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Gut Microbiome Testing: How to Use This Powerful Tool in Practice

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Gut Microbiome Testing: How to Use This Powerful Tool in Practice

The gut microbiome has emerged as a pivotal player in health and wellness. Beyond its digestive functions, this complex community of microorganisms has become increasingly recognized for its role in shaping our health and susceptibility to diseases. Gut microbiome testing offers a unique window into the microbial universe inhabiting the human gastrointestinal tract. This innovative testing approach has become a game-changer in deciphering the dynamic connection between our gut microbiome and individual health.


What Is the Gut Microbiome?

Humans are inhabited by microorganisms collectively called the microbiota. The human microbiome is comprised of an estimated one hundred trillion bacterial cells. The gut microbiome specifically refers to the community of bacteria, viruses, fungi, and other microbes residing in the gastrointestinal (GI) tract. The gut alone accounts for 70% of the human microbiota. Collectively, these commensals play a vital role in preserving human health. They function to break down dietary fibers and other food components, synthesize vitamins, modulate the immune system, and protect the gut from the colonization of pathogenic microbes. (19, 30)

Disturbances in the gut microbiome, called dysbiosis, have been implicated in the pathogenesis of numerous systemic health conditions. Dysbiosis has been linked to GI conditions, like inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), along with systemic diseases like obesity, type 2 diabetes, and allergies (4). The bidirectional communication pathways between the gut and various body systems, such as the gut-brain, gut-heart, gut-liver, and gut-thyroid axes, underscore the influence of the microbiome on total-body health and how disruptions in the normal balance can be implicated in systemic disease manifestations. Furthermore, fecal microbiota transplantation (FMT) experiments have demonstrated the therapeutic potential of restoring a healthy microbiome in certain conditions, such as insulin resistance and IBD.

When to Order Gut Microbiome Testing

Hippocrates has been quoted as saying, "All disease begins in the gut." Appreciating that the microbes that live in the human body outnumber human cells by 10:1 and acknowledging the complex roles they play in human physiology, it's no wonder that scientists and doctors are increasingly looking to the gut for answers related to human health and dis-ease. With the increasing amount of evidence accumulating to implicate the gut microbiome's role in various facets of health, it's not entirely outrageous to suggest gut microbiome analysis has a legitimate role in any personalized approach to medicine. 

But let's narrow this down and discuss some of the most common indications for gut microbiome testing in functional medicine. One of the most common, and perhaps the most obvious, reasons to order stool testing for patients is to better understand the root causes of digestive symptoms and GI disorders. Dysbiosis is implicated in the pathogenesis and clinical manifestation of bloating, abdominal pain, nausea/vomiting, gastroesophageal reflux disease (GERD), Barrett's esophagus, eosinophilic esophagitis (EOE), functional gastrointestinal disorders (FGIDs), IBD, celiac disease, adverse food reactions, and GI cancers (14).

Given the intricate relationship between dysbiosis, intestinal permeability, and various health conditions, gut microbiome testing can be applied to a broader array of symptoms. Leaky gut, or intestinal hyperpermeability, can present not only with digestive symptoms but also symptoms like brain fog, fatigue, joint pain, headaches, rashes, and acne. Furthermore, studies have linked leaky gut to the following health conditions:

Types of Gut Microbiome Tests

Various methods are employed to assess the gut microbiome, with DNA-based sequencing and culture techniques as prominent approaches. DNA-based sequencing techniques, such as 16S rRNA gene polymerase chain reaction (PCR) amplification, offer a comprehensive view of microbial communities in a stool sample. 16S rRNA gene sequencing provides taxonomic information, capturing the diversity and functional potential of the microbiome, but may lack the ability to differentiate between live and dead microbes. The GI-MAP by Diagnostic Solutions is a popular stool test that utilizes quantitative PCR (qPCR) technology to screen for over 50 commensal and pathogenic bacteria, viruses, parasites, and yeast. (19)

On the other hand, culture techniques involve isolating and growing microorganisms in a controlled environment. Although they offer insights into the viability, cultivability, and functional characteristics of microbes, culture methods may underestimate diversity due to the challenges of culturing anaerobic species. Culture methods are also more time-consuming compared to DNA-based sequencing. The Microbiology Analysis by Genova Diagnostics is an example of a culture-based stool analysis. (19)

Integrating both methods may yield a more comprehensive perspective on the gut microbiome, capitalizing on the strengths of each while acknowledging their inherent limitations. The GI Effects Comprehensive Profile by Genova Diagnostics uses both PCR and stool culture as dual methods for evaluating the gut microbiome. Ultimately, the choice of methodology depends on the specific goals of the analysis, emphasizing the importance of considering the strengths and limitations of different gut microbiome testing techniques in the context of the intended clinical or research application.


