Exercise and Chronic Fatigue Syndrome tends to be a “hot button” to many patients. The reality is that mild exercise is important. I have (and continue to) use WII Fit to track weight and monitor activity levels. There are some extremely mild exercises — just shifting balance, and progression up to yoga and step exercises. The key is never to progress aggressively — just add a minute a day at most, or move up one more step for one exercise in their exercise scale for one exercise.
What does the literature say about Gut Bacteria and Exercise?
The first article of interest is not listed on PubMed, but may be read here. The gut microbiota, dietary extremes and exercise 9 June 2014 doi:10.1136/gutjnl-2014-307305 which found “ The results provide evidence for a beneficial impact of exercise on gut microbiota diversity but also indicate that the relationship is complex and is related to accompanying dietary extremes.“
- Exercise induction of gut microbiota modifications in obese, non-obese and hypertensive rats. Petriz BA, Castro AP, Almeida JA, Gomes CP, Fernandes GR, Kruger RH, Pereira RW, Franco OL. “These data indicate that non-obese and hypertensive rats harbor a different gut microbiota from obese rats and that exercise training alters gut microbiota from an obese and hypertensive genotype background.” 
Exercise attenuates PCB-induced changes in the mouse gut microbiome. Choi JJ, Eum SY, Rampersaud E, Daunert S, Abreu MT, Toborek M.  “Our results show that oral exposure to PCBs can induce substantial changes in the gut microbiome, which may then influence their systemic toxicity. These changes can be attenuated by behavioral factors, such as voluntary exercise.” – this is significant to those who suspect some chemical like organo-phosphates is a contributing factor.
Exercise-induced splanchnic hypoperfusion results in gut dysfunction in healthy men. van Wijck K, Lenaerts K, van Loon LJ, Peters WH, Buurman WA, Dejong CH.  “Splanchnic hypoperfusion is common in various pathophysiological conditions and often considered to lead to gut dysfunction. While it is known that physiological situations such as physical exercise also result in splanchnic hypoperfusion, the consequences of flow redistribution at the expense of abdominal organs remained to be determined. This study focuses on these effects” — this is double significant because hypoperfusion is seen in SPECT scans of CFS patients, as well as being the major part of Hemex/Berg model of CFS. Hypercoagulation contributes to the shift of gut bacteria!
So, hypercoagulation will make it harder for the gut to return to normal — and it will also cause you to tire faster when exercising. Even mild short daily activity (I would not say exercise in the usual sense), will have a slow and positive effect on gut bacteria,