A reader contacted me and ask “What about Stevia and gut bacteria?” After discovering that Sorbitol causes gut problems, the reader wondered if other “healthy alternatives” may have issues if you are dealing with a gut bacteria dysfunction. Yes, they have some healthy aspects — but they may also have issues to people with microbiome challenges.
The dominant bacteria is health individuals is Lactobacillus reuteri, which can be low (or non-existent) in patients with CFS and other conditions.
“it was found that lactobacilli and bifidobacteria tested were able to utilise [stevia] steviol glycosides as a carbon source only to a very limited extent.”  – in other words, does not encourage these species 🙁 it does not kill them — just starves them,
“Taking into consideration the broad application of Lactobacillus reuteri in functional foods, the aim of the research was to evaluate the influence of stevia glycosides on its growth. Six Lact. reuteri strains were tested for their ability to grow in the … impaired the growth of analysed strains… it is necessary to evaluate the influence of stevia glycosides on other groups of micro-organisms in further research.” 
Antimicrobial potential of extracts from Stevia rebaudiana leaves against bacteria of importance in dental caries… against 16 bacterial strains of the genera Streptococcus (n= 12) and Lactobacillus (n=4) 
“bacteroides were the most efficient in hydrolyzing Stevia sweeteners to steviol” 
The bottom line seems to be that stevia is utilized by very few bacteria which for cavity fighting is ideal. On the flip size, it appears to starve or inhibits some beneficial bacteria. The literature is no clear if this is good or bad for microbiome dysfunction.
There is one last study  that raises a concern, “. Among patients with allergic diseases, allergy to stevia and stevioside was found in 16.0% AR patients, 34.0 % BA patients, or 64.0 % AE patients. Avoidance of stevioside-containing foods significantly decreased sensitization to stevia and stevioside in patients.” which is a concern because Allergy is a big player in inflammatory bowel disease.
Additionally, with an up regulated immune system we find that “Immune up regulatory response of a non-caloric natural sweetener, stevioside”  which adds more fuzziness.