On my commute today I had a conversation with an old colleague whose teenage daughter had a physical brain trauma(included cerebral ischemia) in January. As she described her symptoms, I recognized a lot of symptoms that are often seen with CFS. I also recall reading some articles about gut shifts seen with physical trauma.

Cognitive impairment is common with CFS and other autoimmune conditions.

• The bidirectional gut-brain–microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease.[2017]
• The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders.[2018]
• “Specifically, Bacteroidales and Clostridiales, the two most prevalent bacterial taxa in mouse gut (Eckburg et al., 2005; Krych et al., 2013), were inversely regulated by traumatic spinal cord injury (SCI): Bacteroidales decreased while Clostridiales increased (Fig. 2, B and C). Significant changes in these taxa were accompanied by lesser but consistent changes in minor taxa, including Anaeroplasmatales, Turicibacterales, and Lactobacillales (Fig. 2 A). Open-field locomotor (Basso mouse scale [BMS]) scores were negatively correlated with the relative abundance of Clostridiales and Anaeroplasmatales, suggesting that the proportion of these bacteria can predict the magnitude of functional recovery and might be useful as a biomarker of injury severity” [2016]
• In conclusion, our results are the first to show specific changes in the microbiota due to a change in brain function, and also to surgical stress following tissue injury, with the likely involvement of the autonomic nervous system and goblet cells under certain conditions.  [2016]
• “Higher percentages of Clostridiales and lower expression of Bacteroidales in high-energy diets were related to the poorer cognitive flexibility in the reversal trials. ” [2015]
• Clostridium butyricum attenuates cerebral ischemia/reperfusion injury in diabetic mice via modulation of gut microbiota.[2016]
• Dysbiotic microbiome in patients with stroke and TIA: ↑ genera Enterobacter, Megasphaera, Oscillibacter, and Desulfovibrio; ↓ genera Bacteroides, Prevotella, and Faecalibacterium correlating with disease severity. ↓ TMAO in stroke/TIA group compared with patients with asymptomatic atherosclerosis [14]

Bottom Line

The number of bacteria taxonomy identified is lower than with other conditions but it is definitely work creating a profile on. An example with the demo ubiome result is shown below.

Analysis Web Site:  http://microbiomeprescription.azurewebsites.net

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.

Today I got a comment from someone with Hashimoto’s thyroiditis, often co-morbid with CFS, IBS etc.  I thought that I would check to see if there had been any microbiome work done on this condition. I was delighted to see a February, 2018 article, “Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients.”  and converted it results into a profile that can be applied to uBiome results.

This is added to the existing series shown below

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

Analysis Web Site:  http://microbiomeprescription.azurewebsites.net

A reader wrote gave me access to their latest uBiome

“I’ve been following your probiotics protocol. I’ve been taking L. Reuterii, a mix of bifidobacterium and symbioflor 2.

Comparing the Before and Now Samples

Overall, there have been a significant improvement is the all profiles with Gout being the sole item with significant increase.

Bacteria Shifts

Apart from two phylum (small populations usually), things have improved. As I have mentioned before — recovery is not a straight line recovery. It is moving from one island to the next until you back to your original harbor.

Class

Moving down to the class level, we see better clarity. Remember the criteria was to focus on items > 150%.  All of them went down

Looking at High Family items we see that we succeed in reducing them.

So where do we go next?

The latest result have good list of changes:

As well as avoids

It is interesting to note that bacillus probiotics is on the take list, but one specific one is on the avoid list: bacillus subtilis probiotic

Some concerns

Candidatus Saccharibacteria: 31x normal only (14.49% of Samples) phylum have this

Candidatus Saccharimonas 22x normal only (0.97% of Samples) genus

The only known item to reduce this are macrolides, for example azithromycin.

For the very high Methanobacteriaceae (35.75% of Samples) family, we see coconut (lauric acid and myristic acid) and bile are items that will decrease it

Bottom Line

It was nice to see objective improvement in the microbiome by following earlier suggestions. The suggestions were successful for reducing high bacteria (the specific goal sought).

The new analysis sight allows both high and low to be adjusted for. We will likely see in a few months what the latest recommendations caused to change.

REMEMBER: Adjust for one shift may induce other shifts.

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.

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’.