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2.1.5 Microbiome testing

2.1.5 Microbiome testing


Dysbiosis and biofilms in the various microbiomes sits at the root of this disease model. Given the implications and progression described in the disease model, reviewing your medical history, from early childhood forward would be suggested. A common progression would be an early childhood infection / biofilm formation in the ears/nose/throat/sinuses that progresses to the gut (and sometimes lungs), before translocating to sex organs and urinary tract. Skin microbiome dysbiosis - eczema, acne, dandruff, fungal nails, etc is also common. 

Gut microbiome


Certain gut microbiome tests are useful in getting a rough understanding of the species present in your GI tract (with a focus on the large intestine), along with the metabolites they consume / produce and if any of these are toxic / relevant to your metabolic alterations. Currently there is no single "perfect" microbiome test available. There are a range of tests with strengths and weaknesses. For upper GI data, endoscopic biopsy / aspirate is currently the method-of-choice. Safer, easier and non-invasive methods for collecting upper GI data are desperately needed.

As the stool specimens are not homogenised, very different counts of species can be obtained from different parts of the same specimen. False negatives are common. This can create confusion for anyone who is used to interpreting various reports at face value. Any species counts need to be interpreted with low confidence.

However, the “overall trends” of species diversity and overgrowth can be useful in making decisions around changes to eating habits, supplements and other interventions, for example, consuming bismuth compounds and / or codonopsis / Dang Shen tea for inhibiting sulphur reducing bacteria and promoting bifidobacteria, or taking Akkermansia probiotics and/or pomegranate, if low or missing, along with a supportive diet.

Biomesight
For diversity / abundance testing and recommendations around dietary changes, Biomesight provide some useful reports and importantly, allows record-level data export to CSV for further detailed analysis, which can be used with the information here to make decisions around interventions. NB. fungal species are not reported.

A Biomesight data analysis tool is now available (currently in beta), which will quickly interpret exported Biomesight CSV files against aspects of the disease model:
https://bornfree.life/2024/biomesight-tool/

Biomesight are offering a discounted test, thanks to our ongoing collaboration with Remission Biome:
https://shop.biomesight.com/collections/frontpage/products/gut-microbiome-test-snapshot
(Use discount code RemissionBiome for 50% off)


GI-MAP
For enhanced pathogen testing, also including parasites, along with reporting on GI related markers, a GI-MAP report provides more information, however the report lacks the detailed species diversity information provided by eg. Biomesight.
USA vendors:
https://www.dhalab.com/shop/gi-map-gi-microbial-assay-plus/
https://labtestshop.com/tests/gi-map-stool-test/
AU vendors:
https://healthandharmony.net.au/shop/gi-map-test-kit-gut-microbiome-stool-sample
https://elementalhealthandnutrition.com.au/product/gi-map-diagnostic-solutions/
UK, EU vendors:
https://smartnutrition.co.uk/shop/comprehensive-stool-test-gi-map-pathogen-plus-uk-and-europe-igimap/
https://www.ibsclinics.co.uk/product/gi-map/
https://ifu-wolfhagen.de/shop/stuhl-test/stuhl-und-verdauungsanalyse-pilze-gr-parasitologie-bakterien-bauchspeicheldruese-entzuendungsparameter/
IN vendors:
https://www.ithrive.shop/products/gi-map-stool-analysis-offered-by-diagnostic-solution-laboratory-us?variant=44135044612310

Other – sinuses, oral, lung, urinary tract and sex organ microbiome


If you have a known or suspected infection in any mucosal tissue, then combining qPCR and Next Generation Sequencing (NGS) 16S methodology can help identify the species present and help with decision-making processes around remediation. Reviewing your entire medical history since birth and highlighting / testing tissues with recurring issues would be highly appropriate.

They normally supply a "Level 1" report (targeted qPCR), followed by a "Level 2" report (NGS), a few days later. It's common that the Level 1 report results will be less than helpful.

MicrogenDX offer a range of different testing and reports, for different tissues. These are available to US and international customers.

https://microgendx.com/patients/microgendx-patient-test-service-dm-intl

Limitations:
1. Does not show Lyme species.

Circulating microorganisms - tick-borne, systemic infections


As anyone who has spent time around Lyme disease and tick-borne infections will tell you, getting good data on circulating and intracellular microorganisms is traditionally very, very difficult. Even if you have access to quality testing, the lifecycle of these species can make many of them difficult and expensive to quantify. However, Legionella and Rickettsia species frequently show up in Biomesight and other microbiome reports.

If you have a reason to suspect intracellular species are going to be included in your collection of pathogens:
MicrogenDX can provide "shotgun" metagenomic sequencing of samples to US customers for "research only" purposes and an extra fee, if your doctor contacts them.
ArminLabs EliSpot and TickPlex tests are able to detect a wide range of pathogenic species - https://arminlabs.com/en/tests/elispot
MDL can provide comprehensive data via their OneSwab test - https://www.mdlab.com/testing/vector-borne/
Vibrant Wellness Tick-borne test has a wide range of inclusions and uses multiple methodologies -
US / Worldwide: https://shop.drjabanmoore.com/products/copy-of-vibrant-wellness-tickeborne-complete-1-0
US / Worldwide: https://labtestshop.com/tests/vibrant-tickborne2_panel/

Similarly, elimination of intracellular species has additional challenges to other microorganisms. Getting the immune system restored to normal functionality and ongoing use of circulating biofilm breakers is a key part of resolving these infections. Specific anti-microbials can be used to manage and accelerate this process.

Fermenting species identification


Once you have collected accurate microbiome data, you can use it to identify overgrowth of any species which produce alcohol and/or acetaldehyde using this table.

Notes and considerations:
1. Some species produce alcohol from carbohydrates or lactic acid.
2. Other species produce acetaldehyde when provided with alcohol and may otherwise be harmless.
3. Some produce both.
4. Some probiotic species are also included for accuracy, however these are not considered problematic under normal circumstances.
5. Some species found outside the gut that only produce acetaldehyde may benefit from alcohol produced in the gut or from dietary intake. Therefore, you may have difficulties remediating overgrowth of these species in other tissues until moderate - severe fermentation by the gut microbiome is remediated.
6. This list is comprehensive, but not exhaustive. It will be added to as a comprehensive literature review is completed and GenBank entries processed.
7. It's a very interesting observation that all of the species known to be causal for common issues like acne and dandruff to various cancers are found in this list.
8. Many microorganisms possess at least some capacity to degrade proteins (e.g., to obtain nutrients), but not all are well‐known or clinically significant for their proteolytic activity. The table below highlights species commonly cited in the literature for notable or well‐characterized proteolysis.