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Now that we can compare whole microbiomes, has there been investigations on the effect of garlic (or diallyl disulfide, its main ingredient) on intestinal flora? From the proven antimicrobial activity, it should work like antibiotics. But does it leave "good bacteria" counts untouched?

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From studies,

lactic acid bacteria were found to be more resistant to GP (garlic powder) compared to the clostridial members of the gut microbiota. While for most bacteria the antimicrobial effect was transient, the lactobacilli showed a degree of resistance to garlic, indicating that its consumption may favour the growth of these beneficial bacterial species in the gut. Once the strains of other bacteria (eg: Bacteroides ovatus, Bifidobacterium longum DSMZ 20090 and Clostridium nexile A2-232) became resistant, they retained their resistant phenotype upon sub-culturing. Garlic intake has the potential to temporarily modulate the gut microbiota (reference).

Overall garlic can prove to be beneficial, because it seems to have more of an effect on detrimental bacteria like Helicobacter pylori (H. pylori), even when its strains were resistant to antibiotics. Overall garlic was found to be more detrimental to pathological bacteria when compared to normal gut flora (reference). Garlic’s diallyl disulfide has also been found to effectively cause cell death in Candida albicans which is a fungus in our gut which if not kept in check can cause health problems (reference).

Inulin and fructooligosaccharides present in garlic can also serve as nutrients for the probiotics colonizing your body (reference).

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