Hey do you think microbiota dysbiosis could cause circadian disturbance? Most articles go in an opposite direction and say its lifestyle causing circadian disturbance…But my disturbance is resistant to lifestyle… I just have primary circadian problem that might be even my worst symptom… Most resistant and almost lifelong. 

Asked by a Reader

In keeping to “gold standard” of information instead of bloggers’ urban myths and ideologies, I head over to the National Library of Medicine studies.

• “gut microbial metabolites influence central and hepatic clock gene expression and sleep duration in the host and regulate body composition through circadian transcription factors”[2020]
• “Findings have suggested that gut microbiota play a major role in regulating brain functions through the gut-brain axis. A unique bidirectional communication between gut microbiota and maintenance of brain health could play a pivotal role in regulating incidences of neurodegenerative diseases. ” [2021]

Sleep, circadian rhythm, and gut microbiota [2020]

First, a more precise definition of circadian rhythms from the above study.

A fundamental part of eukaryotic life, circadian rhythms are endogenous, entrainable biological processes that oscillate in a 24-hour period in concert with the circadian environment of the earth. Circadian rhythms can be found at an intracellular level and have the ability to impact all aspects of metabolism (11). The mammalian circadian rhythm is orchestrated by a master clock, located in the suprachiasmatic nucleus (SCN) of the hypothalamus (12). The master clock follows the 24-hour light-dark cycle (the diurnal cycle) and coordinates the release of neurotransmitters such as serotonin and norepinephrine. Serotonin and norepinephrine are present at higher levels during wakefulness, while melatonin peaks during the night, regardless of the diurnal or nocturnal sleep cycles across species… The peripheral circadian clock is a system of organs within the 22 body which collect
environmental and internal signals in order to direct the expression of circadian clock genes

And then we read:

• “food intake can disassociate peripheral clock periodicity from the master clock; when this happens, greater immune system activation and metabolic dysfunction occur”
• “Dysbiosis and metabolic consequences resulting from circadian clock disruption may be due to increased permeability of the intestinal epithelial barrier “
• “gut microbial metabolites such as the short-chain fatty acids butyrate and acetate may influence clock gene expression“
• “Leone et al. found that a lack of gut microbiota, and consequently a deficit of microbial metabolites, resulted in markedly impaired central and hepatic circadian clock gene expression (40), suggesting the possibility that gut microbiota play a role in propagating circadian rhythm at the molecular level”
• “Serotonin deficiency elicits the loss of the circadian sleep-wake rhythm”
• “The microbes of the gastrointestinal tract exhibit circadian rhythm, and their composition oscillates in response to the daily feeding/fasting schedule.

The Role of Microbiome in Insomnia, Circadian Disturbance and Depression [2018]

The characteristics of the gastrointestinal microbiome and metabolism are related to the host’s sleep and circadian rhythm. Moreover, emotion and physiological stress can also affect the composition of the gut microorganisms. The gut microbiome and inflammation may be linked to sleep loss, circadian misalignment, affective disorders, and metabolic disease. 

Circadian misalignment and the gut microbiome. A bidirectional relationship triggering inflammation and metabolic disorders”- a literature review [2020]

On the other hand, peripheral clocks are found in the nucleus of almost every single cell (eg, enterocyte, hepatocyte, myocyte, adipocyte), and they show circadian rhythms and oscillations that are dependent and independent of the circadian rhythms from the master clock. While the master clock responds mainly to light/dark cycle, peripheral clocks respond to other zeitgebers (eg, temperature, diet, timing, and content of food intake), which indirectly regulate the central clock …
However, Parabacteroides, Lachnospira, and Bulleida were specific to the human GI tract. Lachnospira was unique in that it was the dominant species that were affected by time and behavior (energy consumption early during the day) [114]. However, it is not fully understood why some species increase with clock time throughout the day. One of the theories is that some species are bile resistant, so they increase during the day as the food is ingested, and bile is secreted (eg, Oscillospira and )

A day in the life of the meta-organism: diurnal rhythms of the intestinal microbiome and its host [2015]

“We found that up to 20% of all commensal species in mice and humans undergo diurnal fluctuations in their relative abundance, resulting in rhythmic changes of the entire bacterial community over the period of one day.  For instance, the common mouse and human commensal genus Lactobacillus increases in relative abundance during the resting phase (the light phase in a mouse) and declines during the active phase.”

