Microbiome shift linked to Autoimmune conditions

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 .

Original post at: https://cfsremission.com/2018/04/20/microbiome-shift-linked-to-autoimmune/

  • 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

Actinobacteria phylum B 7
Actinobacteria phylum H 7
Actinobacteria phylum L 10
Bacteroidetes phylum H 18
Bacteroidetes phylum L 11
Chloroflexi phylum H 1
Cyanobacteria phylum L 2
Euryarchaeota phylum H 3
Euryarchaeota phylum L 1
Firmicutes phylum B 5
Firmicutes phylum H 19
Firmicutes phylum L 15
Fusobacteria phylum H 10
Fusobacteria phylum L 2
Lentisphaerae phylum L 1
Proteobacteria phylum H 16
Proteobacteria phylum L 10
Synergistetes phylum L 1
Tenericutes phylum L 1
Verrucomicrobia phylum H 1
Verrucomicrobia phylum L 11
Low Verrucomicrobiae again is a distinctive item

Actinobacteria class B 7
Actinobacteria class H 7
Actinobacteria class L 10
Anaerolineae class H 1
Bacilli class H 6
Bacilli class L 5
Bacteroidia class H 17
Bacteroidia class L 10
Betaproteobacteria class H 5
Betaproteobacteria class L 2
Chloroflexi class H 1
Clostridia class B 5
Clostridia class H 16
Clostridia class L 14
Deltaproteobacteria class H 3
Deltaproteobacteria class L 3
Erysipelotrichia class H 2
Erysipelotrichia class L 1
Flavobacteriia class L 1
Fusobacteriia class H 10
Gammaproteobacteria class H 13
Gammaproteobacteria class L 6
Methanobacteria class H 3
Negativicutes class H 11
Negativicutes class L 6
Verrucomicrobiae class L 10
Suspects are:

  • High Fusobacteriales
  • High Selenomonadales
  • High Verrucomicrobiales
Actinomycetales order H 3
Actinomycetales order L 1
Anaerolineales order H 1
Bacillales order H 1
Bacillales order L 1
Bacteroidales order H 17
Bacteroidales order L 10
Bifidobacteriales order H 3
Bifidobacteriales order L 5
Burkholderiales order H 5
Burkholderiales order L 2
Clostridiales order B 5
Clostridiales order H 16
Clostridiales order L 14
Coriobacteriales order B 7
Coriobacteriales order H 3
Coriobacteriales order L 3
Desulfovibrionales order H 3
Desulfovibrionales order L 3
Enterobacteriales order H 13
Enterobacteriales order L 3
Erysipelotrichales order H 2
Erysipelotrichales order L 1
Flavobacteriales order L 1
Fusobacteriales order H 10
Lactobacillales order H 6
Lactobacillales order L 5
Methanobacteriales order H 3
Pasteurellales order H 1
Pasteurellales order L 3
Pseudomonadales order H 1
Selenomonadales order H 11
Selenomonadales order L 6
Verrucomicrobiales order L 10
Vibrionales order H 1
Vibrionales order L 1
At this point we are starting to see some strong suspects:

  • High Bacteroidaceae
  • High Enterobacteriaceae
  • High Fusobacteriaceae
  • High Nocardiaceae
Acidaminococcaceae family H 2
Anaerolineaceae family H 1
Bacteroidaceae family H 15
Bacteroidaceae family L 5
Bifidobacteriaceae family H 3
Bifidobacteriaceae family L 5
Catabacteriaceae family L 1
Clostridiaceae family H 5
Clostridiaceae family L 3
Clostridiales Family XI. Incertae Sedis family H 1
Clostridiales Family XIII. Incertae Sedis family L 1
Coriobacteriaceae family B 7
Coriobacteriaceae family H 3
Coriobacteriaceae family L 3
Corynebacteriaceae family H 1
Desulfovibrionaceae family H 3
Desulfovibrionaceae family L 2
Enterobacteriaceae family H 13
Enterobacteriaceae family L 2
Enterococcaceae family H 2
Erysipelotrichaceae family H 2
Erysipelotrichaceae family L 1
Eubacteriaceae family H 1
Eubacteriaceae family L 3
Flavobacteriaceae family L 1
Fusobacteriaceae family H 10
Lachnospiraceae family H 10
Lachnospiraceae family L 9
Lactobacillaceae family H 4
Lactobacillaceae family L 5
Methanobacteriaceae family H 3
Nocardiaceae family H 2
Oscillospiraceae family H 4
Oxalobacteraceae family H 4
Pasteurellaceae family H 1
Pasteurellaceae family L 3
Peptostreptococcaceae family H 2
Peptostreptococcaceae family L 2
Porphyromonadaceae family H 5
Porphyromonadaceae family L 6
Prevotellaceae family H 8
Prevotellaceae family L 3
Pseudomonadaceae family H 1
Rikenellaceae family H 4
Rikenellaceae family L 2
Ruminococcaceae family B 5
Ruminococcaceae family H 11
Ruminococcaceae family L 11
Staphylococcaceae family H 1
Staphylococcaceae family L 1
Streptococcaceae family H 2
Sutterellaceae family H 1
Sutterellaceae family L 2
Veillonellaceae family H 8
Veillonellaceae family L 6
Verrucomicrobiaceae family L 10
Vibrionaceae family H 1
Vibrionaceae family L 1
More clear suspects:

