What is Microbiome Prescription?

The Mission Statement

Microbiome Prescription mission is the modification of the microbiome to reduce, relieve or eliminate human misery. Misery may be the rate of deterioration from Alzheimer’s or Parkinson’s; disability from Myalgic encephalomyelitis, chronic fatigue syndrome, long COVID and other post infection conditions; neurological disorders, etc.

More and more medical conditions have microbiome dysfunctions associated with them. There are published papers for the following: acne, adhd, allergic rhinitis (hay fever), allergies, alopecia (hair loss), alzheimer’s disease, amyotrophic lateral sclerosis motor neuron, ankylosing spondylitis, anorexia nervosa, asthma, atherosclerosis, autism, autoimmune disease, Barrett esophagus cancer, bipolar disorder, brain trauma, carcinoma, celiac disease, cerebral palsy, chronic fatigue syndrome, chronic kidney disease, chronic lyme, chronic obstructive pulmonary disease, chronic urticaria (hives), colorectal cancer, coronary artery disease , covid-19, Crohn’s disease, cystic fibrosis, deep vein thrombosis, depression, eczema, epilepsy, fibromyalgia, functional constipation / chronic idiopathic constipation, gallstone disease (gsd), gastroesophageal reflux disease , generalized anxiety disorder, gout, graves’ disease, hashimoto’s thyroiditis, hypercholesterolemia (high cholesterol), hyperlipidemia (high blood fats), hypersomnia, hypertension (high blood pressure, iga nephropathy , inflammatory bowel disease, insomnia, irritable bowel syndrome, juvenile idiopathic arthritis, liver cirrhosis, metabolic syndrome, mood disorders, multiple sclerosis, multiple system atrophy , neuropsychiatric disorders (pandas, pans), nonalcoholic fatty liver disease, nonceliac gluten sensitivity, obesity, obsessive-compulsive disorder , osteoarthritis, osteoporosis, parkinson’s disease, psoriasis, rheumatoid arthritis (ra), spondyloarthritis , rosacea, schizophrenia, sjögren syndrome, sleep apnea, small intestinal bacterial overgrowth , posttraumatic stress disorder, systemic lupus erythematosus, type 1 diabetes, type 2 diabetes, ulcerative colitis.

There have been several recent studies that found that the severity of symptoms is associated with the severity of microbiome dysbiosis. The condition may not be microbiome in origin, but many symptoms of the condition have a strong microbiome association.

The Organization

Microbiome Prescription(MP) is an academic orientated research and development entity. MP’s goal is to develop the best in class models of the complexities of the microbiome and how to alter it as a complete eco-system. There are three legs that it rests upon:

  • Studies on the US National Library of Medicine and equivalent sources
  • Data from the Kyoto Encyclopedia of Genes and Genomes on the many bacteria involved
  • Annotate donated microbiome samples transferred or uploaded from direct-to-retail microbiome testing companies.

The third legs is fed by people wishing to contribute to our mission by uploading their own sample and be able to obtain immediate predictions of what may reduce their misery. The key aspect is immediate feedback which rewards their contribution in a concrete and personal sense.

Microbiome Prescription works directly with the microbiologists and senior staff of some direct-to-retail providers. It publishes direct to the web many of the results of its investigations. Some of the methodologies and algorithms as trade-secrets, but the suggestions generated and the evidence trail for making them are not.

MP is a firm believer in working pro-bono with others that are taking a similar position. For example, it is working with Biomesight.com, a UK firm, on a study on long COVID. MP is providing the data analysis using novel techniques to identify the bacteria that appears to be key players with this condition.

In the for-profit world, it will develop custom exclusive algorithms or application programming interfaces to a customer for remuneration. Often the custom algorithms will be far more process intense than the simplified ones provided on it’s citizen-science web-site. Algorithms are usually unique to a customer needs, preferences and risk factors. For example, an algorithm for a company that sells 10 different probiotics mixtures will determine the best one and potentially provide feedback on a superior formulation that would better address their customer needs as a future offering.

Algorithms using data from Kyoto Encyclopedia of Genes and Genomes requires a firm to obtain the appropriate license for commercial use.

Information about Modelling

  • Studies on the US National Library of Medicine and equivalent sources
    • As of June,2022 a total of 2,453,332 studies have been identified as potential interest for review for a textual analysis program to identify studies warranting manual review.
    • 6,137 studies has been the source of data captured into the production database
  • 3,063 Donated microbiome samples
    • 1,316 have been annotated with a total of 37,786 annotations
  • 13,863 different bacteria (identified by their NCBI identifier) have been found in the uploaded samples with the infrastructure being able to handle 2,424,520 different bacteria
  • 2,094 different microbiome modifiers have been found with a total of 1,845,160 interacts
  • 417,075 statistically significant bacteria relationships have been found (proprietary data and process)
    • This allows us to identify potential microbiome modifiers for bacteria that lacks any literature

Modelling Validation

The original scope of the project was myalgic encephalomyelitis(ME), a condition with no accepted treatment and a massive number of clinical studies on different ways attempting to treat it. This allows us to take samples of people with this condition (194 annotated samples) and compare the suggestions modelled only from the microbiome against clinical studies of various treatment for ME. After preliminary tuning, the suggestions and clinical studies were in substantial agreement on what improves ME. This has also included agreement on which antibiotics should be used against the literature. This has been further validated by patients with ME doing multiple samples using the suggestions generated with both the degree of microbiome dysbiosis being reduced and symptoms improving. These patients has allowed their data to be used in public case studies, for example: Evidence of ME/CFS improving using Microbiome Data.

MP has also been used by two autism specialists on multiple patients with good results being reported.

Often case studies reveal additional factors to be consider in the model, resulting in a continuous evolution of the model.