If you have uploaded/transfered your 16s or shotgun sample to Microbiome Prescription and then logged in. You will see the page below.

Select your latest sample (if more than one) and then click on the link at the bottom right.

This will take you to a page like the one shown below. Select one or more of the conditions you have and click [Get Report] at bottom. The page shows how many bacteria shifts matches that reported in the literature (in this example 27 studies) and how strong you ranked against other people (67%ile).

The result is a long report. The key sections are:

• Significant Bacteria Shifts: the most significant bacteria of those matched
  • Note: above we have 27 studies, the number of bacteria may be less.
• Cross Validated Suggestions: Items reported from studies that help ME/CFS and which we also computed will help correction bacteria shifts.
• Probiotic Species Impact by R² associations: The probiotics that are computed to help most using a private data source
• Additional Suggestions: Items not cited in studies but computed to will help correct bacteria shifts.

Examples Report Treatment Suggestions for CFS Patient.html. NOTE: the reports will be different based on your microbiome.

Cautionary Note

The suggestions are likely to differ from those computed elsewhere on the site. The studies usually just indicate lower or higher amount and lacks precision on how much lower or higher is significant. This results in different bacteria being selected.

The preferred way is to use Symptoms

And then select your symptoms.

While this usually gives better results, it does not give links to studies which MDs often want to see.

BEST PRACTICE is to do what both methods agree upon.

The youtube below does a walk thru of using MicrobiomePrescription.com with a person with ME/CFS, had COVID and Autism. MicrobiomePrescription.com is a free site with world class artificial intelligence system connected to a comprehensive database.

A few highlights from the video:

Correctly Predicted symptoms from their microbiome alone

Symptoms are strongly associated to particular microbiome patterns. These patterns can be used to “guess” the symptoms that they are likely to have. As shown below, for many people it is very accurate!

PREMISE: If we correct the microbiome dysbiosis. then the symptom should be less severe or disappear.

Suggestions agree with Clinical Experience of working

The antibiotics with [CFS] are ones that have been used in studies with some good responses reported. In particular, a similar combination is used successfully by Dr. Cecile Jadin with her patients.

Good and Bad Probiotics are Identified

For this person’s sample, 9 probiotics were computed to help and 33 probiotics were computed to hurt.

Goal is Improved Odds, not a Protocol

The suggestions will be different (often very different) from person to person. Each item is computed to independently help. Take what you are comfortable with. Items to avoid should be respected (when practical).

Example of a Cross Validated Report

While working on a pending post [ME/CFS after EBV in Competitive Athlete] on their microbiome sample I was pleasantly surprised to see their top suggestions have literature on the same substances helping reduce EBV. In one sense, I should have expected it, given the premise that I am working off.

Premise: An infection (including virus) alters the microbiome to be optimal for it survival. Correcting the dysbiosis, weakens the infection (i.e. you may starve it of essential metabolites)

I decided to collect these items in this post for people with ME/CFS and positive for EBV, i.e. chronic active EBV (CAEBV)

Suggestions

Note: [More Info] are links to perplexity.ai, the information may be questionable in some cases.

• Vitamins, Minerals and similar
  1. Selenomethionine {Selenium supplement}
     • Selenium deficiency is associated with increased susceptibility to EBV infection and its complications [more info]
  2. Zinc {Zinc Supplements}
     • Zinc is directly required for EBV gene regulation.[more info]
  3.  Silver nanoparticles {Colloidal silver}
     • Inhibition of EBV replication: Silver nanoparticles stabilized in citrate buffer can inhibit EBV replication by up to 70% [more info]
  4. Magnesium Compounds {Magnesium supplements}
     • Magnesium plays a critical role in the immune response to Epstein-Barr Virus (EBV), particularly in individuals with genetic defects affecting magnesium transport: [more info]
  5. alpha-tocopherol {Vitamin E}
     • Vitamin E has demonstrated inhibitory effects on Epstein-Barr Virus (EBV) transformation of human B cells, particularly under conditions of oxidative stress: [more info]
  6. Vitamin C
     • Effect of high dose vitamin C on Epstein-Barr viral infection [2014]
• Herb or Spice
  • Olea europaea {Olive leaf}
    • Olive leaf extract (OLE) has been shown in multiple studies to have significant antiviral and antioxidant activity against Epstein-Barr Virus (EBV): [more info]
  • Azadirachta indica {Neem}
    • Neem (Azadirachta indica) demonstrates notable antiviral activity against Epstein-Barr Virus (EBV) and other herpes-type viruses: [more info]
  • Allium sativum {garlic}
    • Garlic (Allium sativum) and its organosulfur compounds (OSCs) exhibit notable antiviral activity against Epstein-Barr Virus (EBV) in preclinical studies: [more info]
  • Kaempferol 
    • The Dietary Flavonol Kaempferol Inhibits Epstein–Barr Virus Reactivation in Nasopharyngeal Carcinoma Cells [2022]
  • Commonly recognized antiviral medicinal plants in Ayurveda Medicine. Those with [citation] after them have explicit literature for EBV, most have literature for other virus.
    • Zingiber officinale – Ginger
    • Caesalpinia bonducella – Fever Nut or Bonduc Nut
    • Allium sativum – Garlic
    • Glycyrrhiza glabra – Licorice or Liquorice
      • ts antiviral activity is clearly demonstrated by different studies on the herpes simplex virus, Epstein–Barr virus (EBV), [2023] [2020]
    • Ferula assafoetida – Asafoetida or Hing
    • Gymnema sylvestre – Gymnema or Gurmar (Sugar Destroyer)
    • Gossypium herbaceum – Levant Cotton or Cotton Plant
    • Phyllanthus niruri – Stonebreaker or Chanca Piedra
    • Trachyspermum ammi – Ajwain or Carom Seeds
    • Withania somnifera – Ashwagandha or Indian Ginseng
    • Andrographis paniculata – Andrographis or King of Bitters
      •  has a pronounced effect in inactivation or the inhibition of Epstein Virus (EBV) [2021] [2021] [2021]
    • Centella asiatica – Gotu Kola or Indian Pennywort
    • Curcuma longa – Turmeric
      • significantly induced EBV reactivation [2018] [2021]
    • Woodfordia fruticosa – Fire Flame Bush or Dhawai
    • Phyllanthus emblica – Indian Gooseberry or Amla
    • Terminalia chebula – Chebulic Myrobalan or Haritaki
    • Tamarindus indica – Tamarind
    • Terminalia arjuna – Arjuna or Arjun Tree
    • Azadirachta indica – Neem
    • Ficus religiosa – Sacred Fig or Peepal Tree
    • Moringa oleifera – Moringa [2021] [2021]
    • Quercetin [2021]
    • Resveratrol [2023]
    • Saururus chinensis – Chinese lizard’s tail ,  三白草  [2019]

