I have extracted from studies the bacteria that have been associated with various autoimmune-related conditions as well as building pages to apply them to uBiome samples at: http://microbiomeprescription.azurewebsites.net .

• Histamine Issues From Ubiome
• Type 2 Diabetes
• ADHD
• Autoimmune Disease
• Crohn’s Disease
• Chronic Fatigue Syndrome
• Inflammatory Bowel Diseas
• Rheumatoid arthritis
• Fibromyalgia
• Gout
• Histamine Issues
• Irritable Bowel Syndrome
• Depression
• Systemic Lupus Erythematosus
• Metabolic Syndrome
• High Blood Pressure
• Mood Disorders
• Schizophrenia
• Autism
• Ulcerative colitis
• Allergies
• Alzheimer’s disease

Today, I created a “heat map” across all of these bacteria may be interesting to explore what types of shifts tend to be common/indicators.

• B – Out of normal range (high or low)
• H – High
• L – Low

The last column is the count.

Phylum Level

Low Verrucomicrobia, High Fusobacteria are the most common for a shift in a single direction. A shift in Firmicutes away from the normal range is the strongest indicator of potential problems

Class

Low Verrucomicrobiae again is a distinctive item

Order

Suspects are:

• High Fusobacteriales
• High Selenomonadales
• High Verrucomicrobiales

Family

At this point we are starting to see some strong suspects:

• High Bacteroidaceae
• High Enterobacteriaceae
• High Fusobacteriaceae
• High Nocardiaceae

Genus

More clear suspects:

• Low Akkermansia
• High Anaerotruncus
• High Bacteroides
• High Collinsella
• High Escherichia
• High Fusobacterium
• High Prevotella
• High Pseudoflavonifractor

Bottom Line

With so many bacteria involved, determining which bacteria to focus on has lacked a clear rationale.  With some people shifting from one diagnosis to another over time, it is likely best to focus on the ones that seems to the foundations for many diagnosii.

I hope to update the recommendations page in the next few weeks,  to increase the weight of correcting the above items instead of giving each bacteria equal weight. This would be done as an option.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

Over the years I have seen several people move from Chronic Fatigue Syndrome /ME diagnosis into a Lupus diagnosis. Today, it appears that all of these conditions share the same probable cause of a  gut bacteria dysfunction.  As the dysfunction evolves, the diagnosis may evolve – sometimes with a change of disease, other times with additional diagnosis added.

I have gathered up what has been published on PubMed for the Lupus shifts.  Having these shifts does not mean you have lupus — DNA also comes into play. The intent is give some visibility of a slide into another condition (or stepping away from).

Bottom Line

This is one more autoimmune diseases that has been associated with a ‘microbiome signature’.

For readers that have contributed their uBiomes, we have added more profiles from studies with one important enhancement.  A sample of common symptoms are also shown with check boxes above the analysis. When you look at the results, please contribute your symptoms for those listed. There is a link to the full list, but with cognitive fatigue — that list can be too much for many people.

Remember — adding your symptoms increases the value of your uploaded ubiome for research.

Example: Gout

What’s there?

As new studies are published, their information will be added and new ones added, for example for SIBO.

• ADHD – Attention-deficit syndrome
• Alzheimer’s Disease
• Autism
• Autoimmune Disease
• Chronic Fatigue Syndrome
• Diabetes Type 2
• Crohn’s Disease
• Depression
• Fibromyalgia
• Gout (Arthritis)
• High Blood Pressure
• Histamine Issues
• Inflammatory Bowel Disease
• Irritable Bowel Syndrome
• Metabolic Syndrome
• Mood Disorders
• Rheumatoid arthritis
• Schizophrenia
• Ulcerative colitis

A reader messaged me because a member of their family has just gotten a diagnosis of arthrosis. They asked if it could be caused by the microbiome? Arthritis  affect your bones, ligaments, and joints. Often this means joint stiffness and pain.

Arthritis is an umbrella term describing several conditions. It includes:

• osteoarthritis (OA) also known as arthrosis
• rheumatoid arthritis (RA), and
• gout.

