When dealing with Gut/Microbiome issues, people tend to disconnect that the mouth and the gut are connected beyond one passing food to the other. They are often viewed as independent and isolated systems. This is dangerously untrue.
For ME/CFS, your mouth bacteria is different than a healthy person: Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function. [Sep 2018].
And across a much wider spectrum we read:
- Association between periodontal pathogens and systemic disease.
- Chronic oral infection: An emerging risk factor of cerebral small vessel disease.
- Porphyromonas gingivalis, a periodontitis causing bacterium, induces memory impairment and age-dependent neuroinflammation in mice.
- Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. 
- A scope of monolaurin into the mouth and chews until it is fully dissolved – nasty strong taste, but you get use to it.
- Sublingual (dissolve under tongue) B-12
- Using sublingually the following probiotics that come as tablets:
- Symbioflor-1 – per instructions!~
Replace your toothpaste!
Recently, we (for other reasons) decided to swing over to old-fashion homemade toothpaste. Dr.Axe has some formula, from the choices (checking each against what bacteria it modifies and suggestions) I came up with
- 4 tablespoons coconut oil
- 2–4 tablespoons baking soda or a combination of baking soda and sea salt
- 20 drops peppermint essential oil (flavonoids in it are recommended for me)
- small glass jar
Dr. Axe also lists a ton of issues with commercial toothpaste, for example, Triclosan:
Triclosan exposure is practically unavoidable in the United States, but little is known how ingestion may affect our health. Yang and colleagues used mouse models of colitis and colon cancer to see how brief exposures of triclosan could affect inflammation. They observed that triclosan altered mouse gut microbiota and increased inflammation in a TLR4-dependent manner. Triclosan increased the severity of colitis symptoms and spurred colitis-associated colon cancer cell growth.A common antimicrobial additive increases colonic inflammation and colitis-associated colon tumorigenesis in mice 
Natural Source does mean it is safe..
Mouth Wash – Keep the Breath Sweet and the gut Sick!
There are many sites that have formula similar to the above toothpaste. Although you just rinse and spit with commercial mouth wash — some will cling and eventually makes it way to the gut … oh, yes, remember we are also talking about the mouth bacteria — which is constantly acting as a reserve to repopulate the gut… Perhaps not such a good idea after all.
This site reported (via Citizen Science) that dry mouth is associated with a distinctive gut microbiome pattern. The logical conclusion is that the bacteria in the oral cavity causing dry mouth is seeding the digestive system with bacteria that results in the discovered shift.