July 14, 2024
Home » How Probiotics Alter The Gut Microbiome | Part 1


When a person consumes food, it is traveled down to the gut system, where it can be digested and biotransformed into nutrients in the small and large intestines. These nutrients are then absorbed into the bloodstream and are transported throughout the entire body. These nutrients help the digestive system and provide immune support, metabolism, and body growth while helping to regulate the functions of the endocrine system, the central nervous system, and the musculoskeletal system. There are ways to optimize gut health as there are harmful pathogens that can disrupt the gut system through the usage of probiotics. In this 2 part series, we will be looking at what probiotics are and how they alter the gut microbiome. Part 2 will look at how probiotics can help dampen the effects of gut disorders. By referring patients to qualified and skilled providers who specialize in gastroenterology services. To that end, and when appropriate, we advise our patients to refer to our associated medical providers based on their examination. We find that education is the key to asking valuable questions to our providers. Dr. Alex Jimenez DC provides this information as an educational service only. Disclaimer


Can my insurance cover it? Yes, it may. If you are uncertain, here is the link to all the insurance providers we cover. If you have any questions, please call Dr. Jimenez at 915-850-0900.

What Are Probiotics?

The generic definition of probiotics is defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.” Research studies have also stated that probiotics contain live microorganisms intended to maintain or even improve the beneficial bacteria in the gut system. Probiotics make sure that there is a balance of bacteria in the gut as different strands are there to prevent the harmful bacteria from overtaking the gut and intestines, causing a variety of gut disorders. Other research studies have found that there is a range of diseases that are associated with the gut and intestinal tract and when a person uses probiotics will help suppress unwanted gut symptoms.


However, some foods do not have probiotics strains like food-borne bacteria (e.g., the dirt on vegetables) or even fermented foods that are naturally occurring or starter cultures. Some probiotic strains are added to fermented food after they have been pasteurized, and these can include yogurt or kefir as probiotics.


Are Fermented Foods Probiotics?


When probiotic strains are added to fermented foods, they can provide beneficial bacteria to the gut and help dampen the effects of various gut disordersFermented foods contain natural (or added) cultures designed to digest the food during fermentation, creating organic acids and other byproducts. However, not all fermented foods are probiotics, as these organisms are often absent from the consumed product. This is primarily due to the storage and packaging of fermented foods in containers. A few controlled trials of fermented foods have been performed to document their traditional benefits. Research studies have shown that fermented foods contain microorganisms that can reach the gastrointestinal tract and potentially affect cardiovascular, immune, and metabolic health by generating bioactive peptides and polyamines. Many individuals with gut issues should be encouraged to incorporate fermented foods into their diet but not use them as a therapeutic substitute for probiotics.

An Overview Of Probiotics

Since probiotics are live microorganisms that exhibit a wide variety of beneficial health properties for the gut, as studies have shown, probiotics can help dampen the effects of gastrointestinal disorders while also improving the immune system and producing more beneficial bacteria for the gut flora. Probiotics are excellent for gut health as they have different strains to help fight off harmful bacteria that can cause infections and chronic disorders to the gut and the body. Probiotics are also found in fermented foods like kimchi, yogurts, and kefir that can affect cardiovascular, immune, and metabolic health with the bioactive peptides and polyamines that it generates.

How Probiotics Alter The Gut Microbiome


When probiotics enter the gut microbiome, the strains are thought to be highly domesticated cousins from a fraction of the total gut “wild-type” microbiota. Research studies have found that when probiotics are being ingested, they cause significant positive improvements in balancing intestinal permeability and barrier function in the gut system. Not only that, but probiotics can also provide a considerable balance to the gut microbiota and brain functionality. The gut-brain axis needs probiotics to make sure that everything is functioning correctly. Probiotics act as part of the temporary or transient gut microbiota when consumed. Other research studies have found that the impact of probiotics does not reside in the ability to graft in the gut microbiota. They share genes and metabolites while supporting a challenged gut microbiota dealing with gut and gastrointestinal disorders by directly influencing the epithelial and immune cells in the gut and the body.



Utilizing probiotics in a healthy diet can help promote optimal gut health by lowering the effects of harmful bacteria affecting intestinal permeability. When unhealthy bacteria cause havoc to the gut microbiota, it can affect the body as well. The gut is home to all the body’s functions as the gut helps maintain the body’s energy, growth, metabolism, and immune support by keeping the body and the other systems functional. Therefore, probiotics are beneficial to the gut microbiota as they help dampen the effects of the gut and gastrointestinal disorders that are causing discomfort in the gut. Many individuals can incorporate probiotics in food or supplement form to ensure that their gut is happy and filled with beneficial bacteria to support them.



Bell, Victoria, et al. “One Health, Fermented Foods, and Gut Microbiota.” Foods (Basel, Switzerland), MDPI, 3 Dec. 2018, www.ncbi.nlm.nih.gov/pmc/articles/PMC6306734/.

Dimidi, Eirini, et al. “Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease.” Nutrients, MDPI, 5 Aug. 2019, www.ncbi.nlm.nih.gov/pmc/articles/PMC6723656/.

Shahrokhi, Mahsa, and Shivaraj Nagalli. “Probiotics – Statpearls – NCBI Bookshelf.” StatPearl [Internet] Treasure Island (FL), StatPearls Publishing, 25 Nov. 2021, www.ncbi.nlm.nih.gov/books/NBK553134/.

Shi, Lye Huey, et al. “Beneficial Properties of Probiotics.” Tropical Life Sciences Research, Penerbit Universiti Sains Malaysia, Aug. 2016, www.ncbi.nlm.nih.gov/pmc/articles/PMC5031164/.

Wieërs, Grégoire, et al. “How Probiotics Affect the Microbiota.” Frontiers in Cellular and Infection Microbiology, Frontiers Media S.A., 15 Jan. 2020, www.ncbi.nlm.nih.gov/pmc/articles/PMC6974441/.

Zeratsky, Katherine. “Probiotics and Prebiotics: What You Should Know.” Mayo Clinic, Mayo Foundation for Medical Education and Research, 10 July 2020, www.mayoclinic.org/healthy-lifestyle/nutrition-and-healthy-eating/expert-answers/probiotics/faq-20058065.


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The information herein on "How Probiotics Alter The Gut Microbiome | Part 1" 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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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*
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Dr. Alex Jimenez DC, MSACP, RN* CIFM*, IFMCP*, ATN*, CCST
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