Bottom Line

Time of day, time of year, eating time and diet impacts intra-day microbiome population and thus the metabolites being produced. Some of these metabolites have been shown to impact circadian cycle in recent studies. A few bacteria pulled from the studies cited above include:

• Fusobacterium
• Porphyromonas,
• Prevotella
• Bacteroides acidifaciens,
• Lactobacillus reuteri,
• Peptococcaceae
• Eggerthella,
• Anaerotruncus,
• Desulfovibrio,
• Roseburia,
• Ruminococcus

Time of year impacts (and may be a factor for Seasonal Affective Disorder – SAD)

• Helicobacter,
• Bacillus,
• Stenotrophomonas
• Proteobacteria,
• Lactobacillus
• Romboutsia

I was unable to find any 16s clinical studies on SAD

Advice for taking samples

Record the day of the week, time of day, and if female, where you are in your cycle for stool samples. For best consistency (i.e. seeing what actually changed between samples) — make sure all follow up control for these factors as much as possible.

By same data, I mean the same FASTQ files, a detail file of the parts of your sample returned by a 16s machine. This is then processed through software to infer the bacteria. The result is two different reports. If you pass the same files to other providers, you will like get even more different reports. For why, see this post from 2019, The taxonomy nightmare before Christmas…

This post is going to look an actual example.

Krona View

At this level, they look similar – but there is often a 25% difference between the numbers of a species.

Comparing Samples

At the class level you can see some dramatic changes in counts and percentile. At present, I am using percentiles from aggregations of all labs sources.

When I hit 1000 samples from a specific lab, I will doing lab specific percentiles. Current counts — thus we are using an aggregate for percentile for all labs

For items of concern, you can actually drill down manually on the bacteria. For example for Bacilli above.

You can also get the percentile that is lab specific by going to https://microbiomeprescription.com/Library/Statistics?taxon=91061 with no sample and then changing to the lab as shown below.

We find that we are at the 20%ile for biomesight specific samples and 2.4%ile for thryve specific samples. For explanations, you will need to ask the questions to the lab — microbiome prescription just presents the data.

Kegg Probiotic Suggestions

Different input present different outputs.

Dr. Jason Hawrelak Recommendations

One reports 9 items that are not ideal, and the other 8. There is disagreement on Blautia, Desulfovibrio, Lactobacillus, Roseburia and Bilophila wadsworthia

Bottom Line — FRUSTRATION!

The bottom line is that you want to always use the same lab software for comparing samples. Ideally, the same lab for the physical processing. Comparing the same sample that is processed by two different pieces of software results interpretation challenges.

To give a more human context — take a book and ask two people to retell it aloud, one is from the rural areas of Scotland (with thick Scottish accent) and the other from Mumbai India (with thick Marathi accent) with a third person (a native from Bermuda) trying to recall what they heard…. Different choice of words in the retelling with different intonations. That is the human reality — which also applies to labs.

There was a transcription error in a lookup table for biomesight ONLY, as a result

• the ORDER of Clostridiales (mean 48%) was being reported as the rare Tissierellia class (mean around 0.35%)
• This means that Clostridiales was UNDER REPORTED (i.e. 0%) and Tissierellia was over reported.

For most suggestions, this should have zero impact because the defaults do not include class or order numbers.

For End Products, the following would be incorrectly calculated.

• Butyrate
• Vitamin B12 (Cobalamin)

All of the KEGG data is based on Species and Strains – so no impact there.

Visual Representations would be off

Remember “Data Drift” because our data is live

If you upload and get suggestions and then return in 4 months, you may get slightly different suggestions with the identical request. Why?