Probiotics

Only Lactobacillus casei Shirota (Yakult) has studies, Effects of Lactobacillus casei Shirota ingestion on common cold infection and herpes virus antibodies in endurance athletes: a placebo-controlled, randomized trial [2016]

In the above pending post, two probiotics were computed to have significant impact:

• Enterococcus faecium
• Akkermansia muciniphila

Bottom Line

My general advice would be to do the mineral supplementation with appropriate dosage (This Dosages page may help) for at least 2 weeks, then start on some of the Herbs and Spices (Rotating every 2 weeks). Be warned that “die off” like effect may occur with some. Then rotate on to the probiotics for 2 weeks at a time.

–

Postscript and Reminder

As a statistician with relevant degrees and professional memberships, I present data and statistical models for evaluation by medical professionals. I am not a licensed medical practitioner and must adhere to strict laws regarding the appearance of practicing medicine. My work focuses on academic models and scientific language, particularly statistics. I cannot provide direct medical advice or tell individuals what to take or avoid. My analyses aim to inform about items that statistically show better odds of improving the microbiome. All suggestions should be reviewed by a qualified medical professional before implementation. The information provided describes my logic and thinking and is not intended as personal medical advice. Always consult with your knowledgeable healthcare provider.

Implementation Strategies

1. Rotate bacteria inhibitors (antibiotics, herbs, probiotics) every 1-2 weeks
2. Some herbs/spices are compatible with probiotics (e.g., Wormwood with Bifidobacteria)
3. Verify dosages against reliable sources or research studies, not commercial product labels. This Dosages page may help.
4. There are 3 suppliers of probiotics that I prefer: Custom Probiotics , Maple Life Science™, Bulk Probiotics: see Probiotics post for why

Today I had a nice 70 minute discussion with a user. This shows pretty much all of the new features and options for building your own plan. This applies also for ME/CFS. In fact, the top forecasted symptom for him was ME/CFS without IBS. He has no IBS.

There are Captions on this presentation.

Issues are discussed on many choices.

This is based on this April 24,2035 paper: The gut microbiota promotes pain in fibromyalgia. There are two interesting finings:

• “transplantation of a healthy microbiota [FMT] is associated with reduced pain and improved quality of life. ” This option is rarely available since FMT is only authorized for  recurrent Clostridioides difficile infections
• And  “Since mice transplanted with the FM gut microbiota showed reduced levels of specific bile acids (e.g., ursocholate) and bile-acid-metabolizing bacteria (Lachnoclostridium scindens [sic: Clostridium scindens] ), we treated mice that received FM FMT with UDCA, a host-derived primary bile acid metabolized in the mouse gut into various secondary bile acids.^57,58,59 “

This post is running from this data into a model and thus a theoretical protocol (not tried in any clinic) if there is evidence to support a model.

Ursocholate Deficiency

This is available as a prescription drug: Actigall, Urso 250, Urso Forte. More details from WebMD. This is not always possible to get prescribed. This leads us to look for production by bacteria. We find that we have information about it on the KEGG: Kyoto Encyclopedia of Genes and Genomes. Going though databases, we do not find any known bacteria (including probiotics) that produces it 😦 . Going to a secondary data resource we get some bacteria involved in production:

Checking against published literature on National Library of Medicine Citations for Fibromyalgia we see:

• Several blautia species are identified but the above is not cited.
• Collinsella, Clostridium, Ruminococcus gnavus is not reported
• Eggerthella is reported high
• [Clostridium] scindens is high which is contrary to expectations

This is less than ideal. We really want

We have a secondary resource: Bacteria by Symptoms by Lab that are high or low. By lab for Fibromyalgia, we found:

• No matches for Biomesight data
• No matches for uBiome data
• No matches for Thryve data
  • One Blautia species was low

Lachnoclostridium scindens encouragement

We have the list of known items that impacts this species on this page. We note that 80% of the items listed decreases it — we want to increase it.

• High-fibre diet {Whole food diet}
• Rheum × hybridum {Rhubarb} & Rhubarb x Peony {Rhubarb Peony Decoction}
• bacillus subtilis {B.Subtilis }
• Coffee (Caffeine)

Bottom Line — No evidence confirming the proposed mechanism

Science is endless iteration of tossing out hypothesis and then testing them. Revising as needed. In the study, it is probable that FMT does help; the speculation as to the cause appears unsupported and suspect.

No theoretical protocol will be produced.