Prebiotics “is a general term to refer to chemicals that induce the growth or activity of microorganisms (e.g., bacteria and fungi) that contribute to the well-being of their host.” In general, they have been shown to help the growth of one or more bacteria families deemed helpful. As readers of this column know, some commonly deemed healthy bacteria actually pushes the CFS microbiome in the wrong direction – for example Lactobacillus usually suppress E.Coli (which CFS patients are extremely low in). A prebiotic that encourages the growth of bacteria that further shifts an unhealthy microbiome in the wrong direction. “A prebiotic is a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microflora that confers benefits upon host well-being and health.” The gotcha is whether there are benefits for an unhealthy person?

This is the gotcha that is often forgotten:

What is good for healthy individuals (whose microbiome is balanced) may be wrong for people dealing with health challenges!”

This is actually stated well by a article published this year, “Substantiating the safety and mechanisms of action of probiotic/prebiotic formulations is critical.” [2015]

Since prebiotics have only been know since 1995, our knowledge about this “miracle food” is limited and likely very colored by rose-colored glasses (as are all new medical wonders). The ideal study to find are those that are well done with a specific condition such as Chronic Fatigue Syndrome. Be aware that “no results” or “negative results (making it worst)” have a tendency not to get published. I could find zero clinical studies on pubmed for this condition.

• “Specific probiotics also have immunomodulatory and metabolic effects. However, when evaluated in clinical trials, the effects are variable, preliminary, or limited in magnitude.’ [2015]

Trying to tease our the studies

Most foods contains prebiotics naturally. Even something like coffee can qualify – “induced a significant increase in the growth of Bifidobacterium spp. (P<0·05) …also induced a significant increase in the growth of the Clostridium coccoides-Eubacterium rectale group [2015]”. Prebiotics are generally extracts from foods (often from food that are not in a modern western diet).  The key to this Gordian knot may be looking at what increases biodiversity in the gut. IMHO, changing diet is better option than keeping a bad diet and taking prebiotics.

My general impression has been that every disease that influence the gut (or the reverse) has decreased biodiversity. This is the criteria that I am using.

• What increases microbial diversity:
  • barley flakes, brown rice flakes, or a mixture of both increased microbial diversity, as well as a rise in the proportion of Firmicutes and a reduction of the Bacteroidetes phylum [source]
  • “Agrarian diets high in fruit/legume fibre are associated with greater microbial diversity and a predominance of Prevotella over Bacteroides.” [2015]
  • “The low FODMAP diet was associated with higher faecal pH, similar short-chain fatty acid concentrations, greater microbial diversity .. compared with the Australian diet.” [2015] and also improves IBS.
    • FODMAP -> A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols
    • Study on levels in various foods [Oligosaccharide Profile in Fruits and Vegetables as Sources of Prebiotics and Functional Foods, 2014]
• What does NOT increase microbial diversity
  • “the overall microbial diversity was not affected by treatment with [prebiotic dietary fibers such as xylo-oligosaccharides] [2015]
  • Synbiotic Lactobacillus acidophilus NCFM and cellobiose does not affect human gut bacterial diversity but increases abundance of lactobacilli, bifidobacteria and branched-chain fatty acids: a randomized, double-blinded cross-over trial [2014].
  • “Increased pharmaceutical usage … can contribute to reduced gut microbiota stability and diversity.” [2014]
  • “Analysis of fecal microbiota and dietary intake indicated that numbers of healthy gut bacteria decreased, while numbers of unhealthy bacteria increased parallel to reductions in the intake of polysaccharides after following the Gluten Free Diet.” [2010]

Bottom Line

My perception was turned upside down by doing this research, namely:

• Gluten Free Diet does not help a shifted microbiome get back to normal. It may reduce symptoms but moves you away from getting healthy as a result!
• Prebiotics have no effect on biodiversity
• A diet low in specific prebiotic substances is likely healthiest!
  • FODMAP -> A diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols

You may disagree with this — if so, please find PubMed studies that support you and post as comments.  Common alternative medicine and beliefs may be very wrong and based on belief or naive scientific reasoning.