  • Low Akkermansia
  • High Anaerotruncus
  • High Bacteroides
  • High Collinsella
  • High Escherichia
  • High Fusobacterium
  • High Prevotella
  • High Pseudoflavonifractor
Acetivibrio genus L 1
Actinobacillus genus H 1
Adlercreutzia genus L 1
Akkermansia genus L 10
Alistipes genus H 4
Alistipes genus L 1
Anaerostipes genus L 1
Anaerotruncus genus H 8
Bacteroides genus H 11
Bacteroides genus L 5
Bifidobacterium genus H 3
Bifidobacterium genus L 5
Bilophila genus H 2
Bilophila genus L 1
Blautia genus H 2
Blautia genus L 3
Butyricimonas genus H 1
Candidatus Soleaferrea genus L 1
Cetobacterium genus H 2
Citrobacter genus H 1
Clostridium genus H 4
Clostridium genus L 3
Collinsella genus B 7
Collinsella genus H 2
Collinsella genus L 1
Coprobacillus genus H 1
Coprococcus genus H 5
Coprococcus genus L 5
Corynebacterium genus H 1
Desulfovibrio genus H 1
Desulfovibrio genus L 1
Dialister genus L 4
Dorea genus L 2
Eggerthella genus H 1
Eggerthella genus L 1
Enterobacter genus H 2
Enterococcus genus H 2
Erysipelatoclostridium genus H 1
Escherichia genus H 10
Escherichia genus L 2
Eubacterium genus H 1
Eubacterium genus L 3
Faecalibacterium genus H 6
Faecalibacterium genus L 5
Flavobacterium genus L 1
Flavonifractor genus H 2
Fusobacterium genus H 8
Gemella genus H 1
Haemophilus genus L 3
Hafnia genus H 1
Hafnia alvei genus H 1
Klebsiella genus H 4
Lachnoclostridium genus H 1
Lachnospira genus L 1
Lactobacillus genus H 4
Lactobacillus genus L 5
Megasphaera genus L 1
Methanobrevibacter genus H 3
Mogibacterium genus L 1
Morganella genus H 1
Odoribacter genus H 1
Odoribacter genus L 3
Oscillibacter genus H 4
Oscillospira genus L 1
Oxalobacter genus H 4
Parabacteroides genus H 2
Parabacteroides genus L 4
Parvimonas genus H 1
Peptoclostridium genus H 1
Peptostreptococcus genus H 1
Phascolarctobacterium genus H 2
Photobacterium genus H 1
Photobacterium genus L 1
Porphyromonas genus H 2
Prevotella genus H 8
Prevotella genus L 3
Proteus genus H 2
Pseudobutyrivibrio genus L 1
Pseudoflavonifractor genus H 8
Pseudomonas genus H 1
Raoultella genus H 1
Rhodococcus genus H 2
Roseburia genus H 2
Roseburia genus L 3
Ruminococcus genus B 5
Ruminococcus genus H 1
Ruminococcus genus L 6
Sarcina genus H 1
Serratia genus H 1
Staphylococcus genus H 1
Staphylococcus genus L 1
Streptococcus genus H 2
Subdoligranulum genus L 1
Sutterella genus H 1
Sutterella genus L 2
Turicibacter genus L 1
Veillonella genus H 7
Veillonella genus L 2
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.
Likes: pibee


Hi, I live in Cheltenham, I have been diagnosed with ME/CFS and Fibromyalgia for 17 years.

I have recently been diagnosed with D-Lactic Acidosis which causes ME like symptoms. I believe that ME may be cause by D-Lactic Acidosis secondary to Bacterial Overgrowth for a percentage of ME/.CFS patients. Please read the abstract below from researchers who have found D-Lactic producing Bacteria in CFS patients. I had frequent neurological symptoms that were making me very ill.

I am now receiving treatment (Diet consisting of No Carbohydrates or Simple Sugars). The Diet can be tried by anyone as long as they check with their Doctor first.

In Vivo. 2009 Jul-Aug;23(4):621-8.
Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome.

Patients with chronic fatigue syndrome (CFS) are affected by symptoms of cognitive dysfunction and neurological impairment, the cause of which has yet to be elucidated. However, these symptoms are strikingly similar to those of patients presented with D-lactic acidosis. A significant increase of Gram positive facultative anaerobic faecal microorganisms in 108 CFS patients as compared to 177 control subjects (p<0.01) is presented in this report. The viable count of D-lactic acid producing Enterococcus and Streptococcus spp. This study suggests a probable link between intestinal colonization of Gram positive facultative anaerobic D-lactic acid bacteria and symptom expressions in a subgroup of patients with CFS. Given the fact that this might explain not only neurocognitive dysfunction in CFS patients but also mitochondrial dysfunction, these findings may have important clinical implications.
See https://cfsremission.com/2015/09/21/d-lactic-acidosis-sauerkraut-is-not-good-for-you-if-you-have-cfs/

For more studies

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