The Journey Begins with your microbiome

Thanks for joining me!

This is a companion site to the analysis site at: 

https://microbiomeprescription.com/

The intent of this site to assist people with health issues that are, or could be, microbiome connected. There are MANY conditions known to have the severity being a function of the microbiome dysfunction, including Autism, Alzheimer’s, Anxiety and Depression. See this list of studies from the US National Library of Medicine. Individual symptoms like brain fog, anxiety and depression have strong statistical association to the microbiome. A few of them are listed here.

The base rule of the site is to avoid speculation, keep to facts from published studies and to facts from statistical analysis(with the source data available for those wish to replicate the results). Internet hearsay is avoid like the plague it is.

Open data and Open source are our mottos!

Continue reading “The Journey Begins with your microbiome”

Supplements to avoid before bed…

This is based on bacteria identified in Sleep and the Microbiome – Some Notes. Bacteria level shifts through the day and you do not want to feed the bacteria that are associated with sleep issues. This is theoretical lists that ignores the magnitude of shifts.

To Avoid Before Bed

  • arabinoxylan oligosaccharides (prebiotic)
  • bacillus subtilis (probiotics)
  • berberine
  • bifidobacterium longum (probiotics)
  • bile (acid/salts)
  • Burdock Root
  • Fisetin
  • ginger
  • glycine
  • inulin (prebiotic)
  • iron
  • lactobacillus casei (probiotics)
  • lactobacillus reuteri (probiotics)
  • lactobacillus rhamnosus gg (probiotics)
  • omega-3 fatty acids
  • saccharomyces boulardii (probiotics)
  • salt (sodium chloride)
  • Slippery Elm
  • sodium butyrate
  • vitamin d
  • walnuts
  • wheat
From Social Media
From Social Media

Fine to take

These items will have a reducing impact on at least one of the bacteria. Items in bold has the highest impact.

  • Arbutin (polyphenol)
  • bacillus amyloliquefaciens (probiotic)
  • bacillus coagulans (probiotics)
  • Baking Soda (Sodium Bicarbonate)
  • bentonite
  • Caffeine
  • camelina seed
  • cannabinoids
  • chitooligosaccharides (prebiotic)
  • diosmin,(polyphenol)
  • extra virgin olive oil
  • galacto-oligosaccharides (prebiotic)
  • Hesperidin (polyphenol)
  • l-glutamine
  • linseed(flaxseed)
  • luteolin (flavonoid)
  • melatonin supplement
  • N-Acetyl Cysteine (NAC),
  • pyridoxine hydrochloride (vitamin B6)
  • quercetin
  • resveratrol (grape seed/polyphenols/red wine)
  • sodium stearoyl lactylate
  • thiamine hydrochloride (vitamin B1)
  • Vitamin B-12
  • vitamin b3 (niacin)
  • vitamin b7 biotin (supplement) (vitamin B7)
  • Vitamin C (ascorbic acid)
  • xylan (prebiotic)

So we have melatonin supplement, camelina seed and a glass of red wine to take with some B-vitamins at bed time!


Sleep and the Microbiome – Some Notes

A special edition blog for the sleepless… Many studies are looking at the microbiome with co-morbid conditions — making conclusions difficult.

  • “Growing evidence suggests bi-directional links between gut microbiota and sleep quality as shared contributors to health.” [2023]
  • “Contrary to expectations, timed feeding rendered animals more sensitive to stress” [2023] — so eating by the clock and not the light impacts stress negatively.
  • “In older adults, shorter sleep duration is associated with an increase in pro-inflammatory bacteria whereas increasing sleep quality is positively associated with an increase of beneficial Verrucomicrobia and Lentisphaerae phyla.” [2022]
  • Lachnoclostridium (genus) correlates positively with sleep efficiency, Blautia (genus) correlates negatively [2022]
  • “several taxa (LachnospiraceaeCorynebacterium, and Blautia) were negatively correlated with sleep measures” [2017]
  • Blautia and Eubacterium hallii were microbe markers in the sleep-disordered population” [2022]
  • “Relative abundances of Streptococcus salivarius and Veillonella were independent predictors of sleep disturbances in MHE patients” [2022]
  • “class Mollicutes in subjects with poor sleep quality were lower than in the healthy individuals. [2022]
  • “The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers” [2021]

For what reduces Blautia click here (melatonin supplement and camelina seed). Click here for Lachnoclostridium list (also includes melatonin supplement and camelina seed). Since populations change during the day (See Changing your Microbiome Results by when you take your sample!) you want to avoid substances that FEED these bacteria likely 4+ hours before bed. For list of items, see Supplements to avoid before bed…

Shift them to the morning times


Gut microbiome diversity is associated with sleep physiology in humans [2019]

“men with poor sleep (PSQI >5) tended to have lower alpha-diversity compared to men with normal sleep (Faith’s PD, beta= -0.15; 95% CI:-0.30-0.01, p=0.06). Sleep regularity was significantly associated with  robust Aitchison distances (RPCA) and (phylogenetic-RPCA) PRPCA, even after adjusting for site, batch, age, ethnicity, body mass index, diabetes, antidepressant and sleep medication use, and health behaviors”

  • the top 5 positively associated with sleep regularity were Faecalibacterium prausnitzii G, OEMS01 sp0900199405, Oscillibacter valericigenes, Faecalibacterium prausnitzii A, and Faecalibacterium prausnitzii C.
  • [Poorer sleep] associated with Ruthenibacterium lactatiformans, Bacteroides uniformis, Alistipes putredinis, and Escherichia dysenteriae
Association of subjective and objective measures of sleep with gut microbiota composition and diversity in older men: The Osteoporotic Fractures in Men (MrOS) study [2023]
Gut microbiota alterations in response to sleep length among African-origin adults [2021]

Many Probiotics have some effect

My personal experience is that for most probiotics, taking just before bedtime helps with sleep. I say most — because a few of them will actually cause issues with falling a sleep.
If you have single strains probiotics, you may wish to experiment with the impact of individual strains. Take one strain consistently at bed time, with a significant dosage, for a few days to see the impact (if any). One’s that cause wakefulness, may be ones you should take in the morning.