Interpreting Gut Microbiome Test Results

Interpreting gut microbiome test results requires a multifaceted approach that considers various factors. A diverse and balanced community of microorganisms characterizes a healthy gut microbiome. Bacteria are classified according to phyla, classes, orders, families, genera, and species. The dominant gut microbial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. The Firmicutes phylum comprises genera including Lactobacillus, Faecalibacterium, Bacillus, Clostridium, Enterococcus, and Ruminicoccus. Predominant genera in the Bacteroidetes phylum include Bacteroides and Prevotella. The Bifidobacterium genus mainly represents the Actinobacteria phylum. (29

There are three types of dysbiosis, which are not mutually exclusive and may occur concurrently. The three types include:

  1. Loss of beneficial microorganisms
  2. Overgrowth of pathogenic (harmful) or opportunistic (potentially harmful) organisms
  3. Loss of microbial diversity

When interpreting stool results, it's important to keep these three types of dysbiosis in mind, screening for overgrowth and undergrowth of various microorganisms that stray from the normal patterns of a healthy microbiome. Recognizing dysbiosis patterns associated with specific diseases allows for a targeted understanding of how the gut microbiome may contribute to health conditions, facilitating personalized interventions to restore balance and improve overall well-being. The following are examples of noted correlations between diseases and altered gut microbial composition: 

  • IBS: increased Firmicutes-to-Bacteroidetes ratio, decreased Lactobacillus and Faecalibacterium, increased Firmicutes and Proteobacteria
  • IBD: reduced Lachnospiraceae and Bacteroidetes, increased Proteobacteria
  • Type 2 Diabetes: decreased Firmicutes and Clostridia, increased Bacteroidetes-to-Firmicutes ratio
  • Autism: decreased diversity; reduced Bifidobacterium and Firmicutes; increased Lactobacillus, Clostridium, Bacteroidetes, and Desulfovibrio

Integrating Microbiome Testing into Clinical Practice

Microbiome testing can be seamlessly integrated into clinical practice. In the initial patient consultation, a thorough gathering of medical history, symptoms, and lifestyle factors lays the foundation for understanding the patient's health history and possible factors contributing to symptoms. Additionally, medications, supplements, diet, exercise, sleep, and stress are all factors that influence the gut microbiome, providing the interpreting physician with valuable information to consider while understanding future gut microbiome results (29).  

Personalized treatment strategies based on the microbiome results and the patient's greater health context will encompass dietary modifications, lifestyle changes, or targeted interventions tailored to restore microbial balance. Ongoing monitoring and periodic retesting enable adjustments to the treatment strategy and successful monitoring of patient responses to therapeutic interventions. Collaboration with specialists, such as gastroenterologists or nutritionists, in complex cases enhances the multidisciplinary approach to microbiome management.

Therapeutic Interventions Post-Testing

Functional medicine approaches to restoring balance to the gut microbiome prioritize a comprehensive understanding of an individual's health by considering the interconnectedness of various systems and addressing the root causes of imbalances. Instead of merely treating symptoms, functional medicine seeks to identify and rectify underlying issues contributing to disruptions in the gut microbiome. This may involve thoroughly analyzing dietary habits, lifestyle factors, stress levels, and environmental influences. 

Based on these insights, personalized treatment plans are developed, often incorporating dietary modifications, targeted supplementation, and lifestyle adjustments. Dietary modifications may encompass eliminating or reducing certain foods that exacerbate dysbiosis, such as those high in processed sugars or artificial additives, and incorporating a diverse range of nutrient-rich whole foods. Probiotics, beneficial live microorganisms, can be introduced through supplements or fermented foods to restore microbial balance. Prebiotics, non-digestible fibers that promote the growth of beneficial bacteria, are often encouraged by consuming foods like garlic, onions, and certain fruits. Lifestyle changes, including stress management, regular physical activity, and adequate sleep, are crucial in supporting a healthy gut microbiome. These interventions must be tailored to the individual's microbiome profile and clinical presentation. This personalized approach is fundamental to the success of treatments for dysbiosis, as it acknowledges the complexity and variability of the gut microbiome across individuals, ultimately aiming to restore a balanced microbial ecosystem for improved overall health. 

