Listen to Your Gut: the Microbiome, Probiotics, and Prebiotics

I’ve been feeling extra pioneer-womanesque lately, probably because my roommate and I baked our own bread for the first time on Christmas day. It was a baguette, and it was delicious dipped in olive oil, salt, and pepper.


It got me thinking about other foods I buy at the store but that I could make at home. I eat a lot of bread, and I also eat a lot of yogurt. I probably spend a good $50 on yogurt monthly, which isn’t a fortune in the grand scheme of things, but certainly putting that $50 away in savings for a rainy day wouldn’t hurt. So I decided to make my own yogurt.

I eat yogurt daily. I’ve been doing this for years, well before I became a dietitian. I buy 32-ounce containers because the single serve cups are not cost efficient, and they are usually packed with sugar. I buy Greek yogurt, because I think the richer consistency and the extra protein are worth the steeper price. I buy plain, nonfat and I mix in my own fresh or frozen berries and sprinkle on some granola for texture. It’s the perfect midmorning snack for when my 6am breakfast is wearing off, but it’s not quite lunch time yet.

I feared that making my own yogurt would be difficult, and that I’d have to buy fancy equipment and heirloom cultures from Amazon or something.  As it turns out, all you need is a half a gallon of milk, a food thermometer, and a couple tablespoons of plain old yogurt (which, of course, I have in my fridge at all times).  You can even make it in your crock pot!

incubatingyog cheeseclothyog

(My yogurt, incubating and straining. I used this tutorial, and it really is fool-proof:

If I could force feed everyone in America a cup of yogurt a day, I would. Yogurt (like kefir, kimchee, sauerkraut, and miso) is a fermented food. A fermented food is made by adding live, active bacterial cultures to the food. The bacteria feed on the sugars naturally present in the food and produce metabolic end products like lactic acid and alcohol, which are responsible for the distinct tart flavor of these foods. Because the fermentation process partially breaks down the food’s sugars, human digestion of that food becomes a bit easier (it’s why the lactose intolerant can usually tolerate yogurt without experiencing the unpleasant symptoms associated with drinking straight-up milk).  Humans also benefit from eating certain fermented foods because the bacteria help restore and replenish our natural, healthy gut flora.

We humans have a rich and diverse community of bacteria residing in our bodies, and our gastrointestinal (GI) tracts are hosts to the most abundant colonies. For the most part, an individual’s bacterial community remains stable over their lifetime, but the diversity can vary greatly from one person to the next. The cells of the human microbiome (what we call the collective population of microbiota that live in the human body) outnumber human cells 10:1! But because they’re so tiny, all those cells would fit into two pints of Ben and Jerry’s.

It’s known that human microbiota play an important role in gut health, nutrition, and the immune system, and the more diverse your individual ecosystem is, the more beneficial. Gut bacteria feed on stuff that’s indigestible to us, which can free up nutrients we otherwise couldn’t access. For example, gut bacteria release short chain fatty acids from indigestible fibers. These short chain fatty acids feed the cells of the GI tract, which happen to be some of most proliferative cells in the body.* Gut microbes also help build a healthy and robust immune system by “teaching” your immune cells which bugs are harmless and which ones are pathogenic, and stimulating the production of immune cells while simultaneously inhibiting production of pro-inflammatory molecules. This is what we mean when we say the good bacteria keep the bad bacteria in check.

Research into the role the gut microbiota plays in health is booming right now, and there’s a growing body of evidence that the gut microbiome impacts our risk for developing a wide array of health conditions. Gut bacteria has been studied in relation to obesity, type 2 diabetes, heart disease, gastrointestinal disorders, and cancer, and even depression, anxiety, and other mental health disorders. Research is aimed at identifying the characteristics of the dysbiosis (an imbalance of the gut microbiome) that is associated with a disease, and intervening with an antibiotic, a supplemental probiotic, or diet to see if the disease state changes by altering the flora.

Nutrition-specific research looks at how diet influences the composition of the gut bacteria, and what associations exist between diet, microbiome composition, and disease. Human data are very limited in this respect, because it’s really hard to conduct a randomized, controlled trial with diet interventions (as I’ve described in previous posts) without locking people up in a facility for months on end and controlling every aspect of their intake.**

The difficulty with studying the relationship among gut microbiota, probiotics, and disease is that it’s often unclear whether the dysbiosis is causing the disease or if it’s a result of the disease. For example, the effect of probiotic use in treating both Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD – Crohn’s Disease and Ulcerative Colitis) has been extensively researched with mixed results, even though patients with both disorders have been shown to have messed-up gut flora1,2.

There is one condition, however, that gives hope to microbiome researchers and fuels the ongoing examination of how fixing the microbiota could eradicate disease: Clostridium difficile infection (C. diff).