Ken Lassesen

Bacteria are very very rarely bad or good

A reader messaged me this

hello I do not want to bother, I have a question in the laboratories of my country, in the microbiota tests they put veillonella as virulent, but in a recent publication of microbiome prescription I saw that it could be a solution, why do the laboratories attribute virulence to it?

My Answer

That is equivalent to saying “Italians are criminals”. Why would someone say that? “Some Italians belong to the Mafia”

Veillonella is a genus of gram-negative, anaerobic bacteria that are commonly found in the human oral cavity, gastrointestinal tract, and respiratory tract. While some strains of Veillonella can cause infections, particularly in individuals with compromised immune systems, the majority of strains are considered to be non-virulent or opportunistic pathogens. Some studies have suggested that Veillonella may play a role in certain disease states, such as periodontal disease, but more research is needed to fully understand the potential pathogenic mechanisms of this genus.

From https://chat.openai.com/chat

For a lab to creditably state that, the lab would need to identify the specific strain. Veillonella is a genus, composed of many species, each species is composed of many strains. In terms of our Italian allergy, Italians come from many regions of Italy (species), within each regions are many families (strains). There may be some of these families that tend to being Mafia, others may tend to be priests (and eventually Popes).

Yin-Yang

My attitude is that Yin and yang is a better way of viewing bacteria. Bacteria are out of balance. Too many poor people results in high crime rates (out of desperation), Too many rich people results in low class mobility (the only people that get ahead are their friends, “old school ties”). The “right balance” for a well functioning society varies by country — for example, Iceland versus Haiti. Similarly, your DNA and diet influences what the right balance should be.

This family’s favorite and most effective probiotic is Mutaflor, an Escherichia coli probiotic. All E.Coli is not bad, trying to eliminate all E.Coli is likely a very dumb choice.

Changing your Microbiome Results by when you take your sample!

While working on a different blog post, I came across this study with a nice collection of charts to illustrate the importance of taking samples at the same time of day! It also makes implication that microbiome testing firms should be asking for the time of day that samples was taken (and provide gender, age and time of sample reference ranges — if they want to be creditable)

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock [2015]

Showing Gender Differences (M, F)
Differences with Sleep Issues (BMal1 Circadian Clock Protein)

See The Circadian Clock Protein BMAL1 Acts as a Metabolic Sensor In Macrophages to Control the Production of Pro IL-1β [2021] for more information on BMAL1

Bottom Line

I have often compared the microbiome to a city. If you do a opinion survey, when in the city you take the survey and the time of day has a huge impact. Taking it at 7am in the morning, you will be bias for office workers. At 2pm, likely female shoppers. At 4am likely make shift workers.

Interesting Successful Clinical Trial for Long COVID and ?ME/CFS ?

A key take-away is the importance of bacteria that triggers coagulation and inflammation.

A reader forwarded me this link,

A Randomized Controlled Trial of the Efficacy of Systemic Enzymes and Probiotics in the Resolution of Post-COVID Fatigue

The study concludes:

This study demonstrates that a 14 days supplementation of ImmunoSEB + ProbioSEB CSC3 resolves post-COVID-19 fatigue. The proposed supplement regimen significantly reduces the burden of both, physical and mental fatigue and is effective as an early intervention in the recovery of COVID-19 patients, many of whom continue to experience severe fatigue including muscle weakness and “brain fog” several months after initial infection. 

The substances used are very familiar to readers of my CFS Remission blog. They are:

  • Bacillus coagulans LBSC (DSM 17654)
  • Bacillus subtilis PLSSC (ATCC SD 7280)
  • Bacillus clausii 088AE (MCC 0538)
  • Serratiopeptidase,
  • Bromelain,
  • Amylase,
  • Lysozyme,
  • Peptidase,
  • Catalase,
  • Papain,
  • Glucoamylase
  • Lactoferrin

Some quick notes with citations for new readers:

This points back to the research and demonstration done by Dave Berg at Hemex Labs . “Berg and Joseph Brewer studied coagulation in CFS patients and concluded that approximately 85% of chronic fatigue syndrome patients had hypercoagulation, “[src].

My personal experience with the Hemex approach is good and put me into remission in 2000. Objective measurements showed coagulation in some parts of the coagulation cascade with piracetam and heparin being my favorite cocktail (both taken sublingual).

Reservations

The study ended at two weeks with no ongoing tracking of patients. My observations of ME/CFS people over several decades has been that short term remission is common with a slow regression back to fatigue. An excellent examples are ME/CFS in Australia doing Fecal Matter Transplants with remission within 48 hours and relapse in 4-8 weeks. Just as some bacteria (bacillus cited above) reduces coagulation, other bacteria triggers coagulation. If those triggering bacteria are not adequately suppressed then the fatigue and brain fog will return over time. Think of a leaking dike, you bring in the pumps and remove the water behind the dike, 3 weeks later the water is back — you need to fix the leak in the dike also.

A reader pointed out that the product is available on Amazon for $40. So a cheap experiment to try! If you do try it– please add your experience as a comment on this post.

Condition Progression Using the Microbiome

Today I ran some queries to see how many progressions between the conditions that I have could be inferred from the current data. The following were used:

  • The taxon must be exact matches (no parent of a taxa or taxa children)
  • We count the number of times that the taxa shifts are the same direction, or are different
  • Each condition must share at least 10 bacteria.
  • All of the data (with sources) can be found here for people to dig further into relationships.

