Prebiotics – the care and feeding of Probiotics

I have intentionally avoid dealing with prebiotics in the past. Instead, I have advocated ‘raw appropriate seasonal food’. The microbiome has evolved with seasons, and having fresh strawberries or blueberries in January may contribute to microbiome dysfunctions (speculation). A reader forwarded a study that changed my perspective because the results of one specific prebiotic was very desirable!

  • “To explain why some E. coli mutants do not grow as well on mucus in vitro as their wild type parents yet are better colonizers, we postulate that each one resides in a distinct “Restaurant” where it is served different nutrients because it interacts physically and metabolically with different species of anaerobes.” [2015]
  • “When E. coli Nissle 1917 is the only E. coli strain in the streptomycin-treated mouse intestine, it appears to use arabinose, fucose, galactose, gluconate, mannose, N-acetylgalactosamine, and sialic acid to colonize (Table 2 and (58)). In contrast, E. coli Nissle 1917 does not appear to use ribose to colonize (Table 2).” [2015]
    • Dr Myhill states the same here and advises “Eat figs, hazelnuts, chickpeas!”

Below is what I could find on various types of prebiotics. For example, for mannan oligosaccharide – I could not find any suitable studies.

For most prebiotics, the results were less than ideal – increasing Bifidobacterium with a decrease of other bacteria.

Xylooligosaccharides and/or Pectin

“Purified xylooligosaccharides from Miscanthus × giganteus (M×G XOS) were used in an in vitro fermentation experiment inoculated with human fecal microbiota. A commercial XOS product and pectin were used as controls. Decreases in pH by 2.3, 2.4, and 2.0 units and production of short-chain fatty acids (SCFA; acetic acid, 7764.2, 6664.1, and 6387.9 μmol/g; propionic acid, 1006.7, 1089.5, and 661.5 μmol/g; and butyric acid, 955.5, 1252.9, and 917.7 μmol/g) were observed in M×G XOS, commercial XOS, and pectin medium after 12 h of fermentation, respectively. Titers of Bifidobacterium spp., Lactobacillus spp., and Escherichia coli increased when fed all three substrates as monitored by qPCR.” [2016]

Pectin is from fruit. Apple Pectin capsules are available from Now, Solgar etc. or buy in bulk and make your own capsules ($15 for 2 lbs on Amazon)

One source of Xylooligosaccharides.

Fructooligosaccharides (FOS)

“Fructooligosaccharides (FOS) are one of the most studied prebiotics, selectively stimulating the growth of health-promoting bacteria in the host. However, there is increasing evidence that commensal gut bacteria, such as Bacteroides fragilis, Clostridium butyricum, Enterobacter cloacae, and even the pathogenic Escherichia coli BEN2908, are also able to metabolize FOS in vitro, and in some cases, FOS displayed adverse effects.” [2015]


“By stimulating bifidobacteria, …. These potential beneficial effects have been largely studied in animals but have not really been proven in humans.”[1999]

“All inulin-type prebiotics are bifidogenic – stimulating the growth of Bifidobacteria species. The effects they have on other gut organisms are less consistent….intra-individual response to an identical dose of the same inulin-type prebiotic, in terms of stimulation of total number of Bifidobacteria and individual Bifidobacteria species, can be variable.” [2008]

  • Inulin is typically made from chicory.

Galactooligosaccharides and Maltodextrins.

“a higher proportion of bifidobacteria (25.77%) was seen in the total bacterial population after cultivation on a prebiotic mixture than on the control medium (7.94%). The gram-negative anaerobe count significantly decreased …and the Escherichia coli count decreased” [2015]

“the galacto-oligosaccharide product was more bifidogenic(… much of this growth was attributed to growth of B. longum. …)  and potent in inhibiting E. coli than the other products tested.” [2014]

Almonds and Almond skins

“Significant increases in the populations of Bifidobacterium spp. and Lactobacillus spp. were observed in fecal samples as a consequence of almond or almond skin supplementation. However, the populations of Escherichia coli did not change significantly,” [2014]