• We based our detection of high and low from the examples uploaded. Lat month, 104 new samples were added. That’s a 6% growth/month.
• We add more new studies every month – often dozens. This impacts our suggestions. At present we have 5500 studies that we extract information from.
• Studies are increasing every month on 16s microbiome
  

When this site was started, there was one dominant player in retail-provider: uBiome. In June 2018, the first ThryveInside sample was uploaded, A year later, in May 2019, the first American Gut sample. A year later, in July 2020, BiomeSight started rolling in significant numbers — for 10 months, BiomeSight was the most frequent upload type every month. At present, I support 8 upload types and provide an API for any lab that wishes to do a direct transfer. BiomeSight lead the way here. Statistics are here for those interested.

In an early post, The taxonomy nightmare before Christmas…, The quote below says it all!

My #1 Measuring Stick

The first three labs, uBiome, Thryve and American Gut, all used the NCBI Bacteria Taxonomy systems. These are number and thus easy to store in the database and economic to do analysis on. This is a critical foundation. There are problems using names, because names change overtime. One bacteria has 237 different names. As illustrated below — same bacteria was discovered by many different people. Each person gave it a name and published papers using that name. In time (especially with DNA techniques) it was realized that they were all the same!!

NCBI is an unique identifier just like social security number is for American. Unfortunately, Canadians have SIN numbers. Other nations have Person Numbers. The same thing has happened with lab equipment. The problem is matching identities. With non-Americans in the US, some are issued TIN numbers (and thus we are good for US identity), others do not have TIN numbers. A person is like a bacteria.

Case Studies With Microba and BiomeSight

Microba does not use NCBI numbers. Microba uses the Genome Taxonomy Database (GTDB https://gtdb.ecogenomic.org/) for taxonomic classification. The question arises, who attempts the mapping of the GTDB identifiers to NSBI — Microba or MicrobiomePrescription or no-one?

With cooperation from them (namely, they provided a reasonably complete list of the GTDB identifiers that they used), I was able to create a mapping table between those names and NCBI numbers that was not 100%, but sufficient to give meaningful results.

With BiomeSight.com, they added the numbers to their database. I always prefer the lab to take ownership of the mapping – there can be many nuisances specific to the lab equipment that they are using.

Popular Medical Tests that cannot be added to the data

There are two main reasons that these cannot be added:

• They only measure selected bacteria (see below)
• Their unit of measure is different. One counts the number of hex nut in a mixture of 1000 nuts; the other counts the number of packages of hex nuts (with a different number of nuts per package) in a carton of nuts. They are simply too different.

Lab Name	Bacteria Reported
Bioscreen (cfu/gm)	17
Biovis Microbiome Plus (cfu/g)	40
DayTwo	76
Diagnostic Solution GI-Map (cfu/gm)	34
GanzImmun Diagnostic A6 (cfu/gm)	72
GanzImmun Diagnostics AG Befundbericht	25
Genova Gi Effects (cfu/g)	28
Genova Parasitology (cfu/g)	7
InVitaLab (cfu/gm)	23
Kyber Kompakt (cfu/g)	11
Medivere: Darm Mikrobiom Stuhltest (16s limited)	16
Medivere: Darn Magen Diagnostik (16s Limited)	16
Medivere: Gesundsheitscheck Darm (16s Limited)	17
Metagenomics Stool (De Meirleir) (16s Limited)	53
Smart Gut (ubiome 16s – Limited Taxonomy)	23
Verisana (cfu/ml) aka (kbe/ml)	11
Viome (No objective measures)	29

For these test, users must transcribe whether the test indicated too high(↑) or too low (↓) levels. I give the ability to indicate how much…

How the labs represents varies greatly. Their units are not compatible.

Suggestions are based on these rough values and uses the same logic. A key limitation is that their normal ranges are likely computed assuming a bell curve and not Kaltoft-Moltrup Ranges. You may be acting on items that are in the typical ranges seen.

Issue of Missing Hierarchical Layers

If you look at “My Biome View” on Microbiome Prescription, you will see the hierarchy (per NCBI). Most labs do not give the full hierarchy in their reports. Often they will skip layers. The clearest example is Microba. They provide information in only 4 files.

But when this upload is viewed, you see all of the levels!

A more extreme example is the CosmosID’s PDF files, where they only list the species and strains!

