat diarrhea and is also present in dairy foods. It is hence commonly used. Lactobacillus endocarditis, an exceedingly unusual disorder, is accompanied by high mortality and poor response to treatment. ” – OUCH!

  • “In recent years, infections caused by Lactobacillus and Bifidobacterium made up 0.05% to 0.4% of cases of endocarditis and bacteremia. In most cases, the infections were caused by endogenous microflora of the host or bacterial strains colonizing the host’s oral cavity. According to a review of cases of infections caused by bacteria of the genus Lactobacillus from 2005 (collected by J.P. Cannot’a), 1.7% of infections have been linked directly with intensive dairy probiotic consumption by patients. ” [Lactic acid bacteria and health: are probiotics safe for human?]. [2014]

Some more citations…’ bacteremia is a bad bacteria infection, endocarditis is a bacteria infection of the heart. It has been only in the last few years

Bottom Line

Probiotics are generally safe. No probiotic is 100% safe. To me, soil based bacteria are likely more beneficial then lactobacillus because they went along with our ancestor’s diet long before we started domestication of milk producing animals. There may be considerable basis to the hygiene hypothesis which would result from our modern pathological obsession with sterilization of food in the belief that all bacteria are bad.

The general belief is that issues arise with a weak immune system, after surgeries, and with a “leaky gut”.

Fudge Factors in determining Butyrate, H2, SO2, NH4, histamines producers…

A reader messaged this to me:

People like (and expect) absolute certain answers. Statistician and Artificial Intelligence Engineers NEVER expect absolute answers… they expect fuzzy answers and just work with it.

There are two problems with determining levels from the microbiome:

  • Correct identification of the bacteria from the test
  • Determining if the bacteria produces the substance.

Accurate Bacteria Identification is HORRIBLE

For a basic understanding see these prior posts:

So with the same data (FastQ) files, the number of bacteria producing each of the above will vary greatly.

Most Labs use INFERENCE data to identify producers

By inference, I mean looking at a sample with high butyrate etc and then (stupidly) looking at the bacteria that your specific lab identify there (see above!) and then publishing a paper that high X bacteria produces butyrate etc. Even having an alleged “sterile” environment with only one bacteria is questionable to assert (besides the behavior of a bacteria placed in “extended isolated confinement” is different – as it is with humans). Not many years ago, breast milk was deemed to be sterile. Improved testing resulted is this myth being disproved in Lactobacillus Bacteria in Breast Milk [2020], Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health.[2020], Characterization of potentially probiotic lactic acid bacteria and bifidobacteria isolated from human colostrum.[2020]

These studies are used by many labs to determine amount being produced.

Microbiome Prescription Use Genetics

Is the bacteria capable of producing the chemical? Surprise, surprise, surprise… this list disagrees with the inference studies above. We still have the challenge of labs reports misidentifying the bacteria. Which is more reliable? Well, with genetics, we do not know if the production process is turned on or not. We do know which ones are incapable of producing.

The Wish List

I have tossed this request over to a person that has the academic skills (and creativity) to explore. Take the FASTQ files and the data from KEGG: Kyoto Encyclopedia of Genes and Genomes and see if you can determine the amount of genetic material producing each of these products. We totally side-step the key point of failure — identifying the bacteria!

That is, create software that takes in FASTQ files and provide estimates for all of the applicable Enzymes present! Remove bacteria naming from the process.

Possible software includes: Piphilin, Tax4Fun, PICRUSt2, PICRUSt

Human Analogy

You want to be rich. So you look at the rich and see expensive cars, big homes, trophy spouses etc. So you deduce that you just need to have those and you will become rich!! After all, there is a strong statistical association!! The alternative is to look at wealth production (the genes) and you see a different picture: high yield stocks, inherited money, professional licenses, etc. It is the same with looking at what bacteria produces.

PDF Reports for KEGG and OATS Targets

Today I looked at a sample and when I looked at raising butyrate, there were ZERO bacteria selected. In other words, there were no butyrate bacteria reported by the lab. This could be defect with the reference library used by the lab or a hundred other reasons. I was also hit by requests for suggestions from OATS test.

I did a series of detail posts on OATS in an Autism context which some may find informative:

I have created A Priori Reports for Pub Med reported conditions and it seems logical to create the same for compounds produced using KEGG: Kyoto Encyclopedia of Genes and Genomes data. Some examples are: Histamine (reduce), Butyrate (increase), and for SIBO(decrease): Hydrogen, Methane

This is experimental.

Logic Used

KEGG reports at the strain level using the full genome of each strain. From this information, we approximate the species genome (assuming the strains in the species are reasonably representative).

If the existing tests are 100% accurate at identifying all of these strains…. , we should have a smile. The reality is that tests do not report on many strains, and often disagree on species!! The problem is that they are not “safe” in their identification. For why, see these three posts:

To get around this defect, I used patterns from AI where dealing with imprecise data is normative. I assume that we could get reasonable suggestions by imagining that every species listed is present in equal amount and then generate suggestions from this synthetic microbiome.

Where is it available on the site?

Main Public Menu

The most commonly asks are under Information From Studies. They will produce a PDF download.

Using OATS Test Results

I have created a video of using both of these pages with explanation of what and how we are doing things.

I have also added a new feature beside Using OATS test to pick probiotics. The new page presents more choices

and produce a PDF report that aggregates the suggestions over everything marked out of range.

You will see a summary of what you entered:

A list of items to take or to avoid

Logged In – Advance Display

The “kitchen sink” is available after logging in and setting display level to advance. KEGG Derived Data appears on the menu

Under this menu are two items: one for compounds (like Organic Acids) and one for enzymes (like the one that creates histamine).

On these pages you can get the list of bacteria used for each calculation.

Cross Validation

I usually do some spot checks for reasonableness of suggestions. I picked the highest value item to reduce histamines: Thyme, and was lucky to find a study specifically for this.

Impact of Thyme Microcapsules on Histamine Production by Proteus bacillus in Xinjiang Smoked Horsemeat Sausage [2021] “Results showed that histamine accumulation was suppressed by thyme microcapsule inhibitory effect on the histamine-producing bacteria and the reduction in the transcription of hdcA and hdcP genes. “

So the suggestions appear to be reasonable.

Bottom Line

This is all an academic exercise for me. I do believe that this approach will likely produce superior results than random trial and error; or relying on influencers for approaches. As always, review with your medical professional before starting.