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The Microbiome Functions and Functional Medicine Part: 2 El Paso, Texas

In the last article, we talked about how the microbiomes in our body worked and functioned. As well as learning what each microbe does in our bodies but mostly in our gut. When we are learning more and more about the microbiome, we discover many exciting things that our bodies are capable of as well as being the workers in our intricate immune system. In today’s article, we will be taking a look at what polyphenols does to our microbiomes as well as specific vitamins that are very helpful to our gut and going in-depth more with SCFAs (Short Chain Fatty Acids) and the Tight Junction.

The Role of Polyphenols in Microbiome Balance

Polyphenols, or phenolic compounds, are considered a type of micronutrients, and they are plentiful in plants. They have been well-studied for their role in the prevention of chronic diseases such as CVD, cancer, and neurodegenerative diseases. They also have antioxidant properties, and there are several hundreds of polyphenols that are found in edible plants that serve a giant purpose of defending our bodies against ultraviolet radiation or aggression by pathogens.


To figure this out, think of it like this: The bacteria in our large intestine releases polyphenols from the plants we eat in our diets. It is then transformed into a diet composition that alters the bacterial ecosystem (through the prebiotic effects and antimicrobial properties) to make our gut happy.

Here are some of the microbes that are in polyphenols:
  • Phenolic acids: These are derivatives of benzoic acid and derivatives of cinnamic acid.
  • Flavonoids: These microbes contain flavonols (e.g., quercetin), flavones, isoflavones (e.g., phytoestrogens), flavanones, anthocyanidins, and flavanols (e.g., catechins and proanthocyanidins)
  • Stilbenes: These microbes are resveratrol
  • Lignans: these are minor in the human diet and are linseed oil
Surprisingly some factors affect the polyphenol content of plants, and these include:
  • The ripeness at the time of harvest
  • The environmental factors (exposure to light, soil nutrients, pesticides)
  • processing and storage
When we eat organic fruits and vegetables, they have more polyphenol content that is usually, due to growing under slightly more stressed conditions. Which requires the plant to generate a stronger ‘defense and healing’ response to the environment, and only 5–10% of the total polyphenol intake is absorbed in the small intestine. And 90-95% polyphenols that are linked to fibrous components must be liberated through hydrolysis by bacteria in the large intestine.

Surprisingly some polyphenols do not show up in plasma in humans after ingestion, and a large quantity is metabolized by intestinal bacteria or used to neutralize various pro-oxidizing agents in the intestinal lumen.

Clostridium and Eubacterium (which are both Firmicutes), are the primary metabolizers of polyphenols. Studies theorized that higher polyphenol intake may play a role in shaping the Bacteroidetes to Firmicutes ratio (e.g., inflammatory response potential, obesity, etc.) and can be harmful to our bodies.

However, more recent studies have shown effects of inhibition on Clostridium and Staphylococcus of polyphenols such as grape seed extract, in favor of Lactobacillus and other studies have demonstrated potent inhibition of phenolic compounds thymol (thyme) and carvacrol (oregano) on Escherichia, Clostridia and other pathogens, while simultaneously leaving Lactobacilli and Bifidobacteria have been unaffected.

Here are some other examples of some polyphenols:
  • Resveratrol increases Clostridia, Lactobacillus, and Bifidobacteria
  • Blueberry phenolics increase Bifidobacteria
  • Phenolic compounds in tea suppress C difficile and C perfringens
  • Catechins (found in high doses in teas and chocolate) act on different bacterial species (E. coli, Bordetella bronchiseptica, Serratia marcescens, Klebsiella pneumonia, Salmonella cholestasis, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus subtilis) by generating hydrogen peroxide and by altering the permeability of the microbial membrane
  • Some studies have shown that polyphenols can interfere with bacterial cell signaling and quorum sensing (environmental sampling)
  • Polyphenols can also cause bacterial populations to stop expansion through signaling interference
  • Some research indicates certain polyphenols may be able to block the production of bacterial toxins (H. pylori and tea/wine polyphenols)

The Applications for A Diet


When it comes to eating a healthy diet, variety does matter. The colors, the types of fibers each organic food has, and whether you are going to do it daily or weekly. When you are trying to be in a healthy lifestyle, it always starts with the food. When you are looking for fresh produce, try to emphasize fresh, organic, and minimally processed versions of polyphenol-rich foods. However, don’t boil produce. Instead, try steaming then, and it is the best, but roasting or light frying is not only better, but it tastes so good.

