El Paso Functional Medicine
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Maintaining Gut Flora Balance


For individuals with stomach issues, can maintaining gut flora balance promote and improve gut health?

Maintaining Gut Flora Balance

Gut Flora Balance

Maintaining gut flora balance is part of optimal digestive health. Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tract. The type and amount of bacteria present depend on their location in the body which could be the small intestine and colon. This is the storage housing for waste/stool, and the colon comprises hundreds of different types of bacteria, which have specific jobs and functions.

Unhealthy Flora

The more common pathogens are bacteria that can cause illness if left unchecked, including germs like streptococcus/strep throat or E. coli/urinary tract infections and diarrhea. Other common germs found in the colon include: (Elizabeth Thursby, Nathalie Juge. 2017)

Clostridioides Difficile

  • C. diff overgrowth can cause watery foul-smelling stools daily, and abdominal pain and tenderness.

Enterococcus Faecalis

  • Enterococcus faecalis is a cause of post-surgical abdominal and urinary tract infections.

Escherichia Coli

  • E. coli is the most common cause of diarrhea in adults.
  • This bacteria is present in almost every healthy adult’s colon.


  • Klebsiella overgrowth is associated with a Western diet that consists of various meat and animal products.


  • Bacteroide overgrowth is associated with colitis, which causes painful inflammation of the colon.

Healthy Flora

Healthy bacteria like Bifidobacteria and Lactobacillus, help maintain gut flora balance and keep the unhealthy bacteria in check. Without healthy flora, the entire colon can become overrun by bad flora, which can result in symptoms like diarrhea and/or illness. (Yu-Jie Zhang, et al., 2015) These protective, microscopic germs have important functions that include:

  • Assisting with vitamin synthesis – vitamins B and K in the small intestine.
  • Increases immune system function.
  • Maintaining regular bowel movements.
  • Maintaining a clean colon naturally without the need for colon cleansers.
  • Destroying the unhealthy bacteria.
  • Preventing unhealthy bacteria overgrowth.
  • Breaking up gas bubbles from food fermentation.

Bacterial Dismantling

Whether labeled as healthy bacteria or unhealthy, they are both single-celled organisms that can be destroyed quite easily. Sometimes, it is necessary, like when having to take antibiotics to kill a strep throat infection. However, the antibiotics also kill the beneficial bacteria, which can lead to compounding problems that can include: (Mi Young Yoon, Sang Sun Yoon. 2018)

  • Bowel irregularity – diarrhea and constipation.
  • Yeast overgrowth – can cause itching, burning around the anus and lead to vaginal and oral yeast infections.
  • Dysbiosis – the technical name for a lack of healthy bacteria or a bacterial imbalance.
  • Complications for individuals suffering from irritable bowel syndrome.

There are different ways to destroy bacteria including.

  • Individuals who need to take antibiotics to cure an infection. (Eamonn M M Quigley. 2013)
  • Chronic laxative use.
  • Fiber supplementation overuse.
  • Prolonged diarrhea – can flush out the bad and good bacteria.
  • Stress
  • Completing a bowel prep, like those required for a colonoscopy.

Diagnosing Gut Flora Issues

Many times, problems with gut flora will correct themselves, and no action is required. However, individuals facing chronic bowel problems, like colitis or inflammatory bowel disease, may require medical intervention of their colon’s bacteria.

  • Comprehensive Digestive Stool Analysis/CDSA is a stool test that checks what type and amount of bacteria are present, nutrient absorption rates/digestion speed, and how well food is digested.
  • If there is a significant difference in the proportion of unhealthy versus beneficial bacteria, a healthcare provider may suggest taking a probiotic or a live microbial supplement to help repopulate and maintain gut flora balance.

Gut Dysfunction


Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. The Biochemical journal, 474(11), 1823–1836. doi.org/10.1042/BCJ20160510

Zhang, Y. J., Li, S., Gan, R. Y., Zhou, T., Xu, D. P., & Li, H. B. (2015). Impacts of gut bacteria on human health and diseases. International journal of molecular sciences, 16(4), 7493–7519. doi.org/10.3390/ijms16047493

Yoon, M. Y., & Yoon, S. S. (2018). Disruption of the Gut Ecosystem by Antibiotics. Yonsei medical journal, 59(1), 4–12. doi.org/10.3349/ymj.2018.59.1.4

Quigley E. M. (2013). Gut bacteria in health and disease. Gastroenterology & hepatology, 9(9), 560–569.

Post Disclaimer

Professional Scope of Practice *

The information herein on "Maintaining Gut Flora Balance" 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.

We provide and present clinical collaboration with specialists from various disciplines. Each specialist is governed by their professional scope of practice and their jurisdiction of licensure. We use functional health & wellness protocols to treat and support care for the injuries or disorders of the musculoskeletal system.

Our videos, posts, topics, subjects, and insights cover clinical matters, issues, and topics that relate to and directly or indirectly support our clinical scope of practice.*

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

email: coach@elpasofunctionalmedicine.com

Licensed as a Doctor of Chiropractic (DC) in Texas & New Mexico*
Texas DC License # TX5807, New Mexico DC License # NM-DC2182

Licensed as a Registered Nurse (RN*) in Florida
Florida License RN License # RN9617241 (Control No. 3558029)
License Compact Status: Multi-State License: Authorized to Practice in 40 States*
Presently Matriculated: ICHS: MSN* FNP (Family Nurse Practitioner Program)

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