The user who submitted this would see the following My Biome View…

Microbiome Prescription “completes” the data by summing up each level into the level above if missing. So I sum the count of all of the species in a genus to get the genus count if it was missing from the upload. There is an unfortunate gotcha. you may have 8000 in a genus and the sum of the species is 6000. If the lab provided the genus count, then we are good — no need to create a record with 6000. If we must create this level, then we are missing 2000 and higher levels are underreporting!.

This issue is also seen in some lab results. They scale the numbers so that the species that they report adds up to the count for the genus. What they do not report on is dropped from all of the parent levels.

When you use the Krona Chart, if there are no “unknown section” the0n this ignoring the not identified is a possible issue with the lab results. You can also do this on the My Biome View by comparing the numbers of the parent to the sum of the children – if they always match, then assume that the not identified are ignored.

Inconsistent Numbers

Above we have the case of the genus count being more than the sum of it’s species. This is a good state, because the numbers are more accurate. We have the unidentified bacteria being identified as least at the genus level.

I have also found cases where the sum of the species exceeds the genus. This can legitimately happen when alternative hierarchies are used. It becomes a problem when we attempt to keep everything in one hierarchy (“There can only be one!”)

As a result, if the sum of the species (using NCBI hierarch) exceeds the genus, then we update the genus number for consistency (if we do not do that, then Krona charts can look bizarre — which a user emailed about).

Bottom Line

“Different strokes for different folks” is the problem. In accepting data from 9 different sources, I need to harmonize. The key that I play in is NCBI. This is a huge benefit because it is used with KEGG: Kyoto Encyclopedia of Genes and Genomes, which really enhances analysis.

Right Solution

It is simple, the labs should add to their websites equivalent pages seen on Microbiome Prescription — but only using their lab results. If their staff lacks the skills, I am a professional developer and can be contracted to do a lot of the backend coding (at my usual commercial rates ).

If you wish to be pro-active.

• Verify that every bacteria shown on my biome view is shown on the lab results page. If it is not, they are skipping elements of the hierarchy
• Verify that the count agrees, if not look at what is added up
• Contact the provider and ask for automatic transfer to be implements. Code wise it is very simple, a few hours of work at most for most developers. What is needed is documented here, including a test site!

I cannot fix the root issue — inconsistent data. You are their customers and by being vocal, you can make a difference. If the upload is correct and complete — I make no modifications, it is only for problematic uploads.

In an earlier post, I had illustrate the problem of whether L.Reuteri produced histamine. The answer is “Not sufficient information to answer” — why is shown below. It depends on which strain you have! The source (human/not human) is not sufficient. In general, the probiotic species is insufficient to answer the histamine question.

• Individual strains of Lactobacillus paracasei differentially inhibit human basophil and mouse mast cell activation [2016] “Thus, L. paracasei CNCM I‐1518 could not only inhibit mouse mast cell and human basophil activation 19, but also protect mice from Salmonella Typhimurium infection 31, induce regulatory T cells in skin inflammation model 32, and improve allergic rhinitis in children 33. These studies, which focused on one or a few strains of bacteria, did not permit an accurate comparison of the effects of different bacterial strains.“

Lactobacillus Casei and Paracasei

On many studies, this is reported to reduce hay fever and allergies. If you check the web, you will find that it is also reported as a histamine producer. How can this be true since increased histamines would make allergies worst. The answer is simple. BOTH ARE CORRECT when you look at the fine print… (and you need the fine print that may be missing on the probiotic label).

• “histamine production were found in … Lactobacillus casei 18, isolated from cider)” [2013]
• “According to the results,  Lactobacillus casei CCDM 198 exhibited the best degradation abilities…. significantly (P < 0.05) reduced BAs (putrescine, histamine, tyramine, cadaverine), up to 25% decline in 48 h.” [2020]
• ” Lb. paracasei subsp. paracasei CB9CT and another strain (CACIO6CT) of the same species that was able to degrade all the BAs were singly used as adjunct starters for decreasing the concentration of histamine ” [2016]
• “Seventeen isolates were found that were able to degrade tyramine and histamine in broth culture. All 17 isolates were identified by 16S rRNA sequencing as belonging to Lactobacillus casei.” [2012]

For Lb Casei and Paracasei, most of the studies suggests that it degrades histamine.