The results are below for those with 65% the same or more. Some are very expected, some are not

  • Chronic Fatigue Syndrome with
    • ME/CFS with IBS
    • ME/CFS without IBS
    • ME/CFS with IBS vs ME/CFS without IBS DOES NOT SHOW UP because they only have 5 bacteria in common
  • Small Intestinal Bacterial Overgrowth  (SIBO) was not expected with
    • Colorectal Cancer
    • Rheumatoid Arthritis (RA),Spondyloarthritis (SpA)
    • Parkinson’s Disease
    • But expected with Irritable Bowel Syndrome
    • NOTE: Progression from one condition to another condition may be depend on DNA or epigenetics. If there is a high match up, it should be viewed as increased risk that may be mitigated with adjustments of the microbiome.
Condition NameCondition NameSame Direction PercentageDifferent Direction Percentage
Alzheimer’s diseaseChronic Kidney Disease86.713.3
ADHDChronic Kidney Disease85.714.3
Chronic Fatigue SyndromeME/CFS with IBS85.714.3
Chronic Urticaria (Hives)Obesity85.714.3
Chronic Fatigue SyndromeME/CFS without IBS85.214.8
Chronic Urticaria (Hives)obsessive-compulsive disorder84.615.4
Chronic Urticaria (Hives)Ulcerative colitis83.316.7
Colorectal CancerSmall Intestinal Bacterial Overgrowth  (SIBO)83.316.7
Histamine Issues,Mast Cell Issue, DAO Insufficiencyobsessive-compulsive disorder83.316.7
Brain Traumahypertension (High Blood Pressure83.316.7
Allergic Rhinitis (Hay Fever)Chronic Fatigue Syndrome83.316.7
Ankylosing spondylitisRosacea83.316.7
Parkinson’s DiseaseAnorexia Nervosa83.316.7
rheumatoid arthritis (RA),Spondyloarthritis (SpA)Small Intestinal Bacterial Overgrowth  (SIBO)83.316.7
Brain TraumaMultiple Sclerosis81.818.2
Hyperlipidemia (High Blood Fats)Multiple Sclerosis81.818.2
hypertension (High Blood PressureNonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic81.818.2
Graves’ diseaseBipolar Disorder81.818.2
Chronic Urticaria (Hives)Inflammatory Bowel Disease81.318.8
Stress / posttraumatic stress disorderSystemic Lupus Erythematosus80.819.2
ME/CFS without IBSLong COVID8020
Chronic Kidney DiseaseBipolar Disorder8020
Alzheimer’s diseaseMultiple Sclerosis8020
ADHDobsessive-compulsive disorder78.621.4
gallstone disease (gsd)Ulcerative colitis78.621.4
OsteoarthritisLong COVID78.621.4
Systemic Lupus ErythematosusAnorexia Nervosa77.822.2
ADHDMultiple Sclerosis77.322.7
Chronic Urticaria (Hives)Nonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic76.923.1
Parkinson’s DiseaseSmall Intestinal Bacterial Overgrowth  (SIBO)76.923.1
Chronic Urticaria (Hives)Long COVID76.523.5
Gastroesophageal reflux disease (Gerd) including Barrett’s esophagusLong COVID76.523.5
Chronic Kidney DiseaseSystemic Lupus Erythematosus76.223.8
hypertension (High Blood Pressureobsessive-compulsive disorder7624
Inflammatory Bowel DiseaseSmall Intestinal Bacterial Overgrowth  (SIBO)7525
Histamine Issues,Mast Cell Issue, DAO InsufficiencySchizophrenia7525
Multiple SclerosisSmall Intestinal Bacterial Overgrowth  (SIBO)7525
Nonalcoholic Fatty Liver Disease  (nafld) NonalcoholicStress / posttraumatic stress disorder7525
Chronic Kidney DiseaseGraves’ disease7525
gallstone disease (gsd)Nonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic7525
Cerebral PalsyParkinson’s Disease7525
RosaceaType 1 Diabetes7525
Chronic Urticaria (Hives)Crohn’s Disease73.726.3
Chronic Urticaria (Hives)Psoriasis72.727.3
DepressionME/CFS with IBS72.727.3
neuropsychiatric disorders (PANDAS, PANS)Parkinson’s Disease72.727.3
Irritable Bowel SyndromeOsteoarthritis72.727.3
Histamine Issues,Mast Cell Issue, DAO InsufficiencyInflammatory Bowel Disease72.727.3
Chronic Fatigue SyndromeFunctional constipation / chronic idiopathic constipation72.727.3
AsthmaCeliac Disease72.727.3
rheumatoid arthritis (RA),Spondyloarthritis (SpA)Hidradenitis Suppurativa72.727.3
ADHDAlzheimer’s disease72.227.8
AllergiesPsoriasis72.227.8
Brain TraumaParkinson’s Disease72.227.8
DepressionFibromyalgia72.227.8
AtherosclerosisHistamine Issues,Mast Cell Issue, DAO Insufficiency7228
Inflammatory Bowel DiseaseUlcerative colitis71.828.2
Chronic Kidney DiseaseStress / posttraumatic stress disorder71.428.6
AtherosclerosisME/CFS with IBS71.428.6
ADHDFunctional constipation / chronic idiopathic constipation71.428.6
Ankylosing spondylitisGastroesophageal reflux disease (Gerd) including Barrett’s esophagus71.428.6
rheumatoid arthritis (RA),Spondyloarthritis (SpA)Rosacea71.428.6
Chronic Kidney DiseaseLong COVID70.629.4
gallstone disease (gsd)rheumatoid arthritis (RA),Spondyloarthritis (SpA)70.629.4
Multiple SclerosisAnorexia Nervosa70.629.4
Inflammatory Bowel DiseaseNonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic70.429.6
hypertension (High Blood PressureInflammatory Bowel Disease7030
Cerebral PalsyLong COVID7030
Chronic Kidney DiseaseCOVID-1969.630.4
Cerebral Palsyobsessive-compulsive disorder69.230.8
Cerebral PalsyPsoriasis69.230.8
