Utilizing Advanced Stool Testing to Explore the Impact of Diet on the GI Microbiome

Hippocrates is said to have stated “All diseases begin in the gut.” 2000 years later, advancement in gastrointestinal testing, like the GI360™ stool profile from Doctor’s Data, allows medical professionals to ascertain what is in the gut, and how it might be contributing to health and disease.

The gastrointestinal tract (GI) is a person’s first line of defense and the largest interface between the outside world and our bodies. The microbial ecosystem in the GI, referred to as the gut microbiome, is partially responsible for maintaining human health and is also associated with various diseases. A healthy gut microbiome needs greens, beans and berries to steer clear of dysbiosis.

Our intestines are populated by trillions of microorganisms that have protective, structural, and metabolic roles. Metabolically, the gut microbiota functions to produce vitamins and synthesize amino acids. It is also involved in the fermentation of dietary fiber into short-chain fatty acids (SCFAs) like butyrate. The microbiome ensures protection from pathogenic colonization by competing for attachment sites and nutrients as well as through its ability to produce and secrete antimicrobials. In addition, a healthy gut microbiome is essential for the development and homeostasis of the immune system. Structurally, certain bacteria in the microbiome have been shown to strengthen the mucosal layer of the intestinal wall, which works as an obstacle to the uptake of proinflammatory molecules and antigens.

Dysbiosis is a term used to refer to a microbiota community associated with a diseased state that can be differentiated from the microbiota community associated with a healthy control state. The abundance and diversity of a person’s microbiome can be assessed via multiplex PCR molecular technology, utilized by the GI360™ profile. Many factors can alter the ecosystem of the GI tract including antibiotics, psychological and physical stress, radiation, altered peristalsis, and dietary changes.

A healthy microbiome is largely achieved by increasing the number of “good” bacteria in the gut, which can be accomplished in a variety of ways. When it comes to healthy microbiome abundance and diversity, the patient’s diet must be considered.

 

Soluble Fiber

Fiber is categorized as insoluble dietary fiber (IDF) or soluble dietary fiber (SDF). The 2018 Institute of Medicine daily total fiber (DTF) recommendations range from 25g (women) to 38g (men) per day. The average American DTF intake is only 16.2g. Vegetables have different ratios of insoluble to soluble fiber. Fibrous green produce, for example, is composed of roughly 1/3 soluble fiber to 2/3 insoluble fiber. If leafy greens make up the bulk of fiber consumption, of the 16.2g fiber intake only 5.39 grams would be attributed as SDFs. Some sources state the optimal daily intake of soluble fiber as 15-20g for males and 10-15g for females, well above what is typically achieved via common diets.

IDFs have a beneficial effect on bulking fecal material, decreasing transit time and improving bowel motility, but are only minimally utilized by gut bacteria. In contrast, SDFs form a gelatinous substance to be easily accessed and metabolized by fiber-degrading butyrogenic species (e.g., Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides fragilis, Bifidobacterium family, Clostridium family and Lactobacillus family) to produce beneficial SCFAs. The abundance and diversity of these microbes can be precisely determined via GI360™ testing.

Beneficial SDFs are found in many foods, most abundant in legumes and starchy beans (lentils, kidney beans, chickpeas, etc.), as well as oat and rice bran, bananas, apples, Jerusalem artichokes, onions and chia seeds. Soluble fiber in supplement form is available in inulin, chicory root, psyllium husk, apple pectin and a variety of gums (acacia, guar, etc.).

The primary SCFAs, butyrate, propionate and acetate, are produced by commensal bacteria via fermentation of SDFs and intestinal mucus glycans. The SCFAs produced provide energy for intestinal cells and regulate the actions of specialized mucosal cells producing anti-inflammatory mucins that constitute the mucus barriers and gut active peptides facilitating appetite regulation and euglycemia. Fermentation of SDFs is also an important energy source for enterocytes contributing to the homeostasis of colonic regulatory T cell populations. The SCFAs also contribute to a more appropriate acidic and anaerobic microenvironment that disfavors dysbiotic bacteria and yeast growth. Abnormal SCFAs levels may be associated with dysbiosis, compromised intestinal barrier function and inappropriate immune and inflammatory conditions. Stool chemistries, including the SCFAs butyrate, acetate, propionate, and valerate, are reported as part of the GI360™ profile.

While probiotics may be a consideration in increasing the population of certain beneficial microbes, the fiber feeding approach is most comprehensive with respect to supporting a healthy GI environment, microbial community, and sustained provision of butyrate and other SCFAs.