Worked Example

We use L. Casi and L. Paracasei from Custom Probiotics, for two main reasons, they are the cheapest per BCFU, they have no fillers, pre-biotics, etc so we do not have to deal with counter-indicated formulation that often happens with commercial probiotics blends (often using a marketing-driven formulation).

So looking up the strains, I see Lc-11 and Lpc-37, Time to search for information on these:

On LPC-37

• Lacticaseibacillus paracasei Lpc-37® improves psychological and physiological markers of stress and anxiety in healthy adults: a randomized, double-blind, placebo-controlled and parallel clinical trial (the Sisu study) [2020]
• The immune system in healthy adults and patients with atopic dermatitis seems to be affected differently by a probiotic intervention [2008] use Lpc-37
• The influence of Lactobacillus Paracasei LPC-37 on selected properties of fermented sausages [2015]

On Lc-11

• Obesity and gut microbiome: review of potential role of probiotics [2021] “In obese women, the administration of a probiotic mix composed of L acidophilus LA-14, L casei LC-11, L lactis LL-23, and B bifidum BB–06, improved BW composition after an 8-week supplementation period. A”
• Title: Enumeration of probiotic strain Lactobacillus casei Lc-11 using viability real time PCR [2019]
• I also found this table that is helpful for those taking antibiotics.
  

Bottom Line

IMHO, you need to:

• Know every strain in your probiotics (not just species!)
• You need to be able to locate studies using that strains (Lb. Casei Snakeoild may be just a marketing name to hide that fact that the manufacturer/packager does not know the strain)
  • I have seen some product literature claiming benefits from a different strain because they were the same species —FALSE LOGIC.
• Ideally, you will find some relevant studies using these strains — ideally on humans!

If you are using antibiotics, you may wish to search for the probiotics antibiogram. Ideally, the manufacturer/seller would provide all of that information with a simple email requesting it.

This is an area that I became aware of a decade ago and used this knowledge to discard some suggestions and take other suggestions based on the physical characteristics of the brain. This has major implication for brain fog, autism, ME/CFS, depression, Alzheimer’s, Long Haul Covid and many many more conditions.

The literature

“Research on disease-modifying treatments for  central nervous system  [CNS] diseases have generated a cemetery of failed drugs, rejected in part because of their incapacity to cross the BBB” [3,4,5,6,7]. 

The Molecular Weight [MW] threshold of BBB drug transport of small molecules has been demonstrated previously in studies of drug penetration into the brain.^33, 34 Blood–brain barrier permeation decreases 100-fold when the size of the drug is increased from an MW of 300 Da, which corresponds to a surface area of 50 square angstroms, to an MW of 450 Da, which corresponds to a surface area of 100 square angstroms.³⁵

Drug transport across the blood–brain barrier [2012]

• Disease-Induced Modulation of Drug Transporters at the Blood–Brain Barrier Level [2021] Hints that some infections/conditions may drop the threshold lower.
• Low Molecular Weight (poly)Phenol Metabolites Across the Blood-Brain Barrier: The Underexplored Journey [2021]

I remember that for my treatment of ME/CFS back in 2000, Low Molecular Weight Heparin was what was advocated. It was found far more effective than normal heparin (and costed 30+time more!!)

Getting information on Molecular Weight

What is Da? It’s Dalton — “Measure of molecular weight or molecular mass. One molecular hydrogen molecular atom has molecular mass of 1 Da, so 1 Da = 1 g/mol.” This information is often available on Wikipedia in the left hand column as molecular mass. i.e. 457.483 g·mol⁻¹ –> 457 Da

Information is also available at https://pubchem.ncbi.nlm.nih.gov/

If there is a choice, you want the smallest number. Remember we are talking 100x LESS getting thru with an increase of weight by 50%! Some examples:

• Piracetam: 142.16 g/mol – this has always been an excellent removal of brain fog for me!
• Niacin: 123.11 g/mol — also helps me with brain fog
• Vitamin C: 176.12 g/mol
• alpha-Lipoic acid: 206.3 g/mol
• Quercetin: 302.23 g/mol
• Curcumin: 368.4 g/mol
• Vitamin D: 384.6 g/mol
• Rutin: 610g/mol
• Heparin (compound): 1134.9 g/mol – hence why low molecular weight heparin worked better!
• Cyanocobalamin (Vitamin B12): 1355.4 g/mol — would not expect any impact on cognitive issues
• Antibiotics:
  • Tetracycline: 444.4 g.mol
  • Doxycycline: 444.4 g.mol
  • Minocycline: 457.5 g/mol
  • Azithromycin: 749 g/mol
  • Vancomycin 1449.2 g/mol