Challenges and Considerations in Microbiome Testing

While offering valuable insights, gut microbiome testing can present challenges to clinicians and patients. One major challenge lies in interpreting results due to the complex and dynamic nature of the microbiome. Understanding the intricate relationships between different microbial species and their functions requires expertise, making result interpretation a nuanced process. Clinicians, especially those still familiarizing themselves with microbiome analysis, may need help translating test results into actionable insights for personalized treatment plans. To address this challenge, clinician consulting services with microbiome testing companies prove to be an extremely helpful resource. Collaborating with experts allows clinicians to seek guidance in result interpretation, ensuring a more accurate and clinically relevant understanding of the microbiome data. 

Ethical considerations and patient privacy concerns also arise in the era of genetic testing, including microbiome analysis. As genetic data is inherently sensitive, safeguarding patient privacy and ensuring informed consent becomes critical. Clinicians should communicate clearly with patients about the potential implications of microbiome testing, including the storage and use of genetic information. 

The Future of Microbiome Testing

The future landscape of gut microbiome testing appears promising, with continuous technological innovations and expanding applications across various medical disciplines. The integration of cutting-edge sequencing technologies, coupled with ongoing research efforts, can transform microbiome testing into a powerful tool for precision medicine, offering tailored solutions for disease prevention, diagnosis, and treatment.

Future developments within the field of gut microbiome testing are expected to be characterized by breakthroughs in sequencing technologies, allowing for a more comprehensive and nuanced analysis of the vast microbial communities inhabiting the human gut. One such example of an emerging technology is metabolomics. Metabolomics is the study of small molecules produced during cellular processes, offering insights into the functional aspects of biological systems. In gut microbiome testing, metabolomics provides a functional perspective by identifying and quantifying the metabolites produced by the microbial community, contributing to biomarker discovery, understanding host-microbe interactions, and enabling personalized and targeted therapeutic interventions. It enhances our understanding of the dynamic interplay between the gut microbiome and host health, facilitating a more comprehensive approach to precision medicine. (2, 19

Ongoing research endeavors are actively exploring the intricate relationships between the gut microbiome and diverse health conditions. As our understanding deepens, microbiome testing could become a routine component of diagnostic and therapeutic strategies. Efforts to establish robust reference databases and develop standardized methodologies are underway, aiming to enhance the reproducibility and reliability of microbiome analyses (28). Additionally, advancements in artificial intelligence are being harnessed to decipher complex microbial patterns and predict disease risks based on microbiome data.


Gut Microbiome Testing: Key Takeaways

Gut microbiome testing stands at the forefront of modern clinical practice, offering a profound understanding of the intricate microbial ecosystems within our bodies. With the capability to identify microbial compositions, functional activities, and their dynamic interplay, this diagnostic tool holds immense potential to revolutionize personalized healthcare. The insights gleaned from gut microbiome testing enhance our comprehension of individual health and pave the way for targeted interventions, marking a transformative shift toward precision medicine. As we unravel the complexities of the gut microbiome, its integration into clinical practice heralds a new era in healthcare, promising more tailored and effective approaches to address diverse health conditions on an individual level.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article


