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CDSA Interpretation - Microbiology

CDSA Report - Microbiology

Continuing my series on interpreting the sometimes confusing results of the Comprehensive Digestive Stool Analysis (CDSA) today we're going to look at the Microbiology section.


Beneficial Bacteria

By now almost everyone has heard of so called "beneficial" or "friendly" bacteria, thanks mainly to probiotic yoghurt advertising that seems to be everywhere these days. Beneficial bacteria are in basic terms seen as the good guys within a huge community of bugs that inhabit our gastrointestinal (GI) tract.

A lot of research has gone into understanding their role over the past few decades. Some of their benefits include:

- Physical crowding out of less desirable microorganisms
- Production of antimicrobial substances to keep pathogens at bay
- Breaking down bacterial toxins
- Production of short-chain fatty acids (SCFAs) which keep GI tract cells healthy, provide a source of energy and help to maintain a healthy GI tract pH.
- Digestion of proteins
- Digestion of lactose
- Production of important nutrients such as vitamin K
- Interactions with the immune system i.e. beneficial bacteria help to regulate the immune response and have been found to reduce risk of certain allergic diseases

On the CDSA report the levels of beneficial bacteria are represented on a scale from 0 or NG (for No Growth) to 4+ which represents an optimal amount present.

The CDSA tests for beneficial bacteria belonging to three genera which have so far been found to play the largest positive role in human health. These are:

- Lactobacilli
- Bifidobacteria
- Escherichia coli (E.coli)

You may be familiar with Lactobacilli and Bifidobacteria from probiotic foods, drinks and supplements. E.coli is usually associated with causing food poisoning but most species are actually a normal part of our intestinal microflora and some have beneficial effects. In Europe there is actually a probiotic supplement that contains only E.coli - a strain called E.coli Nissle 1917. The product is called Mutaflor

Ideally you want each of the 3 beneficial bacteria markers to be 4+ or at least 3+. If any are significantly lower (particularly Lactobacilli and/or Bifidobacteria) then this indicates deficiency and potentially serious health consequences. Low levels of these beneficial bacteria can open the door for less desirable microorganisms such as bacteria and yeast to proliferate. Low beneficial bacteria and high levels of other microorganisms is referred to as gut dysbiosis and can lead to leaky gut syndrome, food allergies/sensitivities, nutritional deficiencies and various vague symptoms of fatigue, pain, cognitive dysfunction and changes in mood. Beneficial bacteria deficiency has also been linked to irritable bowel syndrome (IBS), autoimmune disease (e.g. rheumatoid arthritis), asthma, and even colon cancer.


Additional Bacteria

This section of the CDSA report deals with bacteria that are not considered beneficial to health. It includes both non-pathogenic and pathogenic (disease-causing) strains of bacteria.

Like the Beneficial Bacteria section the levels of various bacteria detected in your stool sample are displayed on a scale of 0-4. Bacteria marked NP for non-pathogen shouldn't cause too much concern but may be a confirming sign of beneficial bacteria deficiency that needs to be addressed before more troublesome bacteria are able to colonise. Those bacteria marked PP for potential pathogen may cause symptoms and disease only at high levels (3+-4+). The graph on the CDSA report will be marked yellow at the levels where these bacteria are considered pathogens. Any bacteria marked P for pathogen are considered dangerous in any amount and would include species of E-coli responsible for gastroenteritis (food poisoning). These are marked in red on the CDSA graph.



Mycology is the term used to describes fungi, yeast and mold. A common microorganism that many will be familiar with is Candida ablicans, which can take both fungal and yeast forms and is responsible for many common yeast infections (thrush, athlete's foot etc).

On the CDSA report the mycology section works exactly the same as it does for the Additional Bacteria section with NP, PP and P designations and coloured indicators signifying at what levels a particularly microoganism might become a health concern.


Dysbiosis Index

On older CDSA reports a Bacterial Dysbiosis Index score was included. This was a bar with a scale from 0-20 divided into optimal, slight, moderate and severe sections. It was an arbitrary score based on the microbiology results as well as markers such as stool pH and SCFA concentrations and ratios. It gave a simple to read indicator of whether bacterial dysbiosis was a concern for the patient but I believe it has been discontinued most likely because it was not likely to be a particularly accurate representation.


Sensitivity to Microbial Agents

This page of the CDSA report is intended to identify the best antimicrobial drugs and natural substances (herbs, nutrients) to treat any infections that may have been identified. The report gives the Minimum Inhibitory Concentrations (MICs) for a handful of agents. The MIC is the minimum dose of a substance needed to inhibit further growth of the pathogen identified. Unfortunately the labs don't usually test the actual pathogen isolated from your stool sample but use a generic reference based on that particular species of bacteria, yeast etc. However, this is still a useful guide for treatment as it lets you know the best drug or natural option to choose and the dose required to eradicate the infection.


Implications for Treatment

The information above provided by the CDSA can be useful where gut dysbiosis is suspected. The aim of any treatment for such a situation would depend on exactly what was found but generally involves taking antimicrobial substances as advised on the Sensitivity to Microbial agents report (or something else at your doctor's discretion) and the use of probiotic and prebiotic foods and supplements to restore beneficial bacteria levels to the healthy range.


Interpretation of other CDSA markers:

CDSA Interpretation: Digestion and Absorption Markers

CDSA Interpretation: Metabolic Markers