Vitamins that help our Microbiome

When we are older, we tend to lose specific vitamins that actually helps us and our bodies to be healthier. Here are some of the vitamins that are really good for our gut and can help us prevent leaky gut.

Vitamin D

Vitamin D controls the development of gut-associated lymphoid tissue in our bodies. It is trafficking between gut dendritic cells, and they can differentiation of T-regs and T-reg function in our gut. But the expression of VDR, which influences IL (interleukin) production and tight junction integrity to help our gut.


When it comes to our gut, here are some of the effects of Vitamin D on the gut microbiome. The higher the Vitamin D levels are, they will allow commensal bacteria to secrete more AMPs (antimicrobial peptides). When patients take a high dose of Vitamin D, over 5 weeks can lead to a significant reduction in Pseudomonas spp and Shigella/Escherichia spp in upper gut intestines.

Another thing that Vitamin D does is that it can increase T cell differentiation in the colon. A lack of T-regs increased the incidence of asthma, allergies, autoimmune, and autism. But T-regs can prevent the development of aberrant immune responses such as autoimmune and food sensitivities. We here at Injury Medical Clinic, talk about functional medicine to our patients and try to help them recover from their ailments.

Because Vitamin D exposure fluctuates seasonally for many individuals, it has been observed that lower Vitamin D levels in the winter tend to lead to changes in the intestinal microbial balance. This will make our bodies have a decreased level of Bacteroidetes and an increased level of Firmicutes. This is the reason for ‘winter weight gain’ in many individuals as F: B ratio changes.

Vitamin A


This is a retinoic acid that is required by dendritic cells (DCs) to induce T-cells (and B cells) which are the “tracking and regulation system” of the mucosal immune response. Because of this, T-cells must differentiate into T-regs to maintain a ‘calm and cool’ system or immune tolerance to both our environment, symbiotic organisms, and food.

Omega-3 Fatty Acids


We talked about Omega-3s in a previous article as they are one of the many supplements that we can’t produce in our bodies. It can be mostly found in fish, and some plants can contain omega-3s. But it is a vital team player when we are trying to be healthy and can prevent a leaky gut. Not only that but omega-3s are crucial importance to more youthful skin.

SCFAs (Short Chained Fatty Acids)


SCFAs (Short Chained Fatty Acids) are well-studied to demonstrate anti-inflammatory properties in the large intestine. They are the primary source of fuel for cells lining the intestinal epithelium of the large intestine. They contained:  Butyrate, Proprionate, Acetate. In a previous article, we discussed what SCFAs do when we eat fatty food. It can be both good or bad, depending on what kinds of food you consume. SCFAs act on G-protein coupled receptors to induce differentiation of T-cells, but also on those GPRs in DCs. They can both be direct and indirect influences on our gut.

SCFAs can produce bacteria and can directly impact T-reg production. And that SCFAs inhibit the mucosa and competitively inhibit opportunists. Some foods that provide higher resistant starch will typically yield the most short-chain fatty acids upon microbial fermentation

Tight Junction Modulations

Microbial influence

The tight junctions are the gateways between the epithelial cells. In a previous article, we took a look at what the tight junction is. They control the flow of nutrients, macromolecules, and other substances that are usually allowed to pass through without cellular diffusion or absorption.


All in all, we covered a lot of information about what polyphenols does as well as specific vitamins and supplements that can help our bodies prevent a leaky gut. The microbiomes in our collection and the use of functional medicine can be beneficial in helping us not only to a better, healthier life but, a working, functional body for us when we are older. Tomorrow we will end this three-part series with foods and tips to have a healthy microbiome in our gut and our bodies.

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The information herein is not intended to replace a one-on-one relationship with a qualified health care professional, licensed physician, and is not medical advice. We encourage you to make your own health care decisions based on your research and partnership with a qualified health care professional. Our information scope is limited to chiropractic, musculoskeletal, physical medicines, wellness, sensitive health issues, functional medicine articles, topics, and discussions. We provide and present clinical collaboration with specialists from a wide array of 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 support, directly or indirectly, our clinical scope of practice.* Our office has made a reasonable attempt to provide supportive citations and has identified the relevant research study or studies supporting our posts. We provide copies of supporting research studies available to regulatory boards and the public upon request. 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 contact us. Dr. Alex Jimenez DC, MSACP, CCST, IFMCP*, CIFM*, ATN* email: phone: 915-850-0900 Licensed in: Texas & New Mexico*