Bottom Line

The concept of “needing to take anti-inflammatories for brain inflammation” is correct — the gotcha is that many of the items you may take will never reach the brain because they are too big! Go thru your lists (and suggestions from others) and trim them down to the light molecular weight ones. You will likely get much better success — I did!

I’ve recently added computations for Methane and Hydrogen using KEGG data to Microbiome Prescription. Checking the contributed symptoms, I had over 120 samples with SIBO indicated. So it was time to test the hypothesis.

Charts

What about the old Methane?

The old computation was done on adhoc gathered associations from the literature. It also did not show any patterns.

Bottom Line

With the obvious path being unsuccessful, then time to examine where we did find associations.

ProductName	Pattern
(4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoate	Between 33%ile to 66%ile
cob(II)yrinate a,c diamide	Between 66%ile to 100%ile
D-tagatose	Between 0%ile to 33%ile
undecaprenyl phosphate	Between 0%ile to 33%ile

EndProduct	Pattern
Vitamin B9 (Folic Acid/Folate)	Between 66%ile to 100%ile
Lactic acid	Between 0%ile to 33%ile
2-Butanone	Between 66%ile to 100%ile
Hydrogen cyanide	Between 66%ile to 100%ile
Methyl thiocyanide	Between 66%ile to 100%ile
Propionate	Between 66%ile to 100%ile
Vitamin K	Between 66%ile to 100%ile
Vitamin B7 (biotin)	Between 66%ile to 100%ile
Sialic acid	Between 66%ile to 100%ile
Norepinephrine	Between 66%ile to 100%ile

EnzymeName	Pattern
succinyl-CoA:acetate CoA-transferase	Between 33%ile to 66%ile
phosphoenolpyruvate carboxykinase (GTP)	Between 33%ile to 66%ile

Definition	Pattern
Pentose phosphate pathway (Pentose phosphate cycle)	Between 75%ile to 100%ile
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P	Between 75%ile to 100%ile
Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P	Between 75%ile to 100%ile
Serine biosynthesis, glycerate-3P => serine	Between 75%ile to 100%ile
Histidine degradation, histidine => N-formiminoglutamate => glutamate	Between 75%ile to 100%ile
Riboflavin biosynthesis, plants and bacteria, GTP => riboflavin/FMN/FAD	Between 75%ile to 100%ile
Tetrahydrofolate biosynthesis, GTP => THF	Between 75%ile to 100%ile
CAM (Crassulacean acid metabolism), light	Between 75%ile to 100%ile
Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysine	Between 75%ile to 100%ile

tax_name	tax_rank	Pattern
Blautia hansenii	species	Between 33%ile to 66%ile
Filifactor alocis	species	Between 66%ile to 100%ile
Bacteroidia	class	Between 66%ile to 100%ile
Bacteroides gallinarum	species	Between 66%ile to 100%ile