C. diff is a gastrointestinal disorder that is characterized by overgrowth of the C. diff bacteria as result of prolonged and/or broad spectrum antibiotic use. We mostly see it in hospital settings. Special precautions must be taken with infected patients because the bug is highly contagious and super resistant to standard precautions like antibacterial hand gel. Healthcare workers have to wear protective gowns and gloves when coming into contact with C. diff patients and we must wash our hands with warm water and soap when leaving the room. The symptoms are wildly unpleasant – diarrhea, abdominal pain, and fever that can last days and lead to inflammation of the colon (colitis). Left untreated, it’s life-threatening. The first line of treatment is an antibiotic (a more specific one that targets C. diff), and most physicians also order a probiotic supplement for the patient to help restore normal flora.

But research has tried out a somewhat… alternative treatment for C. diff, and its efficacy has implications for the potential causal relationship between altered gut flora and disease: fecal microbiota transplant. Yep, it’s exactly what it sounds like. Fecal samples from a healthy person (the donor) are transplanted into the colon of an infected person (one group of researchers named their sample, created from the stool of a healthy, 41-year-old woman, “RePOOPulate”3).  The results show a development of intestinal flora in the recipient that closely resembles that of the healthy donor – and the resolution of symptoms (it worked so well that one controlled study was stopped early because continuing would be unethical4). The hope is that identifying specific strains of helpful bacteria will lead to the development of a preparation in a lab.

So it’s pretty clear for C. diff: an alteration in the microbiota causes the disease, and restoration of healthy flora is a treatment for it. The question is, for what other diseases does this stand true? The literature supports a role for probiotic supplementation in certain GI disorders like infectious diarrhea (C. diff is an example), acute onset diarrhea, and potentially IBS (remember, there are mixed results here, but the vast majority of GI docs recommend probiotics for patients battling this frustrating syndrome).  As for the other diseases like diabetes, obesity, and cancer – the data are growing but the jury’s still out.


Probiotics, Prebiotics, and Synbiotics

I’m sure you’ve read enough about research for one post, so I’ll get on to the useful stuff and give you my recommendations for food and probiotic supplements to keep your gut bugs happy.

My general rule is food first, so I’ll always suggest a daily yogurt or kefir. Some, but not all fermented foods have probiotic benefits. For example, store-bought pickles and sauerkraut started out containing live cultures, but have typically been heat-processed, which kills the beneficial bacteria.  The final product in yogurt-making, on the other hand, does contain live cultures because it’s not heated over 110 degrees during processing.  Research supporting regular intake of yogurt or fermented products is equivocal.  One study showed yogurt eaters (who were healthier eaters overall) have a healthier bacterial profile than non-yogurt eaters5.  Another (a randomized, controlled trial) found development of a beneficial gut flora profile and symptom improvement in IBS patients that drank a fermented milk drink6.  But there aren’t a lot of data to sift through. Further, because we can’t measure what doesn’t happen, we cannot speak to the preventative effects a daily yogurt might have on specific conditions (such as those related to GI function).

Over-the-counter probiotic supplements are live bacteria that are similar or the exact same as the beneficial microbiota in our gut. They come in pill or powder form and they can be pricey. Examples are Align (one study’s researchers found this to be the most recommended brand by GI docs that answered their survey9), Culturelle, Florastor (we use this in the hospital often: it’s actually yeast, not bacteria), and TrueBiotic***. Most drugstores have a generic version too.

This is important: because probiotics are considered dietary supplements, they are not regulated by the FDA, so quality, purity, and viability (a huge consideration in a live product) can vary. Proof of efficacy and safety is not required for companies to introduce a probiotic into the market. You want to make sure you buy a product from a reputable company with a lot to lose should their products prove faulty and need to be discontinued. (This caveat goes for all nutritional supplements, not just probiotics). That being said, complications with probiotic use are rare.

Here are some important things to keep in mind should you decide to go the route of over-the-counter probiotics10:

  1. The label should say the product contains “live, active cultures” – if you can’t find those words, don’t buy it. Taking this a step further…
  2. The label should list the specific genus and species using terms that are well-known among the medical and scientific community (the most commonly used in research – because they have shown to be the most effective – are the bacterial strains Lactobacillus and Bifidobacterium, and the yeast strain Saccharomyces boulardii)
  3. The product should specify the number of viable cells at “the end of the shelf life”, not “at the time of manufacture” (the number needed for a beneficial effect will vary depending on the strain)
  4. The product should have a recommended dosage
  5. The product should have recommendations for storage
  6. Contact info for the company that makes the product should be available so people can report adverse effects (this is how a defective product could eventually get pulled from the market)

Keep in mind that these products introduce a select few microbe strains into your gut, so they won’t do much in the way of repopulating your native flora (remember, there are over 1000 species up in there). When you stop taking them, you may see the benefits go away. One way to ensure your own gut microbiota stay plentiful is to feed them!

Remember how I said some gut bacteria can release short chain fatty acids from indigestible fibers? Those fibers are considered prebiotics. Prebiotics are substances (typically indigestible carbohydrates) that feed the probiotics or natural gut flora in a way that promotes beneficial bacterial growth while inhibiting harmful bacterial growth.  Examples are oligofructose and inulin (found in gum acacia****, green veggies, oatmeal, garlic, leeks, Jerusalem artichoke).