AtherosclerosisOsteoarthritis69.230.8
Bipolar Disorderobsessive-compulsive disorder69.230.8
ADHDAnorexia Nervosa69.230.8
Alzheimer’s diseaseAnorexia Nervosa69.230.8
Hyperlipidemia (High Blood Fats)rheumatoid arthritis (RA),Spondyloarthritis (SpA)69.230.8
hypertension (High Blood PressureOsteoporosis69.230.8
Inflammatory Bowel DiseaseAnorexia Nervosa69.230.8
Nonalcoholic Fatty Liver Disease  (nafld) NonalcoholicAnorexia Nervosa69.230.8
Nonalcoholic Fatty Liver Disease  (nafld) NonalcoholicUlcerative colitis69.230.8
FibromyalgiaNonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic69.230.8
Chronic Kidney DiseaseNonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic69.230.8
Chronic Kidney DiseaseOsteoporosis69.230.8
Chronic Kidney DiseaseInflammatory Bowel Disease68.831.3
Chronic Kidney DiseaseMultiple Sclerosis68.831.3
gallstone disease (gsd)Irritable Bowel Syndrome68.831.3
ME/CFS with IBSCOVID-1968.831.3
Irritable Bowel SyndromeSmall Intestinal Bacterial Overgrowth  (SIBO)68.831.3
hypertension (High Blood PressureBipolar Disorder68.831.3
Allergic Rhinitis (Hay Fever)Systemic Lupus Erythematosus68.831.3
AtherosclerosisSmall Intestinal Bacterial Overgrowth  (SIBO)68.831.3
Chronic Kidney DiseaseColorectal Cancer68.831.3
Chronic Kidney DiseaseDepression68.431.6
gallstone disease (gsd)COVID-1968.431.6
AtherosclerosisLiver Cirrhosis68.331.7
Ankylosing spondylitisLiver Cirrhosis68.231.8
Celiac DiseaseInflammatory Bowel Disease68.231.8
Functional constipation / chronic idiopathic constipationSchizophrenia68.231.8
Stress / posttraumatic stress disorderUlcerative colitis68.131.9
Ankylosing spondylitisBipolar Disorder67.932.1
ADHDDepression67.932.1
Alzheimer’s diseaseParkinson’s Disease67.632.4
Ulcerative colitisLong COVID6733
Osteoarthritisrheumatoid arthritis (RA),Spondyloarthritis (SpA)66.733.3
OsteoporosisCOVID-1966.733.3
Alzheimer’s diseaseInsomnia66.733.3
Amyotrophic lateral sclerosis (ALS) Motor NeuronBipolar Disorder66.733.3
Alzheimer’s diseaseBipolar Disorder66.733.3
Anorexia NervosaLong COVID66.733.3
Anorexia Nervosaobsessive-compulsive disorder66.733.3
AsthmaSystemic Lupus Erythematosus66.733.3
ADHDBipolar Disorder66.733.3
Allergic Rhinitis (Hay Fever)Stress / posttraumatic stress disorder66.733.3
ADHDChronic Fatigue Syndrome66.733.3
AcneStress / posttraumatic stress disorder66.733.3
AcneSystemic Lupus Erythematosus66.733.3
AcneLiver Cirrhosis66.733.3
Allergic Rhinitis (Hay Fever)Sjögren syndrome66.733.3
AllergiesType 1 Diabetes66.733.3
Cerebral PalsyAnkylosing spondylitis66.733.3
Chronic Fatigue SyndromeNonalcoholic Fatty Liver Disease  (nafld) Nonalcoholic66.733.3
Cerebral PalsySystemic Lupus Erythematosus66.733.3
Cerebral PalsyInflammatory Bowel Disease66.733.3
Brain TraumaType 2 Diabetes66.733.3
Brain Traumaobsessive-compulsive disorder66.733.3
Brain TraumaIrritable Bowel Syndrome66.733.3
Fibromyalgiaobsessive-compulsive disorder66.733.3
gallstone disease (gsd)Stress / posttraumatic stress disorder66.733.3
DepressionGout66.733.3
Chronic Kidney Diseaseobsessive-compulsive disorder66.733.3
Chronic Urticaria (Hives)Systemic Lupus Erythematosus66.733.3
Crohn’s DiseaseHistamine Issues,Mast Cell Issue, DAO Insufficiency66.733.3
COVID-19Eczema66.733.3
Histamine Issues,Mast Cell Issue, DAO InsufficiencyLiver Cirrhosis66.733.3
InsomniaLong COVID66.733.3
Inflammatory Bowel Diseaseobsessive-compulsive disorder66.733.3
Inflammatory Bowel DiseaseOsteoarthritis66.733.3
Inflammatory Bowel DiseaseME/CFS without IBS66.733.3
ME/CFS with IBSUlcerative colitis66.733.3
ME/CFS without IBSCOVID-1966.733.3
Liver Cirrhosisneuropsychiatric disorders (PANDAS, PANS)66.733.3
Liver CirrhosisME/CFS with IBS66.733.3
Multiple SclerosisMultiple system atrophy (MSA)66.733.3
Liver CirrhosisStress / posttraumatic stress disorder6634
Inflammatory Bowel Diseaserheumatoid arthritis (RA),Spondyloarthritis (SpA)65.934.1
Celiac Diseaseobsessive-compulsive disorder65.734.3
Celiac DiseaseSystemic Lupus Erythematosus65.634.4
Chronic Fatigue SyndromeSchizophrenia65.534.5
hypertension (High Blood PressureCOVID-1965.534.5
ADHDParkinson’s Disease65.434.6
Sjögren syndromeSystemic Lupus Erythematosus65.434.6
Stress / posttraumatic stress disorderobsessive-compulsive disorder65.234.8
rheumatoid arthritis (RA),Spondyloarthritis (SpA)Bipolar Disorder65.234.8
Chronic Fatigue SyndromeParkinson’s Disease65.234.8
AutismBrain Trauma65.234.8
Multiple SclerosisParkinson’s Disease65.234.8
AtherosclerosisIgA nephropathy (IgAN)6535
AsthmaCOVID-196535
Chronic Kidney Diseaserheumatoid arthritis (RA),Spondyloarthritis (SpA)6535
Alzheimer’s diseaseGraves’ disease6535

The problem with “official” ranges from labs

Ranges are created by labs to be able to give answers to people asking for them. The key word is created. They may have no actually be healthy ranges for your age, gender, diet style etc. Say again! Not actually healthy ranges for you.