Last, we look at what studies reported

Tax Rank	Tax Name	Shift	Distribution	Citation Link
genus	Enterococcus (NCBI:1350 )	High	Distribution	📚 PubMed
genus	Klebsiella (NCBI:570 )	High	Distribution	📚 PubMed
genus	Prevotella (NCBI:838 )	High	Distribution	📚 PubMed
genus	Salmonella (NCBI:590 )	High	Distribution	📚 PubMed
genus	Staphylococcus (NCBI:1279 )	High	Distribution	📚 PubMed
genus	Streptococcus (NCBI:1301 )	High	Distribution	📚 PubMed
phylum	Firmicutes (NCBI:1239 )	Low	Distribution	📚 PubMed
species	Acinetobacter baumannii (NCBI:470 )	High	Distribution	📚 PubMed
species	Bacteroides fragilis (NCBI:573 )	High	Distribution	📚 PubMed
species	Bifidobacterium longum (NCBI:216816 )	Low	Distribution	📚 PubMed
species	Enterococcus faecalis (NCBI:1351 )	High	Distribution	📚 PubMed
species	Enterococcus faecalis (NCBI:1351 )	Low	Distribution	📚 PubMed
species	Enterococcus faecium (NCBI:1352 )	High	Distribution	📚 PubMed
species	Escherichia coli (NCBI:562 )	High	Distribution	📚 PubMed
species	Escherichia coli (NCBI:562 )	High	Distribution	📚 PubMed
species	Methanobrevibacter smithii (NCBI:2173 )	High	Distribution	📚 PubMed
species	Methanobrevibacter smithii (NCBI:2173 )	High	Distribution	📚 PubMed
species	Pseudomonas aeruginosa (NCBI:287 )	High	Distribution	📚 PubMed

Looking at the “usual suspect” for SIBO, Methanobrevibacter smithii, a methane producer, we found only 23 samples with any (and all of the labs associated with these samples reports this bacteria so over 100 (80%) of the people reporting SIBO had none appearing)

Tentatively conclusion, SIBO does not leave any clear tracks in a 16s Sample.

It is that season again — and some areas are reporting much higher levels than usual (with predictions for it getting worst). Some people will load themselves up daily on antihistamine, for example, Diphenhydramine HCl , which impacts over 800 different bacteria. We do have a profile of the bacteria shifts seen on Microbiome Prescription.

Supplements

The bad news is that we have lots of studies, but no good studies — all of them have problems…

” A total of 57 062 articles were derived from searching seven online databases and evidence from 48 RCTs and 10 observational studies were reviewed for methodological quality and risk of bias. No qualitative studies meeting the inclusion criteria could be found, therefore only a quantitative review was performed. ”

Health supplements for allergic rhinitis: A mixed-methods systematic review [2020]

• Association of Serum Vitamin D and Immunoglobulin E Levels With Severity of Allergic Rhinitis [2021] ” vitamin D deficiency is associated with increasing severity of allergic rhinitis symptoms.” [2021 ]
  • “This MR study found no evidence supporting a causal association between serum 25(OH)D levels and risk of AR, AS and NAR in European-ancestry population. ” [2021]
• Effects of vitamin E and selenium on allergic rhinitis and asthma pathophysiology [2021]
  “Our results indicated that vit E could attenuate allergic rhinitis and asthma symptoms; nevertheless, treatment with Se alone was not effective in controlling allergic symptoms. ” [2021]

Probiotics?

Lactobacillus

“Probiotics may be beneficial in improving symptoms and quality of life in patients with allergic rhinitis; however, current evidence remains limited due to study heterogeneity and variable outcome measures. Additional high-quality studies are needed to establish appropriate recommendations.”

A systematic review and meta-analysis of probiotics for the treatment of allergic rhinitis [2015]

Probiotic Potential of Lactobacillus Species in Allergic Rhinitis [2021 – full text] is a recent review with two appearing to be most likely effective (to some extent): Lactobacillus Casei and the closely related Lactobacillus Paracasei with dosages up to 30 billion CFU/day. These happen to be less than the suggested dosages from Custom Probiotic.

Bifidobacterium

If we look at Nat.Lib.of Medicine studies at Microbiome Prescription, we do not see any reports of low Lactobacillus. What we do see is low Bifidobacterium) ( Bifidobacterium longum , Bifidobacterium adolescentis, Bifidobacterium catenulatum) and Clostridium butyricum. Logically those seem better candidates!

• Probiotic NVP-1703 Alleviates Allergic Rhinitis by Inducing IL-10 Expression: A Four-week Clinical Trial[2020], a mixture of Bifidobacterium longum and Lactobacillus plantarum… ” Therefore, NVP-1703 can be treatment option for perennial AR.” [2019]
• [Allergic rhinitis management:environment control and patient education].[2017], combined clostridium and bifidobacterium capsules(called Changlekang) – good results
• Probiotics ( Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2) improve rhinoconjunctivitis-specific quality of life in individuals with seasonal allergies: a double-blind, placebo-controlled, randomized trial [2017] “This combination probiotic improved rhinoconjunctivitis-specific quality of life during allergy season for healthy individuals with self-reported seasonal allergies; however, the associated mechanism is still unclear. “
• Bifidobacterium mixture (B longum BB536, B infantis M-63, B breve M-16V) treatment in children with seasonal allergic rhinitis and intermittent asthma [2017] “Children treated with probiotic mixture achieved a significant improvement of symptoms “

Bifidobacterium longum produces a rich collection of end products (1,380), the absence of which may account for hay fever.

