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.**