At the highest levels of the bacteria are phylums:  (Firmicutes and Bacteroidetes). Almost every bacteria belongs to one of these two phylums. Almost every person in the US would be unhealthy by Indian Standards — well outside of the typical ranges. And almost every person in the India would be unhealthy by US Standards — well outside of the typical ranges. If you are of Indian descent living in the U.S. and eating a mixture of Indian and Western foods… any ideas of what you healthy range should be?

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? [2020]

The classic approach in most labs for other tests (like Vitamin D, iron, etc) is to get a collection of apparently healthy individuals from physically around where the lab is and the assume that the data will be a bell curve/normal distribution. The people are typically self-declared to be healthy – for Americans, this will usually be high in people that have a high body-mass index [BI] (i.e. overweight). We know that a high BI causes changes in the microbiome…. From that data, compute the range — see typical instructions to labs here:  Standard Lab Ranges (+/- 2 Standard Deviations). This assumption is never validated statistically on the data – lack of appropriate skills in the lab is a common cause. If you attempt to validate against almost any bacteria in the microbiome — it will fail, often extremely fail.

Research scientists knows that this is making a huge assumption and will often in their research papers use a method called Box Plot Whisker. It is definitely better but typically require more samples to establish the ranges. A lab manager will opt not to do it when he may only need to do 30 samples to get the Standard Lab Ranges, and may need 150 samples to get a good Box Plot Whisker. Why should he want to increase costs when he can go cheap and claim that he is following standard processes.

Wait! There is More!

Suppose that you get 200 “healthy samples” — we can get the ranges using Box Plot Whisker and that’s it! We now know what healthy ranges are then!!!

WRONG!!! VERY WRONG!!! The National Institute of Standards and Technology (the same people who define how long a foot is, or how many lumens a light bulb has) has made if very clear!!!!

If we have 200 samples, we will likely have 97 different ranges!!

From https://cfsremission.com/2019/12/22/the-taxonomy-nightmare-before-christmas/

Some of the ranges from different ways will be in significant contrast with each. To illustrate this, let us look at samples uploaded from OmbreLabs and Biomesight — they both use the same physical lab that has the same equipment — the difference is the software (“the ways”) that they use on the identically same data file!!!! We are NOT talking about two samples from the same stool; we are talking about one sample only

LabBacteria/Taxa Types
BiomeSight 4193
OmbreLabs6549
uBiome2324
All consumes the same FASTQ raw data — the difference is the software they use

Looking at frequency of detection, we have some good matches at the genus level

Tax_NameBiomeSight
% Detected
OmbreLabs
% Detected
BiomeSight
Average %
OmbreLabs
Average %
Vibrio3.8883.9070.0030.003
Nitrobacter0.2990.3190.0020.002
Prochlorococcus0.1790.1590.0030.003
Ruegeria0.1790.1590.0010.004

And some bad ones!

Tax_NameBiomeSight
% Detected
OmbreLabs
% Detected
BiomeSight
Average %
OmbreLabs
Average %
Rhodothermus90.3711.9140.2750.039
Escherichia80.7425.1830.5360.058
Pedobacter97.96724.0830.9360.014
Alkaliphilus97.18928.6280.3480.011


Whose right? Both are right and both are wrong — there is no standard!!!! Right assumes a shared upon norm or consensus by people concerned.

What is my personal solution?

I am by academics and industrial experience, a statistician, operational research and Artificial Intelligence Software Engineer. The way to get the most probable solution from a difference of opinions, is to build a consensus model — take every ones suggestions and combined them!

At present I have good number of opinions that can be used, and if I get more expert opinions (and permission to use them) I will gladly add them.

I would love to see all of the labs make public the data they used to construct their ranges. Open data. I have discussed that with some of them and they deem it to be “proprietary” data. It is, in that the disclosure may reveal their mistakes and expose their ranges as questionable. Every one’s ranges are questionable (IMHO).

There is no right answer. There is no trustworthy range. A consensus answer is likely a good answer, the best that is available at the moment.

Another ME/CFS person has gone to Firmicutes!

This person sent a request just after this post went out: My gut has gone to Firmicutes!

Reader’s Backstory

I am a 39 year old male from the US whose symptoms appeared at or around the time of puberty.  My case is not particularly severe – in fact it took me until the age of 23 to acknowledge to myself that I had a problem. While I fit the diagnostic criteria for ME/CFS, I specifically suffer from brain fog, low mental and physical energy, food sensitivities, 3 trips to the bathroom each morning, mild joint pain, and unrefreshing sleep. My symptoms have gradually worsened as I’ve aged. Certain vitamins, herbs, and foods have helped me to feel better but these solutions do not last more than a few days max. Nobody else in my family shares my symptoms, and I’m told I didn’t take antibiotics as a child.  My BMI is 22.

Proforma Review

Well you can see the process in this My gut has gone to Firmicutes! post, I thought that I should do a step by step walk thru of the process that I use.

After logging in, I go to [My Profile] and then on the [Overview] panel, click Health Analysis.

