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The human microbiome, more specifically the gut microbiome, has gained considerable attention within the scientific and medical communities in recent years. Research currently being conducted worldwide indicates that the balance of these gut microbes may have a powerful impact on both short-term and long-term health. 

The importance of gut health and microbiome testing has also been popularized in the media, leading to a growing interest from the general public in learning about the benefits of evaluating their gut health. (Allaband 2018) Several companies have made it possible for individuals to purchase a microbiome test kit that can be ordered online, completed at home, and returned for analysis. The reports of these tests, however, often leave consumers scratching their heads and turning to their healthcare providers for help in interpreting the results. 

With this surge of interest and availability of microbiome testing, consumers and patients seek to understand if testing is worthwhile and which testing option is best.

Defining the microbiome

The term “microbiome” is often used to describe the diverse population of microbes in the human body. What it actually defines is the collection of microbial genes, while the collection of microbial organisms living in a specific environment is termed “microbiota.” (Allaband 2018) Microbiota can be found in various locations of the body, including the skin, oral cavity, and lungs. 

The most well-known microbiota is that of the gastrointestinal (GI) tract, particularly in the large and small intestines, which is what popular media often refers to when talking about the microbiome and microbiome testing. Commensal species of microbes present in the GI tract include bacteria as well as viruses, fungi, and parasites. In a healthy individual, these microorganisms coexist harmoniously, starting in the oral cavity and with the highest concentrations located in the small and large intestines. The impact of the microbiome is so intertwined with the body’s daily physiological function that it’s often referred to as the “hidden organ.” (Hou 2022)

Research currently being conducted worldwide indicates that microbes living in the human gut may have a powerful impact on both short-term and long-term health.

The importance of balance

In a healthy microbiome, beneficial bacteria coexist with potentially harmful ones. These "good bacteria" play a crucial role in maintaining health by outnumbering and keeping the harmful microbes from overgrowing. This balance supports both the microbiota and overall health. However, if this delicate balance is potentially disturbed by factors such as infection, illnesses, lifestyle, dietary patterns, or the use of antibiotics, the body may be left more vulnerable to diseases. (Hou 2022) 

Changes to the microbiome’s composition resulting in low levels of commensal species or overgrowth of opportunistic or infectious organisms can lead to imbalances referred to as dysbiosis. A microbiome in dysbiosis, with reduced microbial diversity, increases the risk of pathogenic overgrowth and loss of beneficial microbes. (Peterson 2014) This imbalance disrupts the production of metabolic products by the microbiome, impacting the metabolome—the complete set of metabolites in the body. (Costanzo 2022) Changes in these metabolic products can interfere with normal metabolic functions, leading to inflammation, weakened immunity, and chronic diseases. (Hou 2022) 

A large body of studies conducted in recent years supports a connection between the body’s microbial ecosystem and various health conditions including GI disorders, colorectal cancer, inflammatory bowel diseases (IBDs), asthma, allergies, autism, and other medical conditions. (Hou 2022)(Peterson 2014) With the rising awareness of the significance of gut health in many chronic conditions and diseases, it's no surprise that so much fervor exists surrounding the potential and future of microbiome-based diagnostics. (Allaband 2018)(Turjeman 2022) 

Introducing microbiome testing

Comprehensive stool tests are an excellent tool for identifying pathogenic infections and assessing the microbial composition of the lower intestinal tract, digestive function, and GI immune activity. Healthcare providers may wish to order a gut microbiome stool test for patients presenting with concerns or questions about their gut health. 

Consumer vs. clinical tests

Consumers with concerns or curiosity about their gut health can also order a microbiome test kit online from direct-to-consumer companies. Testing on the customer side entails the simple process of collecting a stool sample at home and sending it back to the company for laboratory analysis. This certainly has expanded access, but these tests often lack the comprehensive analysis provided by tests available exclusively through clinicians. Clinical tests, such as those offered through specialized labs, assess a broader range of markers that are useful for identifying and managing GI or related conditions. These tests also utilize reference ranges validated for clinical populations, enhancing the utility and reliability of the results for informed clinical decision-making. In contrast, direct-to-consumer tests may provide more general information but often lack the depth and clinical relevance needed for precise therapeutic interventions. 

Test methodologies

There are several ways to analyze stool samples, including culturing, microscopic examination, and DNA sequencing techniques, such as 16 rRNA sequencing and shotgun metagenomics. (Allaband 2018) Different clinical stool tests may utilize one or a combination of these methods, with each offering unique insights into the gut microbiota. For example, culturing can identify live bacteria and their antibiotic sensitivities, while DNA sequencing methods provide a comprehensive view of microbial diversity, including difficult-to-culture organisms. The choice of methodology can significantly influence clinical decisions, as some tests might be more suited for diagnosing specific conditions, guiding targeted treatments, or monitoring therapeutic efficacy in patient management.

Consumers concerned about their gut health can now order a microbiome test kit online.

Limitations and benefits

Although research results from studies pertaining to the human microbiome are proving to be extremely exciting, they're far from conclusive. There's still so much that's unknown about the microbiome, its millions of microscopic inhabitants, and the role they play in disease or drug responses. Due to the unique thumbprint of each individual’s microbiome and its ever-evolving composition, a microbiome test may only be able to provide a snapshot of what's transpiring inside the body. Furthermore, as stool samples also vary in amount and variation of bacteria, based on the day, it's likely that each sample provided will produce a different set of results. 

However, stool test results combined with other testing data and the patient’s clinical presentation can allow a healthcare provider to leverage their expertise to provide actionable insights and personalized lifestyle modification steps.  

Although stool analysis reports vary from lab to lab, clinicians can expect to see results providing insights into the following areas:

• Commensal (i.e., beneficial) bacterial, viral, and fungal species and the quantities in which they're present

• Opportunistic bacterial species and the quantities in which they're present

• Pathogenic bacteria, viruses, and fungi

• Markers of digestive function, immune activity, and inflammation, such as elastase and calprotectin

• Bacterial metabolites, such as short-chain fatty acids and beta-glucuronidase

• Antibiotic and botanical antimicrobial resistance (Kasırga 2019)

Data on all of the above can be clinically useful for identifying several GI conditions, such as infections, malabsorption syndromes, and IBDs, and their potential underlying causes, including microbial dysbiosis and intestinal hyperpermeability. (Chen 2020)(Kasırga 2019)(Vanuytsel 2021)

Choosing a microbiome test

Choosing the most appropriate microbiome stool test will depend on various factors including what the healthcare provider is looking to investigate, the patient’s economic constraints and ability to perform the test, test availability, and more. Staying up-to-date on the testing practices of various clinical options can help providers support their patients in choosing the best gut microbiome test kit to meet a patient’s expectations and specific concerns. Before investing in microbiome testing, it's helpful for patients to understand what tests are being conducted and how the insights can help guide clinical decisions. (Allaband 2018)(Tariq 2023)  

The bottom line

GI microbiome testing can help healthcare providers tailor dietary, lifestyle, and supplement interventions to promote a healthier gut environment. (Turjeman 2022) Tailoring recommendations based on comprehensive microbiome test results may significantly enhance patient adherence and health outcomes. Personalized recommendations resonate more with individuals because they directly address their unique health profile, making the advice more relevant and actionable. (Gold 2006)(Kopanitsa 2022) Testing can also aid in the early detection of imbalances in the gut, allowing for timely interventions to prevent recurrence or relapse of health issues and the development of chronic diseases.