top of page

Prebiotics, Probiotics, Postbiotics and everything in between; What’s best for you and your Unique Gut?

plant based, probiotics, prebiotics, postbiotics

Hippocrates once stated, “all disease begins in the gut.” Now more than 2,000 years later, we know that he was onto something hugely important! Your gut microbiome plays a critical role in everything from immune support and energy levels, to metabolism, hormone & blood sugar balance, and longevity. And yet, even in a world with gut health supplements and cookbooks flooding store shelves, most of us have little understanding of what gut health actually is, and the simple steps we can take today to create a thriving gut microbiome to support long-term health.

In this article, we’ll take a look at the latest research on probiotics and how these little bugs affect your gut function.

What you will learn in this article: 

  • A better understanding of your gut ecosystem

  • What probiotics are

  • What probiotics aren't

  • Which probiotics are beneficial

  • How to truly nurture your gut health


Your gut microbiome is a mini-ecosystem, with trillions of tiny bacteria, yeast, fungi, protozoa, archaea, and viruses all working together. These microbes have important functions like food digestion, the synthesis of vitamins, and the production of neurotransmitters (such as serotonin, dopamine, and GABA) that play a key role in determining your mood. The more diverse your gut ecosystem is, the more it thrives. And with a thriving gut, you also improve communication with systemic organs like your heart, liver, and brain, and help build a robust immune system to prevent and attack disease.

So What are Probiotics? 

There are more than 38 trillion bacteria4 in the gut with 8,000 unique bacterial strains in the human gut microbiome. Some of them are essential for everyone, others help to remedy specific conditions, and others still may actually be wreaking havoc on your body.

It is also important to understand that we need a balance of microbes–too much or too few of them can throw off that balance, harming our gut. The most common probiotic bacteria belong in the groups Lactobacillus and Bifidobacterium, and a common yeast is Saccharomyces. When these strains are too high it can lead to dysbiosis7 or an imbalanced gut microbiome, when they are too low and inflammatory strains are too high, it can lead to things like Inflammatory Bowel Disease6, autoimmune conditions5, and more.  Because there are so many different types of microbes, different strains have unique effects on our bodies. 

Some of these bacterial strains are part of what are called probiotics. And they can be a key to unlocking long-term gut health by helping create a vibrant, diverse, and well-balanced community of beneficial microorganisms.

The International Scientific Association for Probiotics and Prebiotics defines probiotics16 as: “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host.”

These microscopic creatures are generally a good thing. They’re a natural, vital part of your gut. And you receive them in small amounts from dirt, interactions with people (and pets), the food you eat (especially fermented foods), and, quite literally, from everyday life. But they can also be added through probiotic supplements.

Should You Take a Probiotic Supplement?

Probiotic supplements have gained popularity over the past several years, and seemingly for good reason, as probiotics are the living gut bugs your microbiome depends on.

While everyone needs probiotics, many of us have questions about whether or not to take supplements. There are so many different strains of bacteria, and everyone’s lifestyle is different, so it’s difficult to say which strains are beneficial for a person at any given time. Overall we all need to maintain the balance of different bacteria, yeast, and other microbes in our gut. Taking the wrong probiotic supplements can change that balance, potentially worsening your gut issues. With so many strains of unique bacteria in the gut, there’s no straightforward conclusion as to which probiotic strains are beneficial across the board.

The truth is just that — it’s complicated. For example, studies3 show a probiotic supplement containing histamine-liberating strains may significantly worsen GI and systemic symptoms in someone who deals with Histamine Intolerance or Mast Cell Activation Syndrome (MCAS), while others are specifically formulated to contain strains that lower histamines. Certain strains like Lactobacillus Reuteri have been heavily studied2 to reduce activity of archaea, the microbes that produce methane gas causing and worsening constipation. Certain strains have been shown in studies1 to help with regulation of the intestinal barrier function, including improving tight junction protein function, balancing intestinal microbial composition, regulating immune-related cytokine expression.

What are the Functions of some of the Most Common Probiotic Strains?

Not only are the strains of probiotic important, it is important to differentiate the right genus, species, and strain for each person’s unique microbial needs. Let’s break it down to make it simpler:

Genus: The type of organism a microbe is classified under. Similar to modern day people being classified as homo sapiens, which differentiates us from animals and other creatures. 

