Current evidence is that bacteria in prebiotic supplements doesn't displace the current gut microbiota or readily take up residence. Once you stop taking any probiotic the fecal microbial and metabolite mix rapidly reverts to its original state, but probiotics may be useful to shorten diarrhea and gastrointestinal distress after courses of antibiotics.
The bacterial strains that appear to offer the greatest positive impact on gut health, like Akkermansia muciniphila and Faecalibacterium prausnitzii, are more difficult to culture and hence are at best minor constituents of prebiotic mixes.
The set of microbial strains in every persons gut is established soon after birth, but the relative proportions can vary dramatically within 24 hours, based primarily on diet.The evidence I've seen shows more promising outcomes from prebiotics that preferentially feed beneficial strains (inulin, transgalacto-oligosaccharides, and laculose), than from probiotics, and the easiest way to get these is to consume them in foods like whole grains and onions/leeks/garlic. Resistant starch and polyphenol intake also appear to favorably modulate the microbiota composition, towards more A. muciniphila, F.prausnitzii and Bifidobacteria spp. and fewer pathogenic Proteobacteria, and this may be one of the the major mechanisms for health benefits of plant-based diets.
If you must take a supplement rather than eat a healthy microbiota promoting diet, I'd recommend inulin (usually sourced from chicory root), as there's a lot of interesting research on it and metabolic endotoxemia, a remarkably fascinating subject. Eg:
Dehghan, P., Gargari, B. P., Jafar-Abadi, M. A., & Aliasgharzadeh, A. (2013). Inulin controls inflammation and metabolic endotoxemia in women with type 2 diabetes mellitus: a randomized-controlled clinical trial. International journal of food sciences and nutrition, 65(1), 117-123.
Inulin-supplemented patients exhibited a significant decrease in fasting blood sugar (8.5%), HbA1c (10.4%), fasting insulin (34.3%), homeostasis model assessment of insulin resistance (HOMA-IR) (39.5%), hs-CRP (35.6%), TNF-a (23.1%), and LPS (27.9%) compared with the maltodextrin group (p<0.05).
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Edited by Darryl, 14 November 2014 - 07:38 PM.