  1. Andrews, L. B., Fullarton, J. E., Holtzman, N. A., et al. (2001). Social, Legal, and Ethical Implications of Genetic Testing.; National Academies Press (US).
  2. Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. V., Jarmusch, A. K., & Dorrestein, P. C. (2021). Mass spectrometry-based metabolomics in microbiome investigations. Nature Reviews Microbiology, 20(3), 143–160.
  3. Boicean, A., Birlutiu, V., Ichim, C., et al. (2023). Fecal Microbiota Transplantation in Inflammatory Bowel Disease. Biomedicines, 11(4), 1016.
  4. Bull, M. J., & Plummer, N. T. (2014). Part 1: The Human Gut Microbiome in Health and Disease. Integrative Medicine (Encinitas, Calif.), 13(6), 17–22.
  5. Caminero, A., Meisel, M., Jabri, B., et al. (2018). Mechanisms by which gut microorganisms influence food sensitivities. Nature Reviews Gastroenterology & Hepatology, 16(1), 7–18.
  6. Cayres, L. C. F., de Salis, L. V. V., Rodrigues, G. S. P., et al. (2021). Detection of Alterations in the Gut Microbiota and Intestinal Permeability in Patients With Hashimoto Thyroiditis. Frontiers in Immunology, 12.
  7. Christie, J. (2023, January 26). 5 Lab Test Can That Help Diagnose The Root Cause of Chronic Bloating. Rupa Health.
  8. Cloyd, J. (2023, February 28). A Functional Medicine Protocol for Leaky Gut Syndrome. Rupa Health.
  9. Cloyd, J. (2023, May 19). The Impact of The Gut Microbiome on Autoimmune Diseases. Rupa Health.
  10. Cloyd, J. (2023, November 20). Could Food Poisoning Be The Reason For Your Chronic Digestive Symptoms? Rupa Health.
  11. Cloyd, J. (2023, December 5). The Impact of Gut Health on Cardiovascular Disease: Insights from Functional Medicine. Rupa Health.
  12. Cloyd, K. (2023, December 5). The Gut-Brain Axis in Clinical Practice: Functional Approaches to Mental Wellness. Rupa Health.
  13. Conner, V. (2022, September 13). Fibromyalgia: Causes, Symptoms, & Alternative Treatments. Rupa Health.
  14. D'Souza, S. M., Houston, K., Keenan, L., et al. (2021). Role of microbial dysbiosis in the pathogenesis of esophageal mucosal disease: A paradigm shift from acid to bacteria? World Journal of Gastroenterology, 27(18), 2054–2072.
  15. DeCesaris, L. (2022, June 6). What Is Gut Dysbiosis? 7 Signs To Watch For. Rupa Health.
  16. DePorto, T. (2023, January 4). The Microbiome Diet: Everything You Need To Know. Rupa Health.
  17. Fowlie, G., Cohen, N., & Ming, X. (2018). The Perturbance of Microbiome and Gut-Brain Axis in Autism Spectrum Disorders. International Journal of Molecular Sciences, 19(8), 2251.
  18. Greenan, S. (2021, December 8). 5 Probiotic-Rich Foods To Eat Instead Of Taking Supplements. Rupa Health.
  19. Jandhyala, S. M. (2015). Role of the Normal Gut Microbiota. World Journal of Gastroenterology, 21(29), 8787.
  20. Kowalski, K., & Mulak, A. (2019). Brain-Gut-Microbiota Axis in AAlzheimer'sDisease. Journal of Neurogastroenterology and Motility, 25(1), 48–60.
  21. Krishnareddy, S. (2019). The Microbiome in Celiac Disease. Gastroenterology Clinics of North America, 48(1), 115–126.
  22. LoBisco, S. (2022, August 17). The Thyroid Gut Connection: How to Nourish Your Microbiome for Better Thyroid Health? Rupa Health.
  23. LoBisco, S. (2022, December 14). How To Build A Healthy Microbiome From Birth. Rupa Health.
  24. McNally, L. (2023, November 27). The Association Between the Microbiome and Cancer. Rupa Health.
  25. NIH Human Microbiome Project defines normal bacterial makeup of the body. (2015, August 31). National Institutes of Health (NIH).
  26. Ohlsson, L., Gustafsson, A., Lavant, E., et al. (2018). Leaky gut biomarkers in depression and suicidal behavior. Acta Psychiatrica Scandinavica, 139(2), 185–193.
  27. Petersen, C., & Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cellular Microbiology, 16(7), 1024–1033.
  28. Puschhof, J., & Elinav, E. (2023). Human microbiome research: Growing pains and future promises. PLOS Biology, 21(3), e3002053–e3002053.
  29. Rinninella, E., Raoul, P., Cintoni, M., et al. (2019). What is the Healthy Gut Microbiota composition? A Changing Ecosystem across age, environment, diet, and Diseases. Microorganisms, 7(1), 14.
  30. Siddiqui, R., Mungroo, M. R., Alharbi, A. M., et al. (2022). The Use of Gut Microbial Modulation Strategies as Interventional Strategies for Ageing. Microorganisms, 10(9), 1869.
  31. Sun, T., Niu, X., He, Q., et al. (2023). Artificial Intelligence in microbiomes analysis: A review of applications in dermatology. Frontiers in Microbiology, 14.
  32. Sweetnich, J. (2023, February 17). 6 Health Benefits of Prebiotics. Rupa Health.
  33. Wei, L., Singh, R., Ro, S., et al. (2021). Gut microbiota dysbiosis in functional gastrointestinal disorders: Underpinning the symptoms and pathophysiology. JGH Open, 5(9).
  34. Wu, Z., Zhang, B., Chen, F., et al. (2023). Fecal microbiota transplantation reverses insulin resistance in type 2 diabetes: A randomized, controlled, prospective study. Frontiers in Cellular and Infection Microbiology, 12(1089991).
  35. Yoshimura, H. (2023, April 3). Functional Medicine Approach to Treatment of Chronic Fatigue Syndrome Symptoms. Rupa Health.
  36. Yoshimura, H. (2023, October 17). What is The Gut-Liver Axis? Rupa Health.

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