Under Potential Medical Conditions Detected, there were no red flags (see 📹 Explaining these measurements).

Similarly, [Bacteria deemed Unhealthy] had no red flags but does have a few bacteria that are not healthy predictors (Eggerthella lenta, Blautia producta, [Clostridium] symbiosum) and Collinsella (90%ile) which is viewed as proinflammatory – not unexpected with ME/CFS. Dr. Jason Hawrelak Recommendations came in at 98.8 percentile, so generally healthy. Blautia is of interest, it is at 36% of the microbiome versus Dr. Harelak preferred 5-10% and one of the highest levels in over 3,000 samples. This seems to be a possible smoking gun. The person is at the 70%iles using PubMed studies for ME/CFS without IBS.

Using the Krona Chart panel we see that the dominant species is Blautia obeum (which lacks any clear condition associations).

The next step is to look under [Visualizations] – Microbiome Tree, to visually scan for unusual disturbances. What I usually look for on the first pass are HIGH Percentiles with a high % of the microbiome. 💥BOOM we had some major ones. The 100%ile means that the value was higher than any of the 3000+ samples

Taxa / BacteriaPercentilePercentage
Firmicutes phylum96%ile97.7%
Eubacteriaceae:99%ile7.7%
Eubacterium99%ile8.1%
Collinsella aerofaciens91%ile1.3%
Blautia100%ile36.2%
Blautia obeum100%ile21.3%
Dorea100%ile7.7%
Dorea longicatena100%ile6.5%
Agathobaculum99%ile3.1%
Agathobaculum desmolans99%ile3.1%

At this point, we have a ton of items that are overgrowth. This is a very atypical sample with a bunch of unusually high shifts. So we will move on to getting suggestions.

Bacteroidetes is 0.43% of the microbiome so we are talking a Firmicutes/Bacteroidetes ratio of 228:1. The normal ration is around 1.5 (The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age, 2009), There is also considerable variation across the world.

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? [2020]

If there was not so many extreme high values, then our suggestion process usually work with both high and low values.

Getting Suggestions

My usual process is doing three methods and looking at the consensus report. The methods are:

Because of the extreme values, I am also doing Percentile in top or bottom 5% [28 taxa picked], For all four of these, I am restricting the suggestions to High Items. We need to reduce bacteria to make room!

The list was interesting — and also typical for ME/CFS patients:

The high-protein/meat diet would also provide B-vitamins listed above. Hesperidin’s best natural source is lemons — which also will provide Vitamin C. The best source for Arbutin is likely Lingonberry (available at IKEA) – for other see Arbutin – Microbiome Prescription Food And Nutrients. For the top items, use Nutrients with Number of Foods – Microbiome Prescription Food And Nutrients to see what foods contains it if you wish natural sources (or as supplements is not available).

There is one interesting diet to consider: Eating traditional Indian (based on chart above) – i.e. meatless high spice diet consisting of a lot of Dal and other foods from Taste of India or Kitchens Of India. Alternatively, spend 6 months at a traditional Ashram in India. This diet appears to result in the lowest Firmicutes/Bacteroidetes ratio.

Probiotics

While there were a few suggestions, the computed impact were relatively low compare to those with negative impact. I would skip probiotics.

Questions from Reader

Q: Does the Consensus View only show me what to increase, or does it also show me what to avoid? 
A: Yes, Just click on the column titles to reverse the order. If you hold the shift key, you can do sorting by multiple columns.

Q: This may seem like a silly comment, but it’s difficult for me to envision a vitamin (such as B1) or a supplement (such as melatonin) significantly influencing the microbiome. I picture large foods filled with bacteria like sauerkraut, or sugary foods like cookies, as the items that would have the biggest impact.  I clearly have a lot to learn.

A: Bacteria feed on chemicals, including vitamins. If you click on the modifier name, i.e. thiamine hydrochloride (vitamin B1), AFTER setting display level to Intermediate, you will see a column called citations:

Clicking on Source Study will show where the data is coming from, with links to the studies.
Some studies are on animals — but the bacteria is expected to respond in the same manner.

Remember: The site works off of actual peer-review studies only. Evidence, not speculation or wishful thinking.

Q: When I adjust the recommendations to include prescription items, I get a whole bunch of prescriptions that show up.  I’ll try to convince my doctor to prescribe!
A: It is not worth the effort — because this is an off-label usage and there will be resistance. Especially since half of the top items in the list are not prescription and similar predicted impact. Hesperidin is in Lemons and Buchu, no prescription needed. Try the other items first, if the next test shows improvement (expected) and a prescription item jumps out far above the others — then it will be a good time to ask.

Q: Random question:  The Probable Symptoms link under My Profile seems to be broken at the moment.  This isn’t the same as the Potential Medical Conditions Detected under the Health Indicators, right?  
A: Correct, the probable symptoms is done by pattern matching. Your numbers are so different that the A.I. was unable to make a reasonable infererence.

Q: I’d think the microbiome would be a really accurate way to predict obesity, but under Potential Medical Conditions I was surprised to see i’m in the 100th percentile for Obesity.  I weighed 120 pounds throughout high school and even now can’t break 150 lbs.  I plan on getting updated samples every couple months, so i’ll be interested to see if my next sample shows something different here.
A. Once we get things changing, we can use the National Library of Medicine Citations for Obesity to see how we want to target further shifts. We know what bacteria is associated with it, we just want to push the same bacteria in the opposite direct from that which was reported.

Course of Action

The first item of concern is simple: make sure that the dosages are adequate to effect changes. Taking a once-a-day supplements that has all of the vitamins listed above is unlikely to have any significant effect. Use the Dosages for Supplements to find the dosages. This can also be found by clicking on the Simplified Suggestions

Quick summary of dosages

After 4-8 weeks (depending on finances), repeat the microbiome test (using the same lab) and see what has changed. Recovery is like steering a sailing ship: it is a continuous set of course correction. Sometimes just a few to get to a safe harbor; other times, you may feel like you are circumnavigating the world.

