The Language of Microbial Culture: Explaining Prebiotics, Probiotics, Synbiotics and Postbiotics

Inline_Probiotics_Post_05.012.17It’s no secret that it’s one of my favorite subjects—the burgeoning field of human gastrointestinal microbiology. I know…it’s easy to get caught up in the comparative excitement of it all.

The microbiota is familiar territory to most Primal types, but with time and research, we come to understand the nuances of the terrain a little better. New terms pop up. Novel discoveries grab our attention. Promising connections become apparent. It feels like a good day to go over a bit of the latest—to provide a little refresher for those who’ve joined us recently and most of all to offer some additional perspective on what we’re learning as studies branch into new depths. 

So without further ado, welcome to Biome 101.

The Cheat Sheet


Okay, most of you don’t need a refresher on this one. But for many, “probiotics” is simply a buzz word for something they vaguely remember is healthy…for some hazy, complicated reason. For those lost souls, here’s the quick and dirty.

The average human gut contains between 1000 and 1150 different species of bacteria and yeast, with the total population count numbering in the trillions—that for the most part, are either harmless or contributing valuable functions to your body and mind.

Competition for prime gut real estate encourages a healthy anti-pathogenic intestinal tract and sound immune function throughout. Essentially, it’s like a an old-growth forest ecosystem, whereby the natural competition of both indigenous plant and animal species works together to maintain a state of healthy equilibrium for the forest biome as a whole, preventing colonization by exotic (aka pathogenic) species. Some of the functions that play out include:

  • secretion of anti-microbial proteins that protect against pathogenic bacteria
  • maintaining and restoring intestinal homeostasis
  • interaction with our in-built immune receptors 
  • metabolizing indigestible compounds and extracting nutrients from the foods we eat

Modern science has thus far managed to create artificial cultures of around 40% of these beneficial gut bacterial strains. These cultures are, essentially, what we know to be probiotics—collections of known beneficial microorganisms that promote the re-colonization and maintenance of healthy gut populations.

And despite their comparatively recent rise to stardom, humans have been making probiotics for millennia. Yogurt, sauerkraut, kefir, kimchi, kvass, raw vinegar—basically any fermented food has the potential to be classed as a probiotic. That being said, not every product with “live cultures” is necessarily a probiotic. To be classed as such, that product needs to promote measurable health improvements in either the gut, oral cavity, vagina, or skin.

Nowadays, it’s all about the probiotic supplements that can guarantee the most CFUs (colony forming units). Call me old school, but I’m more of a quality over quantity kind of guy.


This is where we start getting into less familiar territory for some folks, but it’s actually quite simple. Prebiotics are special plant fibers that nourish the good bacteria already living in your gut—essentially, a hearty meal for your beneficial bacteria. Prebiotics are indigestible fibers that can pass through the gastrointestinal tract and arrive in your gut relatively unscathed, where they’re feasted upon (aka fermented) by trillions of hungry mouths.

Big-name prebiotic sources include green bananas, jicama, raw leeks (I’ll take mine cooked, thanks), dandelion greens, raw garlic, onion, and raw asparagus. Prebiotics are often integrated into probiotic supplements to not only provide a vital food source for the new colonials, but to encourage continued growth of the existing gut flora.


Which brings me very smoothly onto synbiotics. Essentially, this is a technical sounding label to describe products or treatments that combine both probiotics and prebiotics to create a super potion for your nether regions. In the words of the white coats, “because the word alludes to synergism, this term should be reserved for products in which the prebiotic compound selectively favors the probiotic compound.” Got that? No worries. Let’s just look at what it means for your morning supplement or dinner plate.

While you’ll have no trouble locating a good synbiotic (yes, as it happens, I can recommend one that I use every day), there’s also plenty of fermented food pairings that together create a powerful synergistic effect. Classic examples are yogurt and raw honey (yes, please), kefir and chia seeds, or pickled asparagus if you’re feeling more adventurous. Raw apple cider vinegar contains plenty of pectin (a prebiotic) and of course good levels of beneficial bacteria, making it a synbiotic option for those who choose it.


The fourth and final term may be the least familiar concept in the microbiology realm. In a nutshell, post-biotics are the metabolic by-products of the bacteria living in your gut and other microbiomes of your body. Researchers found that these by-products can be utilized to lower blood glucose and therefore show promise as a treatment for prediabetes.

It’s an interesting concept and developing subfield. Because much of the immune-supporting and inflammation-lowering benefits of gut bacteria are actually derived from their metabolic by-products, it stands to reason that providing certain at-risk people with specific post-biotics would go a long way towards helping them. These kinds of applications may make for a powerful in-clinic treatment for certain disorders and gut dysbioses, but it can never replace the long-term maintenance and 24/7 protective powers that an active, healthy gut population can provide. 

