To Soy, or Not to Soy – that is the question

A reader asked about soy  — is it good or bad (or neutral)?  I will look at the microbiome, coagulation and any studies dealing with CFS/ME/IBS/FM that I can find.  I will not look at other health claims / problems with soy (see Soybead Foods – The Good, Bad and Ugly if interested). Tunnel vision is sometimes needed to prevent over-saturation of information

Genus No-soy
Mean (SD) %
Mean (SD) %
Bifidobacterium 4.45 (5.13) 7.53 (9.49)
Unclassified Clostridiaceae 1.53 (2.58) 0.14 (0.22)
Lactobacillus 0.15 (0.19) 0.06 (0.11)

IBS and Soy

  • “There was no significant changes in mean differences of symptoms severity score between the two groups (soy, placebo); however soy isoflavone supplementation could significantly improve the quality of life scores” [2015]
  • “A 2-wk oral treatment with a phytoestrogen-rich soy germ fermented ingredient (SG) prevented the stress-induced hyperpermeability and visceral hypersensitivity in cyclic rats through ER activation, and blocked the increase in colonic proteolytic activity, suggesting that SG can be promising in IBS management.” [2013]
  • “In conclusion, the anti-inflammatory properties of a fermented soy germ extract (FSG – Primasoy) treatment result from two distinct but synergic pathways i.e an ER-ligand and a PAR-2 mediated pathway, providing rationale for potential use as adjuvant therapy in IBD.”[2015]
  • Soy germ fermented with Aspergillus niger M46 resulted..has the potential to be a good dietary supplement for prevention of oxidative stress-related diseases,” [2014]
  • “Patients with food hypersensitivity (FH) differed from other IBS patients in that they had a longer duration of clinical history, a history of FH as children, and an increased frequency of self-reported FH; they also had hypersensitivities to other antigens (eg, egg or soy).” [2010]


  • “Results of statistical analysis using the separation test and intent-to-treat analysis revealed no benefit of soy compared with placebo.” [2011]


Bottom Line

Preferring soy has no apparent benefit unless it is fermented with the right bacteria.

There are major difference between non-fermented soy products and fermented soy products.  Some, like Natto (soy fermented with Bacillus subtilis var. natto) is on my recommended list — not because of the soy, but because of the nattokinease produced by the bacillus subtilis.  Soy fermented with lactobacillus is not recommended, neither is regular (unfermented) soy milk (Bifidobacterium decreased, diversity decreased).

Soy is not used by E.Coli, which means unless you are actively feeding E.Coli by other means you are starving the little E.Coli you have.