Literature on ME/CFS and Firmicutes: I review studies on ME/CFS, Chronic Q-Fever, Lyme etc, and I do not find this pattern being cited. It is a very big 💥 BOOM pattern

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 appears to 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.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.

The information above should always be considered/discussed with your medical professional if possible.

My gut has gone to Firmicutes!

Back Story

I am a 25 year old male from the US, and I have been suffering from constipation, food sensitivities, insomnia, and psoriasis since 2018 (21 years old) after a round of Clindamycin.

This person actually has three samples from OmbreLabs:

  • 2022-09-09: Firmicutes 95% (93%ile)
  • 2022-10-01: Firmicutes 93.5% (88%ile)
  • 2022-11-10: Firmicutes 94.8% (90%ile)

The first thing that I note is that “give it time, it will correct itself” does not seem to be happening. The second thing is these rates appear to be seen in about 10% of the samples.

Drilling down to which Firmicutes are dominating we have (latest sample):

My first impression is that we want to focus solely on reducing the high ones, and make room for the low ones to grow. That is actually a choice on building a consensus. Because of the shear numbers, I am going to use strict study citations. Why? Typically we are sparse on studies and need to infer / estimate likely impacts. In this case, we are going to hit studies everywhere!

For bacteria selection (with only highs) we have:

  • Filter by Standard Lab Ranges – 14 bacteria
  • Kaltoft-Moltrup Ranges – 50 bacteria
  • Box Plot Whiskers Ranges – 58 bacteria

The list of items suggested is atypical with supplements dominating! I attach them below.

PriorityGut Modifier
795.9Hesperidin (polyphenol)
789.3melatonin supplement
774.7luteolin (flavonoid)
774.7retinoic acid,(Vitamin A derivative)
774.7Arbutin (polyphenol)
774.7diosmin,(polyphenol)
774.7vitamin b3 (niacin)
774.7pyridoxine hydrochloride (vitamin B6)
709.2thiamine hydrochloride (vitamin B1)
688.7vitamin b7 biotin (supplement) (vitamin B7)
687N-Acetyl Cysteine (NAC),
656.3linseed(flaxseed)
642.7Vitamin B-12
592.7caffeine,(coffee or non-herbal tea)
563tea
522neem
506.5quercetin,resveratrol
495.6folic acid,(supplement Vitamin B9)
455.7Guaiacol (polyphenol)
438.6low carbohydrate diet
428.5carboxymethyl cellulose (prebiotic)

My suggestion would be a low carbohydrate diet and start taking the supplements above. I would avoid all probiotics, one did show up at the top of the probiotics: bifidobacterium longum bb536 (probiotics) at the strain level, but a strong avoid at the species level which means it is a high risk one

I would use the suggested dosages cited below (AFTER reviewing with your medical professional)

Microbiome ModifierCurrentDosageClinical DosageEst Confidence
Vitamin B1 Thiamine1.8 gm/day709.2
Vitamin B3 Niacin3000 mg/day774.7
Vitamin B6 Pyroxidine200 mg/day774.7
Vitamin B7300 mg/day688.7
Vitamin B9 Folate5 mg/day495.6
Vitamin B12 Cyanocobalamin10 mg/day642.7
Vitamin C30 g/day410.7
Vitamin D50000 UI/day141.3
DO NOT USE A B-COMPLEX. Some B-Vitamins were to be avoided

Questions From the Reader’s Review

In general, I avoid diet styles personally because they lack precision for the content. For example, does doing a Mediterranean diet means drinking the typical amount of wine (10-12 liters of wine per year) with 57 pounds of fish a year as seen by many countries around the Mediterranean? The fish consumption in the Mediterranean region differs greatly from what is claimed to be from that diet.

  1. What exactly is meant by a low carb diet in the research? (50 grams, 100 grams, etc)
  2. I see that sorghum is recommended despite being a carb source (this is further in the consensus suggestions, but on in the blog post), so would this be a high risk item?
    • Suggestions are done independent of each other. In general, we have no idea about interactions. As with all suggestions, the source of the suggestion is available, in this case it was specific for sorghum brans [2015].
  3. Vegetable/fruit juice based diets is one of the diet styles recommended.  Would perhaps following a diet low if solid carbs like rice, bread, potatoes but still consuming orange juice be an idea worth considering?  Getting carbs from juices would essentially prevent any food residue from getting far into the digestive system; therefore, limiting fermentable residue.  I am asking so much about carbs because I have done low carb in the past, and I felt better for a short period of time but worse long term.
  4. How long should the low carb diet be followed?  How strict do I have to be to receive benefits?
    • Suggestions are usually safe to keep to for 4-6 weeks, then their impact on the microbiome should be realized and a retest should be done to get the next course adjustment.
  5. How safe is carboxymethyl cellulose as a prebiotic based on the research?  I am a little concerned about taking it.  I also have a capsule making kit, so I would be able to make my own capsules.
  6. Chitosan has a fairly high at 407.3 on the consensus.  Is there a reason for not including it on your list in the blog post.  I see that one of your posts from CFS remission seem to recommend it for firmicutes overgrowth.
    • The reason to include or exclude is actually shown on the Advance Tab, see below

Getting the Reasons for Suggestions

  1. Change Display Level to Advance
  2. Go to Research Features tab
  3. Find this section and click Advance Suggestions

On the next page select how you want to generate suggestions and then make sure you click the green box

On the next page you will see book stacks (📚) by each suggestion.
Click it:

This will show the studies used to make this decision and why. That is, what are the other bacteria impacted by using this chitosan. Note that there are 42 taxa-studies listed! Focusing on a single bacteria, like firmicutes is not a process that I encourage, that is why I let the AI determine the suggestions based on all of the facts available.

