Reducing Clostridium Genus

A reader forwarded their uBiome results and it was high in Clostridium. Another high bacteria is clostridium asparagiforme reported by Ian Lapkin et al 2017 paper [Index to all posts on Study].


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The Clostridium genus is associated with Crohn’s Disease (some 300+ hits on PubMed) and thus having high levels have a risk of evolving into Crohn’s disease (typical or atypical) and likely a friendlier environment for C. difficile to occur.

Clostridium genus includes Clostridium difficile (Peptoclostridium difficile).. the later is inhibited by Plantain bananas, Bile salts, Lactobacillus casei, Lactobacillus rhamnosus,  Saccharomyces sp. boulardii Enterococcus.

DataPunk.Net Data


  • D-Glucose


  • Trametes versicolor
  • Resistant starch (type II)
  • Polymannuronic acid
  • Navy bean (Cooked)



PubMed Literature

  • “Results showed that co-culture with B. longum IPLA20022 and B. breve IPLA20006 in the presence of short-chain fructooligosaccharides, but not of Inulin, as carbon source significantly reduced the growth of the pathogen. With the sole exception of B. animalis Bb12, whose growth was enhanced,” [2016]
  • “The strain B. longum IPLA20022 showed the highest ability to counteract the cytotoxic effect of C. difficile acting directly against the toxin” [2016]
  • ” cinnamon, rosemary, and turmeric were active against selected Clostridium spp.” [2017]
  • “B. licheniformis improved the growth of the chickens challenged with [Clostridium perfringens] pathogens.” [2017]
  • “Among those, seven Paenibacillus polymyxa strains showed the highest antibotulinal activity and the largest antimicrobial spectrum against C. botulinum strains. ” [2002] – this is in Prescript Assist Probiotics
  • “Ocimum basilicum L. (basil), Rosmarinus officinalis L. (rosemary), Origanum majorana L. (marjoram), Mentha × piperita L. var. Piperita (peppermint), Thymus vulgaris L. (thyme) and Pimpinella anisum L. (anise) against C. perfringens strain…. Minimum inhibitory concentration values were 1.25mgmL(-1) for thyme, 5.0mgmL(-1) for basil and marjoram, and 10mgmL(-1) for rosemary, peppermint and anise.  ” [2016]
  • “The best antimicrobial activity against C. butyricum was found at Abies alba Mill.[European Silver fir oil], against C. intestinale was found at Abies alba Mill.Mill.[European Silver fir oil], against C. perfringens was found at Satureia montana[Winter Savory] and against C. ramosum was found at Abius alba and Carum carvi.[Caraway] ” [2014]
  • ” The most susceptible to chitosan were bacteria belonging to genera Bacteroides and Clostridium (91-97% growth inhibition).” [2006]
  • “Tannic acid, propyl gallate and methyl gallate, but not gallic acid, were found to be inhibitory to the growth of intestinal bacteria Bacteroides fragilis ATCC 25285, Clostridium clostridiiforme ATCC 25537, C. perfringens ATCC 13124, C. paraputrificum ATCC 25780,” [1998]
  • ” Moreover there was a significant decrease in the proportion of Bacteroides, Clostridium and Staphylococcus genera in the faeces of cocoa-fed animals” [2012]
  • “. Slow digestible carbohydrates (human milk glycan, inulin and fructooligosaccharide), insoluble complex carbohydrates and protein diets favor the growth of Bacteroides, Clostridium and Bifidobacterium” [2013]
  • “While this synbiotic yogurt can increase bifidobacterial numbers and decrease clostridial numbers (but not enterobacterial numbers) in some individuals, it cannot modulate these microbial groups in the majority of individuals.” [2012]

Bottom Line


  • Bifidobacterium animalis


  • Bifidobacterium longum and Bifidobacterium Breve
  • Bacillus licheniformis (it does produce histamines, see this post)
  • Lactobacillus casei
  • Lactobacillus rhamnosus probiotics
  • Prescript Assist
  • Streptococcus Probiotics
  • Chitosan supplements
  • Have Chocolate! There is one chocolate that I just picked up which may be interesting to try: from MilkBoy in Switzerland

The herb/spice that seems to be the best candidate is Silver Fir — it impacts multiple species, it is not a common item. You may wish to try more common ones cited above first.

Silver Firsee this technical summary, This page cites options for taking it.

  • “The internal use of Fir Needle Essential Oil is restricted. It should not be used orally because it can be severely sedative in action and produces excess heat sensation in the body. Fatal allergic reaction to it may also be possible even with smallest doses.”
  • Italian Seller for Resin.

Yogurt: No evidence that it will help.

This is strictly an educational post. Always consult with a knowledgeable medical profession before any changes of supplements, diet or medicine.