 

Polyphenols:

Plant polyphenols, bestowing dark or bright colors and astringent flavors, are compounds produced as a defense expression against stressors: pathogens, parasites, predators, and ultraviolet radiation. In vivo research demonstrates therapeutic significance of polyphenol intake at 500mg-1000mg per day (approximately 5-9 fruit and vegetable servings). Over 8,000 phenolic compounds, divided into classes and sub-classes, have been identified and studied with variable clinical application: anthocyanins from deep colored blue and red berries, cranberries, pomegranate, red cabbage, red wine for cardiovascular health; epigallocatechin 3-gallate (EGCG) in green and white herbal tea for inflammation, combating oxidative stress and metabolic dysfunction; and genistein in beans, soy, lentils and peas as a natural phytoestrogen to inhibit breast cancer cells are just a few of these classes of “functional foods.” The high polyphenol content emphasized in several recognized therapeutic diets (i.e., Mediterranean Diet, Paleo Diet, Dietary Approaches to Stop Hypertension (DASH), Wahls Protocol®) remain a foundational pillar in preventive medicine.

A 2020 systematic review demonstrated that polyphenols act as a pre-biotic, increasing the abundance of key microbiome species including Akkermansia mucinifila spp. (A. muciniphila spp.) and Faecalibacterium prausnitzii spp. (F. prausnitzii spp.). A. muciniphila spp., is known as the “sentinel of the gut,” and is a gut bio-health marker in healthy individuals. Using mucin to support gut barrier integrity alters the gut immunological response, reduces gut inflammation and enriches production of SCFAs.

Another polyphenol benefactor, F. prausnitzii spp., is a primary producer of butyrate and was shown to be significantly decreased in Lupus patients resulting in considerably lower levels of pentanoate, a short chain fatty acid (SCFA) with the ability to suppress autoimmunity. A decline in the microbial composition of F. prausnitzii spp. correlates to increased mortality in a number of inflammatory and immune modulated diseases.

 

Avoid a Standard American Diet (SAD)

Overall, those who follow a Standard American style diet are consuming too much saturated fat, refined sugar, trans fats, and refined grains due to high intakes of sugary sweetened beverages, desserts, and processed foods. Conversely, most are not getting enough vitamins, minerals, fluid, or dietary fiber. These dietary choices lead to dysbiosis.  While therapeutic diets (i.e. Low Fodmap, Keto, Carnivore, etc.) can be beneficial, especially in the short term, longer-term use of therapeutic food plans that are inherently low in soluble dietary fiber can also contribute to dysbiosis. Patients following a SAD or low fiber therapeutic diets should assess microbiome diversity and abundance regularly to ensure a healthy and balanced microbiome.

The comprehensive and complementary GI360™ methodologies utilized by Doctor’s Data provide a whole-system view of your patient’s microbiome, including abundance and diversity of keystone bacteria, possible pathogens, viruses and yeast to give providers a foundation for targeted therapies. This objective data, coupled with a full intake and dietary assessment, empowers patients and vastly increases the likelihood of reaching health goals and improving outcomes.

 

About the GI360™ Profile

The GI360™ Profile is a gut microbiota DNA analysis tool that identifies and characterizes the abundance and diversity of more than 45 targeted analytes that peer-reviewed research has shown to contribute to dysbiosis and other chronic disease states. Additionally, the GI360™ Profile utilizes multiplex PCR molecular technology coupled with growth-based culture and ID by MALDI-TOF, sensitive biochemical assays and microscopy to detect and assess the status of pathogens, viruses, parasites and bacteria that may be contributing to acute or chronic gastrointestinal symptoms and disease.

 

For a deep dive into increasing microbiome diversity, different stool testing methods and a ton of clinical pearls on tackling lab report findings in clinical practice, tune in to the New Frontiers podcast with Dr. Julia Malkowski below:

A 360-Degree View of the Microbiome: Practical Strategies for Clinicians

 

Resources

• GI360 Brochure: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/Brochures/GI360+brochure.pdf
• GI360 Collection instructions: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/Collection+Instructions/GI360+or+CSAP+Instructions.pdf
• GI360 Resource Guide: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/Resource+Guides/DDI_GI360_Resource_Guide.pdf
• GI360 FAQs: https://doctorsdata.com/GI360-FAQs
• Webinar: https://doctorsdata.com/Media-Library-Detail/Diseases-Begin-Gut
• Webinar: https://doctorsdata.com/Media-Library-Detail/Gut-Microbiota-and-Stress
• Webinar: https://doctorsdata.com/Media-Library-Detail/GI-Microbiome
• White paper: Doctor’s Data Antibiogram 2022 https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/documents/DoctorsDataAntibiogramPaperJuly2023.pdf
• Doctor’s Data Antibiogram 2023 https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/documents/DoctorsDataAntibiogram2023.pdf
• GI360 Posters and Abstracts: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/News/flipbooks/GI360/GI360PostersAbstracts_protected.pdf
• GI360 Publications: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/News/flipbooks/GI360/GI360_Publications_2020_secured.pdf
• GI Health brochure: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/Brochures/Gastrointestinal+Health+brochure.pdf
• GI360 Sample Report: https://site-akiajqrf22xmaqzsiz6q.s3.amazonaws.com/DDI+Website/Sample+Reports/Sample+Report+GI360.pdf
• “Test and Address: The Clinical Importance of Direct Assessment of Gut Microbial Abundance and Diversity”, The Townsend Letter, January 2023 Issue. Test and Address: The Clinical Importance of Direct Assessment of Gut Microbial Abundance and Diversity – Townsend Letter