Foods

If you pick a diet type, then using the new experimental food component would be suggested as an adjunct tool. I used the KM filter, restricted only to high bacteria as a start point for foods.

At the bottom of the suggestions page, we see the link button

The top items (with nutrients they were selected on) are listed below:

On the avoid list:

The food list takes items like Hesperetin and vitamins, and show the foods higher than typical. It speeds the analysis (and also overload the data that you have).

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 appears to 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.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.

The information above should always be considered/discussed with your medical professional if possible.

Samples over time of ME/CFS Spouse

This is the spouse of someone with significant ME/CFS. It is well known that bacteria is transferred between people in the same household unit.

This raises all sorts of questions — which I am not interested in exploring… “For better or worse, in sickness and in health”

My wink wink suggestion for microbiome issues has been “Snog a lot of pretty young healthy things as the best probiotic” — my wife does not agree…..

Comparison between Samples

The first step that I did was to verify that all samples used the same reference sticks. This means clicking this for each sample first.

New reference tables are uploaded once a week.

This person has processed FASTQ data thru both BiomeSight and OmbreLabs. I am using OmbreLabs data below. Using reference tables uploaded in 2023.

Criteria6/8/20228/4/20229/6/202210/26/2022
Lab Read Quality2.13.83.68.3
Bacteria Reported By Lab534774721775
Bacteria Over 99%ile10326
Bacteria Over 95%ile58272422
Bacteria Over 90%ile99534450
Bacteria Under 10%ile256848127
Bacteria Under 5%ile13281577
Bacteria Under 1%ile53116
Lab: Thryve
Rarely Seen 1%814912
Rarely Seen 5%43806073
Pathogens21343327
Outside Range from JasonH5577
Outside Range from Medivere13131717
Outside Range from Metagenomics9999
Outside Range from MyBioma7788
Outside Range from Nirvana/CosmosId23231919
Outside Range from XenoGene44444949
Outside Lab Range (+/- 1.96SD)38392622
Outside Box-Plot-Whiskers177202153118
Outside Kaltoft-Moldrup206257203292
Condition Est. Over 99%ile0000
Condition Est. Over 95%ile0000
Condition Est. Over 90%ile0000
Enzymes Over 99%ile1418523
Enzymes Over 95%ile11510559112
Enzymes Over 90%ile212192143320
Enzymes Under 10%ile6310693266
Enzymes Under 5%ile294527141
Enzymes Under 1%ile2208
Compounds Over 99%ile373631119
Compounds Over 95%ile289288275281
Compounds Over 90%ile372381361385
Compounds Under 10%ile288255235298
Compounds Under 5%ile192159136216
Compounds Under 1%ile3714431

General Impression

  • After the first sample, the next two had improvements but the last one went the wrong way.
    • Too high and Too low reduce for 2 samples and then increased
    • Too high or too low for Enzymes were the highest for the last sample
  • Most of the third party ranges were constant for the first two samples and most got worst for the last two samples.
  • Compounds are much less indicative of issues.
  • Special Studies are sensitive to lab quality,
    • 6/8/2022 4-14%, top items: ME/CFS without IBS, Poor gut motility, Cold Extremities
    • 8/4/2022 5-17%, top items: ME/CFS without IBS, Poor gut motility
    • 9/6/2022 4- 18%, top items:  ME/CFS without IBS,  Easily irritated
    • 10/26/2022 7 -22%, top items: General: Fatigue, ME/CFS without IBS

ME/CFS without IBS is a consistent top item and we see that the percentage is increasing.

Proposed Approach

Unlike many samples, we see distinct deterioration in several 3rd party criteria. For many samples, there is no change between samples. We will include those in the consensus, namely:

  • JasonH
  • Medivere
  • MyBioma
  • Xenogene

It is interesting to note that one 3rd part criteria improved: Nirvana. To this, we do our usual:

  • Lab ranges
  • Box-Plot-Whiskers
  • Kaltoft-Moldrup

The net result will be more bias to those in the 3rd party criteria cited above. Another way of stating that, we will emphasis more that which everyone agrees are most concerning.

The top suggestions (easily obtained):

The top avoids are:

The downloads are attached:

Food Suggestions

We mostly eat pastured meats and vegetables. No cereals and little in the way of carbs or even fruit. I used to eat linseed crackers in the USA, but here I eat buckwheat instead. Here in Spain we switched from wild Alaskan salmon, to seasonal, local, small blue fish, like mackerel, sardines, etc. Added Rabbit and can eat a lot more quality raw cured pork, if we want to. I have always enjoyed natural wine and Spain has plenty of it. Fresh made coffee and 100% cocoa. Raw goat, sheep and cow’s milk are also available and I do enjoy them with some regularity.

I used the latest sample with the Kaltoft-Moltrup Normal Ranges. The top suggestions are each because of different nutrients that appear significant with Fiber, total dietary and Magnesium, Mg being a common theme.

On the avoid list we have at the bottom:

Remember, foods are filtered to the nutrients that are above typical levels for foods containing the same nutrients. The goal is to reduce the intake of nutrients that have been identified to shift things in the wrong direction.

For most people, if you say reduce folic acid in your diet — most people will not have a clue. The purpose of the food suggestions is to translate a precise item into common foods.

Note: If a food in your diet is not in the list then we deem it as neutral. For example: there are 24 variety of rabbit in the food database, only one shows up in the suggestions from the sample, Rabbit, meat, raw, Oryctolaguscuniculus, (Nyama ya kalulu), which suggests to keep eating rabbit. Similarly for milk, the two that shows up are Milk with Cow’s blood (from Africa) of 626 entries for milk.

The video below may help understand Food Suggestions better.

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 appears to 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.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.

The information above should always be considered/discussed with your medical professional if possible.