Microbiome shift linked to Autoimmune

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

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

Class

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

Order

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

Family

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

Genus

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.