Species: The group of similar species a microbe is related to. Similar to race or ethnicity that groups people together by characteristics or culture. 

Strain: The exact type of that strain formulated to confer a specific benefit by the microbe, which can differ its function. Similar to a person’s family or last name, differentiating them further from those with the same ethnicity and culture based on their behavior and social effects on those around them. 

As science continues to evolve in the area of microbiome testing, and we continue to further explore the vast world of the gut microbiome, we will continue to gain insight and clarity into proper management of the gut, and the role that appropriate gut health supplements can play, and which genus, species, and strain can best benefit or exacerbate specific conditions. For now we know there are 3 predominant friendly genus of microbes that can support a more balanced gut: 

  • Lactobacillus- predominantly found in the end of the colon (the distal colon)8. Lactobacillus support colon motility and reduce constipation. They also help maintain the pH of the colon to prevent it from becoming too basic and allow overgrowth of opportunists, including yeast, sulfur-reducing bacteria, and others. 

  • Bifidobacterium- mainly growing in the right side of the colon, AKA the proximal colon9, these help support motility and prevent backflow into the small intestine to reduce risk of Small Intestinal Bacterial Overgrowth (SIBO), Intestinal Methanogenic Overgrowth (IMO), and more. 

  • Saccharomyces- Friendly species of yeast10 which help manage levels of other opportunistic yeast and fungi, including candida, aspergillus, and other aggressive fungal strains. 

For now, resources such as the US Probiotic Guide can provide evidence-based guidance for choosing the most appropriate probiotic strains for specific conditions.

Are Supplements the Only Source of Probiotics? 

prebiotics, probiotics, postbiotics, plant based, organic, integrative nutrition, married to health

Taking probiotics does not ensure a healthy gut, but there are ways that everyone can improve their gut health through food. In fact, we should look towards food first instead of supplements to maintain our healthy gut microbiome. It’s important to have a diverse population of bacteria in your gut by eating the right foods. Fermented and fiber-rich foods have been found to help gut microbiome diversity and function. Some beneficial fermented foods include:

  • Sauerkraut

  • Kimchi

  • Kombucha

  • Kefir

  • Miso paste

  • Lacto-fermented vegetables

  • Dairy-free yogurt

  • Dairy-free fermented cheese

  • Tempeh

  • Unpasteurized apple cider vinegar

It is also extremely important to understand that we come into contact with billions of microbes per day. This happens when we breathe, eat, hug, kiss, and just be! 

Many of these microbes can turn out to be great for us and some might not be. What decides whether the microbes we come into contact with benefit our bodies is the environment we are creating. The lifestyle full of great fiber, movement, and exposure to nature is creating the environment inside of you to hold on to nurture more probiotic species. 

Will Probiotics Show Immediate Benefits in Our Health? 

It’s vital for us to feed these helpful probiotics with enough of their preferred food, called prebiotics, in order for them to take care of us and provide us with their gifts, called postbiotics. Let’s simplify that with an analogy- think of your gut as a garden; in order for it to become a lush, generous, fruitful garden, it needs to have 2 main inputs- healthy seeds (probiotics) and healthy soil, sun, water, and nutrients to nourish the seeds (prebiotics). When we have those things, the seed transforms into a lush plant that provides us with fruits, flowers, or vegetables- AKA gifts in return for us taking such great care of them. These gifts are known as postbiotics. 

Some think they can supplement their way out of a poor diet or undo years or decades of damage with a quick supplement thrown into the mix. That would be equivalent to a farmer trying to plant their best, most expensive heirloom seeds in dirt that is dry and desolate, that they do not intend to water, or add nutrients to. So, the right input (probiotic) + wrong environment and food (prebiotics) does not = bounty or output (postbiotics). 

If you are planning to introduce a probiotic in your gut’s garden, it’s important for you to start caring for your soil by removing unhelpful lifestyle habits (hyper-refined foods, poor sleep, stress) and start regenerating the land with exercise, fiber, water, and sleep. Since we contain more microbes than human DNA in our body, it’s time we all start thinking about taking best care of those little bugs inside of us, nourishing them well so they want to take care of us in return. The post-biotic produce they give us can affect almost every single aspect of our lives. 

There are quite a few people (and you maybe one of them) that try to eat more plants/fiber and feel terrible. If you listen to many influencers online, they will tell you that plants are poisonous and to replace your kale with sticks of butter and your beans with animal testicles. Fortunately, we have a better plan. 