There are many conditions that distinctive microbiome profiles have been discovered. If you have a uBiome done, I have created pages to compare the ubiome against the published profiles. One of these is rheumatoid arthritis, as shown below (you must have uploaded ubiome to see the results)

The studies used for this page included:

• Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status.
• The Microbiome: a Revolution in Treatment for Rheumatic Diseases?
• Role of the Gut Microbiome in Modulating Arthritis Progression in Mice.
• An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis
• [THE USE OF PROBIOTICS IN PATIENTS WITH RHEUMATOID ARTHRITIS].
• The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment.

A quick search on PubMed found significant research in this direction for osteoarthritis.

• The Microbiome and Bone and Joint Disease. 2017
  • “Although animal studies implicate the microbiome in the development of bone and joint disease, available results are limited and can be conflicting.”
• Akkermansia muciniphila May Determine Chondroitin Sulfate Ameliorating or Aggravating Osteoarthritis. 2017
  • So the microbiome determines the effectiveness of a treatment!
• Metabolic syndrome-associated osteoarthritis. (2017)
  • Metabolic syndrome has a known profile which is on the analysis site.
• Diet-Intestinal Microbiota Axis in Osteoarthritis: A Possible Role. 2016
• Relationship between inflammation, the gut microbiota, and metabolic osteoarthritisdevelopment: studies in a rat model. 2015

I was unable to find studies reporting a specific microbiome profile for osteoarthritis.

For Gout, we find:

• Combined Signature of the Fecal Microbiome and Metabolome in Patients with Gout.
  • “The signatures of microbiome showed being up-regulation of opportunistic pathogens, such as Bacteroides, Porphyromonadaceae Rhodococcus, Erysipelatoclostridium and Anaerolineaceae”
  • “The LefSe method revealed that the phylum Bacteroidetes and its derivative (Bacteroidia, Bacteroidales, Bacteroidaceae as well as Bacteroidales S24_7 group and Porphyromonadaceae), the phylum Chloroflexi and its derivatives (Anaerolineae, Anaerolineales, and Anaerolineaceae), the order Corynebacteriales and its derivative (Nocardiaceae and Rhodococcus), the class Erysipelotrichia and its derivatives (Erysipelotrichales, Erysipelotrichaceae and Erysipelatoclostridium), and the class Negativicutes and its derivative (Selenomonadales) were all higher in the intestinal microbiota from the gout patients. Conversely, the family Vibrionaceae and its derivatives (Photobacterium and Vibrio), the genus Coprococcus 3, Lachnospiraceae NC2004 group, Lachnospiraceae UCG_005, Ruminococcaceae NK4A214 group and Ruminococcaceae UCG_011 were all lower in the intestinal microbiota from the gout patients.”
  • Additionally the metabolites (KEGG) found significant differences.
    

Bottom Line

All of the different types of Arthritis appear to have distinctive profiles according to published studies. There are also metabolite shifts (since these are produced by bacteria — this is expected). Metabolites are the supplies for the body.

One item was very significant — two people may have similar metabolites shifts, and thus the same diagnosis — BUT have different bacteria causing this shift.  If the person has high or low Akkermansia muciniphila,will determine if they have a positive or negative response to Chondroitin Sulfate. This later reality is what I have started to suspect for all of the microbiome caused conditions:

• The symptoms are caused by the metabolite shifts.
  • There may be many combinations of bacteria shifts that can cause a similar  metabolite shift.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

This post looks at three more people that have done 2 microbiome results over time.

Example 1

Following recommendations

 Example 2

This was a series of ubiome done around 2016. A health professional attempted to deal with the microbiome dysfunctions with traditional conventional processes.

Example 3

Treatment is unknown, but by the ubiome numbers, would have occurred after recommendations became available OR have been a natural / spontaneous improvement.

Bottom Line

There is growing evidence that the recommendations appear to:

• Normalize metabolite functions (KEGG)
• Reduce the typical microbiome signature across multiple autoimmune like conditions.

Our base assumption is that symptoms are caused by the shifts. There is no objective way to measure symptoms (and with memory issues often being involved, it makes it a more unreliable evaluation method). We can measure the two above items, and do observe improvements.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.