Bottom Line

I suspect Placebo effect and poor study construction has resulted in the fuzziness for supplements and lactobacillus probiotics. The Nat.Lib.of Medicine profiles points to some specific bacteria that are low and the available studies, appear to suggest that taking those bacteria as probiotics will significantly improve hay fever. The list is:

• Bifidobacterium longum ,
• Bifidobacterium adolescentis,
• Bifidobacterium catenulatum) and
• Clostridium butyricum i.e. Miyarisan

Adequate Vitamins D and E supplementation may also help. I use the word adequate because often the dosages suggested in some studies are insufficient to alter blood level by any reasonable amount in a month (see this post for a formula ) – hence “no effect”.

There is one more path to consider, getting suggestions explicit for the shifts reports.

The results are shown below

We see L.Casei, L. Paracasei and Clostridium butyricum on the recommended list — in agreement with the above. Further down, we see Selenium (cited above) also listed

The above is evidence based on the microbiome shifts seen with hay fever.

This morning I chatted 90 minutes with another data scientist about the microbiome. After the video chat he sent me a link to this recent article: From IBS to ME – The dysbiotic march hypothesis [2020]

” The pathogenesis of the relationship is unknown. Intestinal dysbiosis may be a common abnormality, but based on 1100 consecutive IBS patients examined over a nine years period, we hypothesize that the development of the disease, often from IBS to ME, actually manifests a “dysbiotic march”. In analogy with “the atopic march” in allergic diseases, we suggest “a dysbiotic march” in IBS; initiated by extensive use of antibiotics during childhood, often before school age. Various abdominal complaints including IBS may develop soon thereafter, while systemic symptom like CFS, fibromyalgia and ME may appear years later.”

Related to the above:

• How Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Progresses: The Natural History of ME/CFS [2020]
• Can You Trust Your Gut? Implicating a Disrupted Intestinal Microbiome in the Progression of NAFLD/NASH [2020]
• Microbial transitions from health to disease [2021] “dysbiotic microbial populations may be important in the development of approaches to prevent the progression of disease and to restore health in diseased individuals.”

Personally, I have seen someone progress from GERDs to IBS to Chronic Fatigue Syndrome to atypical Crohn’s disease. The progression is not deterministic, with DNA being a significant factor.

I have had on my todo list, creating a microbiome progression map. I have just added it (based solely on gold-standards PubMed studies). It can be seen via https://microbiomeprescription.com/Library/PubMed

When you click the crystal ball . you will be taken to a new page. For example, IBS

Bottom Line

This is based on PubMed studies which are often hit and miss for depth of analysis and reporting shifts. Over time, I expect data to improve and the forecasts on this page to improve.

A Periodic Review of PubMed for COVID Fecal Microbiome finally found some studies:

One paper reported very very good results!

The optimal eight oral microbial markers (seven faecal microbial markers) were selected by fivefold cross-validation
on a random forest model, and the classifier based on the optimal microbial markers was constructed and achieved an area under the curve (AUC) of 98.06% (99.74% in the faecal microbiome).”

Alterations in the human oral and gut microbiomes and lipidomics in COVID-19 [2020]

“The heatmap showed that the faecal microbial community in CPRs (Confirmed Patients Recovered) was different from that in CPs (Confirmed Patients) and HCs,(Healthy Controls)” [SP is suspected Patient, SPR is suspected Patient recovered] which appears to confirm my hypothesis that most infections will leave a “garbage state” in the microbiome which will generally shift slowly back to the healthy state. This return to a healthy state is not certain and when it fails to happen, then we have diagnosis such as long haul covid, chronic fatigue syndrome, and post-infection syndrome.

More coming…