This was in /r/ketoscience. Am hoping for more discussion about real world situations over here.
Stumbled across http://perfecthealthdiet.com/2011/10/jimmy-moore%E2%80%99s-seminar-on-%E2%80%9Csafe-starches%E2%80%9D-my-reply/ .. don't care about safe starches etc. but this section caught my eye:
"Low-carb diets generally improve immunity to bacteria and viruses, but not all is roses and gingerbread.
Low-carb diets, alas, impair immunity to fungal and protozoal infections. The immune defense against these infections is glucose-dependent (as it relies on production of reactive oxygen species using glucose) and thyroid hormone-dependent (as thyroid hormone drives not only glucose availability, but also the availability of iodine for the myeloperoxidase pathway). Thus, anti-fungal immunity is downregulated on very low-carb diets.
Moreover, eukaryotic pathogens such as fungi and protozoa can metabolize ketones. Thus, a ketogenic diet promotes growth and systemic invasion of these pathogens.
As the fungal infection case studies on our “Results” page illustrate, low-carb dieters often develop fungal infections, and these often go away with increased starch consumption.
Another issue is that mucus is essential for immunity at epithelial surfaces, and glycosylation is essential for the integrity of cellular junctions and tissue barriers such as the intestinal and blood-brain barriers. Thus, reduced production of mucus can impair intestinal immunity and promote gut dysbiosis or systemic infection by pathogens that enter through the gut.
Finally, a very low-carb diet is not entirely free of risks of gut dysbiosis, and not just from fungal infections. Bacteria can metabolize the amino acid glutamine as well as mucosal sugars, so it is not possible to completely starve gut bacteria with a low-carb diet. Nor is it desirable, as this would eliminate a protective layer against systemic infection by pathogens that enter the body through the gut. As our “Results” page shows, several people who had gut trouble on the very low-carb (and generally excellent) GAPS diet were cured on our diet."