If you find yourself in this position do not wait to reach out so we can help you truly get to the root and truly overcome your symptoms. 

Tell me More About These Gifts Our Gut Bugs and the Right Probiotics Can Give! 

If prebiotics are what feed healthy gut microbes, postbiotics are the bioactive compounds/ gifts these microbes leave behind. They can pass significant benefits to the host (which in this case, is you!).

Examples of postbiotics11 include:

  • Functional proteins

  • Secreted polysaccharides (aka carbohydrate chains)

  • Short-chain fatty acids (e.g., acetate, butyrate, propionate)

These byproducts can help with a wide range of functions in the body, including12:

  • Regulating the immune system

  • Reducing tumor formation and growth

  • Reducing blood sugar

  • Reducing cholesterol and risk for cardiovascular disease

  • Repairing the lining of the intestines, reducing intestinal hyperpermeability (aka leaky gut), and instances of or flares of inflammatory bowel disease13

  • Synthesizing vitamins, including vitamin K

  • Increasing nutrient absorption

  • Producing about 7–20% of our body’s daily energy15

Which are Some of Our Favorite Probiotics as Integrative Registered Dietitians and Certified Gastrointestinal Nutritionists?

VSL#3, probiotic, plant based, integrative nutrition, IBS, SIBO

While there are many lifestyle and dietary changes we can make on our own to improve our gut health, those with gut issues may still need to supplement probiotics to help their gut function at its best. High potency, third party tested supplements, with published data, such as VSL#3® can build a better balance of beneficial bacteria in our gut for those with gut issues such as Irritable Bowel Syndrome (IBS), Ulcerative Colitis (UC), and Pouchitis. Because diversity and balance of different bacteria strains is essential for gut health, VSL#3® is a high quality probiotic supplement that contains a beneficial variety of bacteria, specifically VSL#3® contains 8 strains of bacteria that work synergistically. VSL#3® is a medical food and should be used under the supervision of a physician. Always ask your care team before starting a new supplement or medical food. 

Putting it all Together

If you’re working with digestive health challenges, you may benefit from working with a knowledgeable health care team — including a primary care provider, gastroenterologist, and/or a registered dietitian nutritionist — to help you resolve your specific health challenges. However, there’s a lot that most of us can do on our own that will lead to significant health benefits.

Here are a few final thoughts and tips for creating a thriving gut microbiome:

  1. Prebiotics are food for the microbes that live in and on your body. If those microbes are well-fed and taken care of, they will be very happy. And that will help your mood through the gut-brain axis and make you happy, too.

  2. At a minimum, aim for the recommended fiber intake from whole plant foods, but including more can bring even greater benefits.

  3. Aim for a fiber-rich diet from a diverse array of foods. Shooting for 30 or more unique plants14 per week can be a great goal.

  4. When adding more fiber and plant foods, following the low-and-slow rule is a great way to ease your gut microbiome into dietary changes. Rome wasn’t built in a day, and your best gut health won’t be either.

  5. If you’re currently suffering from a GI condition or experiencing chronic GI symptoms, it can be very helpful to work with a knowledgeable and compassionate care team who can help you understand the many nuances of repairing gut tissue and facilitating new microbes to help improve overall health.

  6. Remember, probiotics are not one size fits all and you should be aware of strains and formulations that have been thoroughly tested and properly formulated like VSL#3®.  

With so many different probiotic strains and supplements, understanding how they function in our gut is very important. Our gut health depends on a balance of microorganisms called probiotics, and they produce bioactive compounds called postbiotics that provide us with many health benefits. While probiotic supplements can help us, they don’t always ensure improved gut health on their own, so we should always consider incorporating a variety of plants and fermented foods to maintain our healthy gut microbiome. 

married to health, integrative nutrition, gut health, SIBO Specialist, IBS Expert, Plant based dietitian
James Marin, RD, EN & Dahlia Marin, RDN, LD, CGN

Want more FREE recipes and resources? Click Here

Sign Up for Our Newsletter Click Here

Become our Patient Click Here

Meet the Team: See which Dietitian is right for you! Click Here


  1. Cheng FS, Pan D, Chang B, Jiang M, Sang LX. Probiotic mixture VSL#3: An overview of basic and clinical studies in chronic diseases. World J Clin Cases. 2020 Apr 26;8(8):1361-1384. doi: 10.12998/wjcc.v8.i8.1361. Erratum in: World J Clin Cases. 2021 Jul 16;9(20):5752-5753. PMID: 32368530; PMCID: PMC7190945. 

