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.
- The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders.
- “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” 
- 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. 
- “Higher percentages of Clostridiales and lower expression of Bacteroidales in high-energy diets were related to the poorer cognitive flexibility in the reversal trials. ” 
- Clostridium butyricum attenuates cerebral ischemia/reperfusion injury in diabetic mice via modulation of gut microbiota.
- 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 
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.