We have been led to believe that pathogens have been eradicated in humans. However, that is not the case. There are many pathogens that are highly prevalent in society today. These pathogens can relay symptoms such as headaches, malnutrition, eczema, inflammatory bowel disease, and diarrhea.  

What are Pathogens?

Pathogens are bacteria, viruses, or other microorganisms that can cause disease. The most common pathogens we see today are bacterial pathogens, parasitic pathogens, and fungal pathogens. These pathogens are increasing due to more overseas travel, digestive illnesses, and exposure to/ the transmission of parasitic infection. 

Before a pathogen can be diagnosed, a careful history and testing are required. The most accurate testing to diagnose dysbiosis is a comprehensive diagnostic stool analysis and organic acids test. By performing these tests, the goal is to determine a diagnosis and manage dysbiosis by restoring normal microflora and providing nutrients that will heal the intestinal mucosa. 

Bacterial Pathogens 

The best way to test for a bacterial pathogen is to gain information indirectly. For this type of lab testing an Organic Acid Test should be performed. This allows us to monitor metabolic byproducts and measure biochemicals in the stools that reflect the direct health of the digestive tract. 

Parasitic Pathogens

These parasites cause flatulence, bloating, diarrhea, cramps, constipation, and poor digestion. They thrive by depleting the healthy gut flora, allowing the bad bacteria to overgrow and nutrients to be depleted in order to feed itself. 

Yeasts/ Fungal Pathogens

Practitioners are well aware of fungal pathogens, but it is to be noted that these infections often accompany a parasitic infection. Due to the energy drained from the body by the parasite, this leaves a perfect opportunity for fungal pathogens to appear. 

How Can We Overcome Pathogens?

The first step to overcoming pathogens is to have lab testing performed. Lab testing will provide your practitioner with the necessary information to determine what pathogen is overgrowing in your gut. From here, the plan can be created to properly assess the pathogen and repair a healthy gut. 

There are serum (blood) tests that can detect a pathogen in the body. However, serum testing is not as accurate nor effective. Serum testing results take multiple weeks to receive, whereas stool testing provides a direct look into the pathogen in a matter of days. Stool testing is the most effective approach to determine pathogens throughout the body. A common approach to stool testing is to collect 3 stool samples 48 hours apart from each other. This allows scientists to analyze if there is a pathogen present and its strength. 

Not all pathogen testing searches for the same information. Based on a patient’s individual symptoms, we determine the best company and lab to fit their specific needs. We have a variety of lab companies we work with to ensure our patients receive the best and most accurate care. For more information on the labs we work with, read more here. 


Pathogens are fairly common. Although we have made advances in technology and the cleanliness of the food and water we drink, they are still being found. Pathogens appear as simple symptoms, so if you are experiencing any of these symptoms, I recommended seeing a doctor. The stool test analysis will provide a great deal of information and get you back on track to feeling great with a healthy gut! -Kenna Vaughn, Senior Health Coach 



University, Functional Medicine and Ronald Grisanti, directors. Advanced FDM Testing — Interpretation and Treatment: Stool Pathogens – Bacteria, Parasites and Yeast. Functional Medicine University – The Leader in Online Training in Functional Diagnostic Medicine, 2010, www.functionalmedicineuniversity.com/members/444.cfm.


The scope of our information is limited to chiropractic, musculoskeletal, and nervous health issues or functional medicine articles, topics, and discussions. We use functional health protocols to treat injuries or disorders of the musculoskeletal system. Our office has made a reasonable attempt to provide supportive citations and has identified the relevant research study or studies supporting our posts. We also make copies of supporting research studies available to the board and or the public upon request. To further discuss the subject matter above, please feel free to ask Dr. Alex Jimenez or contact us at 915-850-0900.  



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The information herein on "Pathogens: What Are They?" is not intended to replace a one-on-one relationship with a qualified health care professional or licensed physician and is not medical advice. We encourage you to make healthcare decisions based on your research and partnership with a qualified healthcare professional.

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Our information scope is limited to Chiropractic, musculoskeletal, physical medicines, wellness, contributing etiological viscerosomatic disturbances within clinical presentations, associated somatovisceral reflex clinical dynamics, subluxation complexes, sensitive health issues, and/or functional medicine articles, topics, and discussions.

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We understand that we cover matters that require an additional explanation of how it may assist in a particular care plan or treatment protocol; therefore, to further discuss the subject matter above, please feel free to ask Dr. Alex Jimenez, DC, or contact us at 915-850-0900.

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Dr. Alex Jimenez DC, MSACP, RN*, CCST, IFMCP*, CIFM*, ATN*

email: coach@elpasofunctionalmedicine.com

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Dr. Alex Jimenez DC, MSACP, RN* CIFM*, IFMCP*, ATN*, CCST
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