Clostridium difficile, bacterial census and gut ecology restoration

??????????????????????????????????????????????????????????????????????????????There are many conditions that result at least in part from bacterial dysbiosis, or imbalanced gut bacteria. As gut symbionts, our bacterial microbiome is vital to normal immune function as well as neurologic/brain function and hormonal balance. Some of the diseases or conditions that occur from dysbiosis can be life-threatening! One such example is a Clostridium difficile reaction. This species of bacteria can cause a gut infection usually known as “c-diff”, and this infection is most often acquired in a hospital. One case I recently became aware of was caused by a colonoscopy procedure. Clostridium infections often happen after antibiotic use as a result of the antibiotic suppressing the normal healthy bacteria that keep Clostridium difficile bacteria populations suppressed.

C-diff is usually treated with strong antibiotics such as vancomycin, which reduces the infection but also further imbalances the dysbiosis (as well as encouraging the formation of antibiotic resistant strains of C. difficile). While this may be necessary if there is an acute flareup, long term stabilization is only accomplished through restoration of the microbiome. Often the first step in gut restoration is a bacterial census, or tallying up what bacteria live in your colon.

There are different tests available, but I am going to look specifically at two tests: Metametrix GI Effects Microbial Ecology Profile Stool, and the tests that offer. A sample test of Metametrix can be found here:

A good video that shows the depth of information available from the ubiome test can be seen on this video:

Reviewing these two sources of data immediately should illustrate a critical difference: the Metametrix test report only provides genus but not species specificity. In many cases the genus does not provide enough information without the species. On the other hand, the ubiome test provides many layers of information that can be re-sorted to answer different questions. Data is available all the way down to the species level, and even linked to Wikipedia entries for that specific species. The Metametrix test can show large, genus-level imbalances and generalized patterns, but for someone evaluating not only Clostridium difficile populations, but also the populations of beneficial bacteria that reduce its effects (Streptococcus thermophilus, Lactobacillus lactis, Lactobacillus plantarum, Lactobacillus rhamnosus, Bifidobacterium animalis are examples that come to mind) the Metametrix data set is clearly lacking. What you really need to know is not only what the C. difficile levels are, but also its antagonists! A complete deficiency in antagonists can permit moderate levels of Clostridium difficile to produce disasterous infections.

What other factors can help to restore gut ecology? Here is a short list:

1. Mental: stress is bad for beneficial gut bacteria; relaxation and deep breathing, yoga etc. are good stress reductions, but do what works for you! Freediving is what works for me, as an example. Good stress reduction helps the gut to be a good environment for beneficial organisms.

2. Nutritional: When you choose what you eat, you’re choosing which populations of gut organisms you feed. Feel like a donut? you’re feeding yeast and other less beneficial species! A good green smoothie such as those made with a Nutri-bullet are gut bacteria superfood. McDonalds? quite the opposite. The “Western Diet” is the research standard in producing a sick lab animal, and it does the same for humans!

3. Food Sensitivities: IgG or Immunoglobulin G tests can identify immune sensitization to food ingredients. If you have a food sensitivity, eating that food will initialize an immune inflammatory cascade that makes your gut lining slough off and look more like sunburn-a very poor environment for gut symbionts. In addition, intestinal permeability goes up, pieces of bacterial protein (LPS; lipopolysaccharides) can translocate across the intestinal barrier into the bloodstream and cause a myriad of other problems in the body. Food sensitivities are often foods that we like, eat often, and are otherwise healthy. I’ve seen sensitivity to olives, chicken, flax, dairy, cinnamon as well as pesticides, Agent Orange, food colors and similar ingredients. Getting tested is the shortest road to knowing what to avoid. For someone fighting Cdiff, it may be the only road.

4: Supplements that can help: Kefir decreases the effects of Clostridium difficile toxins, and reduce C. difficile growth. It is also protective against Clostridium difficile. Coconut oil reduces Clostridium difficile as well. Curcumin is a very potent anti-inflammatory that can help to reduce systemic inflammatory reactions and help heal the gut lining. L-Glutamine is also a great supplement to speed healing of the gut and make it a better place for healthy gut bacteria. Of course probiotics can help, with some of the ones showing more different species showing promise (a good example would be from Prescript-Assist).

5. Medical/DIY procedures: the biggest one that comes to mind is FMT or Fecal Microbial Transplant. This is increasingly showing promise and for many individuals helps a great deal. It is probable that its success still depends on items 1-3 above, however, and having a major food allergy, not sleeping enough, or eating poorly can make the newly introduced population of gut bacteria unsustainable, requiring repeat procedures. Use of encapsulated feces is one possibility, although some have expressed concern at potentially causing SIBO or small intestine bacterial overgrowth as colonic bacteria are different than small intestinal bacteria. Every area of the body has an “optimal microbiome” and yet what is optimum varies between individuals. It is important t remember this when comparing microbiomes on test reports!

For more answers and a great deal more information, see my book on Amazon here:   It is also available in print here: . The printed version should be on Amazon as well within one week.

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4 thoughts on “Clostridium difficile, bacterial census and gut ecology restoration

    1. Hi Martyna, the GDX test is more comprehensive in that it also evaluates specific pathogenic bacteria, inflammatory markers, and parasites. Ubiome does not do this, and does not provide all the information down to the genus/species level though it isn’t always necessary. The uBiome test requires more expertise to evaluate and know what’s good or bad and what you should do about it. I offer this service, for example. There is a big price difference too; the gdx test is significantly more expensive. Ubiome is more useful for a pure bacterial census as its data format can mine the data several different ways and compare it to core groups at the phylum, class, order, genus levels.You just have to know how to make something useful out of that!

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