Finally, synbiotics are food or supplement products that contain both prebiotics and probiotics. A true symbiotic will contain a prebiotic that has been shown to selectively feed the probiotic it contains. For example, Bifidobacteria eat oligofructose, but Lactobacillus casei do not8.  Culturelle is an example of a symbiotic (contains probiotic and inulin, a prebiotic).

In case you’re wondering, my yogurt turned out very well. It tastes like, well, yogurt, and the consistency is perfect.

Till next time…

finished yog


1. Shreiner, A, Kao, JY, Young, VB. (2015). The gut microbiome in health and in disease. Curr Opin Gastroenterol.  31(1):69-75.

2. Whelan, K. and Quigley, EWW. (2013). Probiotics in the management of irritable bowel syndrome and inflammatory bowel disease. Curr Opin Gastroenterol. 29(2):184–189

3. Petrof, EO, Gloor, GB, Vanner, SJ, Weese, SJ, Carter, D, Daigneault, MC, Brown, EM, Schroeter, K, Allen-Verco, E. (2013). Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome. 1: 3.

4. van Nood E, Vrieze A, Nieuwdorp M, et al. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 368:407–415.

5. Kong, LC, et al. (2014). Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects. PLoS One. 9(10): e109434.

6. Veiga, et al. (2014). Changes of the human gut microbiome induced by a fermented milk product. Sci Rep. 4:6328

7. Ciorba, MA. (2012). A gastroenterologist’s guide to probiotics. Clin Gastroenterol Hepatol. 10(9): 960-968.

8. Schrezenmeir, J, and de Vrese, M. (2001). Probiotics, prebiotics, and synbiotics – approaching a definition. Am J Clin Nutr.  73(2): 361s-364s

9. Williams, MD, et al. (2010). Probiotics as therapy in gastroenterology: a study of physician opinions and recommendations. J Clin Gastroenterol. 44(9): 631–636.

10. World Gastroenterology Organisation. (2011). World Gastroenterology Organisation Global Guidelines: Probiotics and Prebiotics. Retrieved on 1/4/2015 from:



*Further, in a person with impaired nutrient absorption (and decreased ability to get enough calories from their food) due altered structure or function of their small intestine or pancreas, these short chain fatty acids actually become a super important source of calories.

** This is called a metabolic ward study. It’s quite an expensive endeavor and most wards can only accommodate a small group (8 participants, for example), which makes it hard to extrapolate results from these studies to the general public. Basically people are isolated in a hospital-like ward for a predetermined period of time. Researchers control everything about the environment, including food intakes, humidity, temperature, and light.

***I am not getting paid to promote brands in this blog. If that changes, I’ll be sure to let y’all know.

****Banatrol is a prebiotic medical food made with banana flakes and a proprietary prebiotic blend with gum acacia that’s used in hospital settings for patients with diarrhea (but you can order it for home use too!). It’s a powder you mix up with water and it can be given orally or through a feeding tube.  More info: (No I don’t work for this company, nor am I getting free samples or being paid to say nice things. I just think it’s cool.)



Filed under gastrointestinal nutrition, microbiome, probiotics

6 responses to “Listen to Your Gut: the Microbiome, Probiotics, and Prebiotics

  1. Kari

    Great info!! I recently found out I have a milk allergy…it has been the underlying cause of my constant sinus infections. I have had to pull out all dairy and have been able to find some ok substitutes but yogurt I miss terribly !! The milk free options I am finding are FULL of crazy ingredients and sugar not to mention, they taste funky. Have you ever made this recipe with any other kind of milk? This may be a great option for me if I can use a coconut or organic soy milk!! Let me know what you think 🙂


    • Hey Kari! Thanks for reading! I have not made soy, almond, or coconut milk yogurt but I was thinking about trying it next. The “starter” cultures for the milk version came from regular dairy yogurt, so you would need to replace that. You say you want to avoid the store bought vegan yogurts because of all the extra sugar, which I’m in full support of. Would you be OK with using only the two tablespoons of the store-bought soy/coconut yogurt that you’d need to start your homemade yogurt? Once it’s done, you could then save a little of your homemade yogurt for the next batch, and so on every time you make it, to the point where your cultures are kind of your own, even though you started with store bought yogurt. I’ve also seen some recipes online that use probiotic powders instead of starter yogurt. This one was recommended: Also, this blog has some solid-sounding advice for making vegan yogurt: If you try it, let me know how it goes!!


  2. Jane Dille

    Great article about one of my favorite foods! I remember when I was young my mother, a lover of all things kitchen-gadgety, had a yogurt making machine that fascinated me, but she saved the booty for herself and gave the kids the regular fruit on the bottom kind from the store. I’m excited to try it myself and think I’ll give the vegan option a go too! Thanks!!


    • let me know how it goes! One thing I do wish is that I let it strain for a little longer. I let it go for about 2 hours. to get Greek style, it really needs like 5 hours. But I was too impatient. It’s still good, just more like regular yogurt rather than Greek.


  3. awesome article! you’re so smart & crafty.


  4. Pingback: Drink Milk, or Don’t. But Maybe Read This First. | the informed appetite

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