  2. Ojetti V, Petruzziello C, Migneco A, Gnarra M, Gasbarrini A, Franceschi F. Effect of Lactobacillus reuteri (DSM 17938) on methane production in patients affected by functional constipation: a retrospective study. Eur Rev Med Pharmacol Sci. 2017 Apr;21(7):1702-1708. PMID: 28429333.

  3. Hrubisko M, Danis R, Huorka M, Wawruch M. Histamine Intolerance-The More We Know the Less We Know. A Review. Nutrients. 2021 Jun 29;13(7):2228. doi: 10.3390/nu13072228. PMID: 34209583; PMCID: PMC8308327.

  4. Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016 Aug 19;14(8):e1002533. doi: 10.1371/journal.pbio.1002533. PMID: 27541692; PMCID: PMC4991899. 

  5. De Luca F, Shoenfeld Y. The microbiome in autoimmune diseases. Clin Exp Immunol. 2019 Jan;195(1):74-85. doi: 10.1111/cei.13158. PMID: 29920643; PMCID: PMC6300652.

  6. Gong D, Gong X, Wang L, Yu X, Dong Q. Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease. Gastroenterol Res Pract. 2016;2016:6951091. doi: 10.1155/2016/6951091. Epub 2016 Dec 15. PMID: 28074093; PMCID: PMC5198157.

  7. Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterol Hepatol (N Y). 2007 Feb;3(2):112-22. PMID: 21960820; PMCID: PMC3099351.

  8. Walter J. Ecological role of lactobacilli in the gastrointestinal tract: implications for fundamental and biomedical research. Appl Environ Microbiol. 2008 Aug;74(16):4985-96. doi: 10.1128/AEM.00753-08. Epub 2008 Jun 6. PMID: 18539818; PMCID: PMC2519286.

  9. O'Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol. 2016 Jun 15;7:925. doi: 10.3389/fmicb.2016.00925. PMID: 27379055; PMCID: PMC4908950.

  10. Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therap Adv Gastroenterol. 2012 Mar;5(2):111-25. doi: 10.1177/1756283X11428502. PMID: 22423260; PMCID: PMC3296087.

  11. Wegh CAM, Geerlings SY, Knol J, Roeselers G, Belzer C. Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond. Int J Mol Sci. 2019 Sep 20;20(19):4673. doi: 10.3390/ijms20194673. PMID: 31547172; PMCID: PMC6801921.

  12. Żółkiewicz J, Marzec A, Ruszczyński M, Feleszko W. Postbiotics-A Step Beyond Pre- and Probiotics. Nutrients. 2020 Jul 23;12(8):2189. doi: 10.3390/nu12082189. PMID: 32717965; PMCID: PMC7468815.

  13. Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, Hermoso MA. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol. 2019 Mar 11;10:277. doi: 10.3389/fimmu.2019.00277. Erratum in: Front Immunol. 2019 Jun 28;10:1486. PMID: 30915065; PMCID: PMC6421268.

  14. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium; Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May 15;3(3):e00031-18. doi: 10.1128/mSystems.00031-18. PMID: 29795809; PMCID: PMC5954204.

  15. Takashi Kusu, Hisako Kayama, Makoto Kinoshita, Seong Gyu Jeon, Yoshiyasu Ueda, Yoshiyuki Goto, Ryu Okumura, Hiroyuki Saiga, Takashi Kurakawa, Kayo Ikeda, Yuichi Maeda, Jun-ichi Nishimura, Yasunobu Arima, Koji Atarashi, Kenya Honda, Masaaki Murakami, Jun Kunisawa, Hiroshi Kiyono, Meinoshin Okumura, Masahiro Yamamoto, Kiyoshi Takeda; Ecto-Nucleoside Triphosphate Diphosphohydrolase 7 Controls Th17 Cell Responses through Regulation of Luminal ATP in the Small Intestine. J Immunol 15 January 2013; 190 (2): 774–783.

  16. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014 Aug;11(8):506-14. doi: 10.1038/nrgastro.2014.66. Epub 2014 Jun 10. PMID: 24912386.

275 views0 comments


bottom of page