Human Microbiome Research and What It Means for Primal Living

Researchers are increasingly discovering/re-discovering just how personalized our gut microbiomes really are. A 2013 study examined 252 fecal metagenomes from 207 individuals from both Europe and North America, detecting 10.3 million single nucleotide polymorphisms and 1051 structural variants. Researchers went on to conclude that “individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.” We have ourselves an interesting finding here with promising suggestions for the future of the field: our gut populations are entirely individual, meaning that prebiotic, probiotic, and even postbiotic treatments might be personalized in order to achieve the most benefits. 

Next, the literature continues to emphasize just how important the gut microbiome is in the early stages of a person’s life. I’ve come across several studies that indicate necrotizing enterocolitis, a leading cause of neonatal morbidity, may respond well to prebiotic and postbiotic treatment. Notice that, for once, probiotics aren’t the hero of the bacterial hour, as it appears that prebiotics and postbiotics may be a safer and more effective method of treatment than probiotics in this circumstance.

When it comes to the normal course of things, however, probiotics still take center stage. Research shows that formula-fed infants have smaller, less productive thymus glands, while breast-fed babies are more likely to have healthy, normal-sized thymuses. The missing piece of the puzzle? Largely, the beneficial Bifidobacteria in mom’s breast milk. These probiotics also play a leading role in development of the child’s gut microbiome, while mothers fed probiotics during breastfeeding have been shown to offer increased immunoprotective properties in their breast milk. 

For those of us on the other side of the cradle, scientists have recently found a connection between post-diet weight gain and gut flora. Obese mice were placed on a mini-Weight Watchers diet and then transitioned back to a “normal” Western rodent style of eating. The formerly obese mice quickly surpassed their pre-diet weight, and the one major change that researchers observed was in their gut. Dr. Eran Elinav, head of the research team, noted that “following successful dieting and weight loss, the microbiome retains a ‘memory’ of previous obesity.”

The team began looking into resolutions, and came up with two options: first, to implant formerly obese mice with gut microbes from mice that had never been obese, and second, to supplement with post-biotics. Fecal transplantation is its own conversation, so we won’t go down that road, but the second treatment is an intriguing one. Scientists found that the formerly obese microbiome was degrading the flavonoids in their food at a far greater rate than the non-obese microbiota, which in turn was lowering energy expenditure and inhibiting fat metabolism. By adding flavonoids (a “post-biotic therapy”) to their water, the formerly obese mice didn’t gain any extra weight after returning to a regular diet.

For those with , inflammatory bowel disease (IBD) for years, post-biotics appear to offer a new course of promising treatment that might even be a better option than probiotics alone for some. One study published a few years back indicated that certain commonly-administered strains of probiotics can actually have an inflammatory effect on those suffering from IBD. Researchers concluded that “a potent post biotic can… downregulate ongoing inflammatory processes in IBD tissue.” 

On the subject of bowels…combined with a good prebiotic, we might just be onto a winning formula for those suffering from gastrointestinal issues. Another study found that prebiotics (in the form of galacto-oligosaccharides) improved both stool frequency and consistency in patients with functional constipation. When combined with a probiotic, however, the resultant synbiotic had an even bigger beneficial effect: significantly improved stool frequency, consistency and reduced transit time. There really is no “I” in team.

A similar synergistic effect has been shown to help with plenty of other aspects of our health, including immune function and oxidative stress.

A Primal Approach to Gut Health

Beyond all the personal details and medical interventions, there’s an underlying message for any avid Primal enthusiast: don’t ignore your gut microbiome. Considering how many different conditions have been linked to gut dysbiosis, there’s little hope for attaining long-term, comprehensive health without a healthy gut. 

For those dealing with chronic conditions and wondering about what else they might try, you can consider forking out for fecal genomic testing, work out what bacterial strains work best for you, and seek out optimal synbiotics that work best for your individual gut conditions with the help of a specialist.

For all of us, we can recognize that a well-rounded diet that provides plenty of probiotics and prebiotics will form the fundamental building blocks for optimum and resilient gut health.

Thanks for reading everyone. Have questions, comments, experiences to share? I’m all ears. Take care.

TAGS:  immune health

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending three decades researching and educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates Primal/paleo, keto, and Whole30-friendly kitchen staples.

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35 thoughts on “The Language of Microbial Culture: Explaining Prebiotics, Probiotics, Synbiotics and Postbiotics”

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  1. Whatever you have in Primal Probiotics is amazing…3 days ended weeks of diarrhea. And no…this isn’t a paid review. I’m old and fairly frail, so this was magical for me.

  2. My two year old is having bigtime constipation problems right now. I’m sure that gut bacteria has a lot to do with it, and he was a premi, so I’m wondering how much that comes into play as well. The doctor wants to give him an elephants dose of Miralax, but I am really worried that his whole gut biome will be blown up and there will be some bigger issues after that.
    Anyone have any experience with that? Looking for some help here…

    1. Ugh! Both of my kids (who are grown and would die if they knew that I am talking about this) had constipation problems as toddlers. They were breastfed but both c sections which I know affects their biome. I totally feel your pain. I think I did resort to Miralax and even mineral oil mixed in applesauce at some point. However I also think there was an emotional factor…the bigger deal I made about it, and the more stressed I got, the worse it was. Looking back, I remember yogurt (think it was stoneyfield organic) was helpful. I also baked ground flaxseed (chia was unheard of at the time) into just about everything. Plain yogurt with raw honey and flax seed was something they would actually eat. Hope this helps!

      1. Pear juice or prune juice really helps with constipation, worked for my kids 🙂

    2. before you try Miralax, try pumpkin, it works amazing. It cleared up the constipation within a few days.

      1. And I mixed it with honey to sweeten it up. Also if you want you could mix the pumpkin puree with yogurt.

    3. My oldest daughter suffered with constipation as an infant and her pediatrician told me to give her a soy formula. However he failed to tell me not to give her cow’s milk when she got off the bottle. She suffered with constipation and then had problems with potty training because of the cow’s milk. We didn’t find out until years later through a blood test that she had an intolerance to cow’s milk. After going off of it she no longer had bowel problems and her skin cleared up too. Try getting your child off cow’s milk for a week and see if there is a difference.

      1. Oops! If your whole family is dairy and gluten free as on a paleo diet then not sure what the problem would be.

  3. Question about raw garlic…. I can eat pickled garlic all day long. Does this fit the definition of raw in this context? Same health benefits? I can’t seem to find the answer to this anywhere

  4. Just when you think you’ve heard it all…I didn’t even know post biotics were a thing! There’s always something new to learn! I love raw sauerkraut and use the raw ACV. Enjoy kombucha from time to time. I’m thinking about getting back on a probiotic supplement just to be a little more consistent.

  5. “post-biotics are the metabolic by-products of the bacteria living in your gut and other microbiomes of your body”. So, would that make it the bacteria poop that helps you poop? A self replicating fecal transplant?

  6. Bacillus subtilis is a proven probiotic species (a soil based organism) found in traditional foods. Guess what… it’s also in Primal Probiotics.

    I like to rotate probiotic supplements… we also eat lots of kim chi. One of my favorite dishes is wife’s homemade bone broth (cold), mixed with kim chi, diced avocado and authentic olive oil. It’s so delicious.

    1. Oh my goodness, this sounds amazing! Thanks for sharing. (And to think that the pre-primal me would have found this recipe strange…) 🙂

  7. I’ve always heard antibiotics can negatively impact gut bacteria. Is that enough to warrant upping the probiotics after getting over an illness? If so, for how long?

    Would beer or wine (being fermented) be good probiotics?

    1. The primal probiotics sold on this website say to take up to 10 capsules a day to reestablish gut floral following antibiotics or food poisoning.

    2. Definitely increase your probiotics during/after antibiotic use. As for how long, there are a lot of differentials there.. how long of a course.. what type of antibiotic, etc. I would take extra for about 2 weeks myself.

  8. 2 Questions:

    I find something interesting about this article. I’ve been suffering from IBS-D my whole life. In the last few years, I’ve been trying to follow the FODMAP diet and the list of foods up top are basically a list of foods the FODMAP tells me to avoid (garlic, onions, honey, etc). Do you have any opinion/suggestions on how this *Biotic world maps to those of us on a FODMAP diet?

    I’ve been taking probiotic pills , two a day for a long long time, while following fodmap and probiotics I believe has helped, I still get a stomach ache maybe once a week or so. If taking all these pro-biotic pills are supposed to restore my gut balance, what is it about my gut that I need to do it forever…? Shouldn’t, the probiotics create a colony in there that can then flourish? If something keeps killing them off… what could it be? I feel like I’m continually treating a symptom instead of dealing with the real problem….


    1. Many of those foods you mention are on the FODMAP list to avoid bc they are fermentable… here is where the bacteria come into play… they ferment these foods for their own food.

      Do you eat carbs? Do you have a leaky gut? Do you follow the Primal Blueprint? Do you eat a nutrient dense diet? Restrictive diets often restrict nutrients.

      Keep in mind that not all probiotics are created equal; and no probiotic will ever be as good as the real deal. Fermented foods should always come first… supplements second.

      Since the beginning of time, we consumed fermented foods. In the modern world, we take supplements.

      Introducing fermented foods should be a process. Start with a little and work your way up.

    2. My 38 yr old son has suffered IBS-D,also psoriasis since his early 20’s. A few years ago wanting to lose weight, I went low carb, I lost weight and a side effect, my psoriasis cleared up. I told my son this, so he started eating, low carb (he has never been heavy)for his psoriasis and it also helped with his IBS-D. He still has upsets now and then, but he is much better. Now finding MDA, we both have learned so much more. Do you eat prebiotics to feed the good bugs, eat a verity of foods for different nutrients? My son tries to eat something fermented everyday, bone broth, no gluten, and staying lower carb, higher fat, seems to work well for him. I know it’s an awful infliction, I have watched my son deal with it for years. Might try an elimination diet, to make sure it’s not a food allergy causing the problem. I think my son has a gluten sensitivity, that’s why he got better when he started eating low carb.

  9. Aside from talking with my ruminant microbiologist friends over the years, i didn’t really take the gut microbiome too seriously until I became involved with the first NIH Human Microbiome Project (see: doi:10.1038/nature11209 and doi:10.1038/nature11234). Although the jury still is out on the utility of food-derived probiotics (primarily dairy strains), the current trend toward using fecal transplants for conditions like C. difficile colitis is showing real promise. But until we can come up with certified pharmaceutical grade mixes of probiotic human-derived organisms that actually colonize the gut for long periods of time, I prefer to nurture my resident “natural” microbiota through primal practices and the use of prebiotic powders. Please check with your personal physician before starting any new dietary protocol but for my personal N=1 regimen, I like to add in a bit of inulin, dextrin and resistant starch powders to my protein shake every-other-day. Things can be a bit gassy the first few days but once your flora adapts, perfect Bristol type-4s are the normal end product.

    1. Fecal transplants for c-diff work! I contracted c-diff after a hospital stay, went on endless hardcore antibiotics, a week after the course of antibiotics ended it came back. I performed a home fecal transplant and the symptoms resolved almost immediately. It has been 6 months, and c-diff has not returned. Interestingly, I can now tolerate foods I could not before the transplant.

  10. Great article, Mark! I have a question, would kombucha with chia seeds be a synbiotic?

  11. Thank you, Mark, for another fascinating article! This new science on postbiotic transplants is incredible.

    I was successful in creating a fully functioning digestive system by focusing on my gut biome. I used both food based pre/probiotics and Primal Blueprints probiotics to end a lifetime of constipation, gas, bloating, and immune system ailments. I am grateful every day to have found the Primal Blueprint program!

  12. What about natto, the Japanese fermented beans? So delicious but so stinky.

  13. I think that studies and actual work with gut microbes show that they impact our lives far more than the mainstream would really like to acknowledge. Then again, the mainstream is still working off the food pyramid, which I guess they like because it’s pointy, like their heads?

  14. New to this subject but did I understand correctly ”Scientists found that the formerly obese microbiome was degrading the flavonoids in their food at a far greater rate than the non-obese microbiota which in turn was lowering energy expenditure and inhibiting fat metabolism” Is this one of the reasons why they say if you were fat it is easier to become fat again ? I know metabolism slows down as well when you are dieting as the body thinks its in danger of starvation. And how long do these microbiome remember as in do they have a long lifespan or after 1 year they forget :3 ?

  15. “Yogurt, sauerkraut, kefir, kimchi, kvass, raw vinegar—basically any fermented food has the potential to be classed as a probiotic”

    Do the beneficial bacteria found in these fermented foods survive the “journey” through the stomach and small intestine before finally arriving in the colon?

  16. Does taking charcoal tablets negatively affect the gut? I’ll often take a couple to mitigate the effects of too much beer, but if that happens several days in a row, I worry I’m sucking up all the good bacteria with the charcoal.

  17. This reminds me to make a new batch of garlic dill pickles. I use them in cold potato salad plain yogurt and chopped fresh parsley. Cooked an cooled potatoes for the prebiotic and lacto/bifido probiotic cocktail on top.

  18. Just skip animal proteins and fats, get some fiber and resistant starch instead – done

    1. Mark often picks up some of these kinds of questions in a ‘Dear Mark’ post or, if there are lots, writes a follow-up article. The forums are also used for discussions.