Diet & Nutrition

Optimize Your Keto Diet by Focusing on Your Gut Health

Optimize Your Keto Diet by Focusing on Your Gut Health

Ketogenic diets have been making quite the splash among health and wellness fans recently, and with good reason! Many people who go keto say they just feel better––not to mention the fact that studies indicate eating a high fat, low carb diet can lead to better energy levels, reduced levels of free radicals, and good brain health, among other things.1,2

So, what is the keto diet? In its most basic form, a ketogenic (or keto) diet is one in which you eat mostly fats, some protein, and very few carbs. While there are nuances and small differences in exactly what a keto diet is among the various dietary communities, generally speaking you're talking about 75% fats, 20% proteins, and 5% carbs. Eating this way helps put your body into a state called ketosis, in which it burns fat for fuel instead of carbs. Along with all the other benefits above, being on a keto diet can help you reach your optimal weight, help your body relearn how to manage glucose appropriately, and keep you feeling fuller longer.3

All that sounds amazing––but it can only happen if your body is able to make the most of your dietary efforts. If your gut isn't able to use all that great nutrition you're putting into it, you could be putting in a lot of hard work for nothing.

To optimize your keto diet (and avoid a lot of wasted effort), you'll need to ensure that your body can absorb nutrients––especially fats––appropriately. And to make that happen, you'll need to get your gut microbiome on board.

The Gut Microbiome and the Keto Diet

Your gut microbiome is a key determinant in your digestion––including how your body responds to being on a keto diet. Having a healthy, diverse ecosystem of gut bacteria is crucial for:

1. Helping your body absorb fats.

Fats are one of your main sources of nutrition when you're on a keto diet, so it's important to make sure that your body can absorb them well. Certain specific strains of gut bacteria have been studied for their ability to support the digestion and absorption of fats, with some strains encouraging the production of the digestive enzymes needed to break down certain fats and others supporting the uptake of fat into the intestines for use in the body. In fact, this effect is so pronounced that one study found that mice without a microbiome couldn't absorb fat well at all, appearing to pass most of it through their bodies. In the same study, mice with a specific microbiome quickly absorbed fat.4

2. Supporting optimal nutrient absorption.

The relatively strict nature of the keto diet can make it difficult to get appropriate levels of nutrition unless you're very careful about what you eat and make a concerted effort to get the full spectrum of nutrients you need to stay healthy.

This potential pitfall becomes even more of an issue if your gut microbiome is out of balance, since it’s responsible for helping your body absorb nutrients. Research indicates that a healthy gut microbiome supports your intestinal lining, helps break down certain foods, and produces enzymes to digest food and stimulate the absorption of nutrients.5

Certain strains can even help to manufacture vitamins essential for staying well, including B vitamins (which help your body convert food into energy efficiently) and vitamin K (which is crucial for calcium regulation), so it's clearly important to keep your gut microbiome healthy to make the most of this diet.6

3. Keeping you energized enough to enjoy the benefits of the diet.

Eating fewer carbs can be incredibly good for you––but one downside is that you may find it harder to get enough prebiotic fiber, since these types of fibers are commonly found in relatively carb-heavy foods, and it can be hard to find keto diet-friendly fiber.

And not getting enough prebiotics is a big problem, because your gut uses them to produce short chain fatty acids (SCFAs), which are necessary for maintaining your energy, mood, brain function, and intestinal wall.7

Long story short: without enough SCFAs, you're probably not going to be feeling your best physically and mentally, which puts a big damper on the benefits you could be enjoying from your keto diet.8 But a healthy gut microbiome combined with prebiotic supplementation can help you avoid these effects, keeping you firing on all cylinders.

4. Maintaining a healthy metabolism to support your weight management goals.

If you're using a ketogenic diet for weight management, then you'll definitely want to get your microbiome in on the game. Multiple studies explore how having an unbalanced gut microbiome can affect your basal metabolic rate (how many calories you burn when you're not being active) and contribute to weight gain, while having a balanced gut microbiome can keep everything moving like it should.9,10

5. Doubling down on keto's benefits to your blood sugar.

Being on a ketogenic diet can do wonders for your blood sugar regulation. You see, the way many in the Western world eat now––a diet that's heavy in carbs, and by extension, glucose––is pretty new for us as a species, meaning that our bodies haven't adapted for it yet. So when you eat a bunch of carbs, you flood your body with glucose, overwhelming its natural responses and setting yourself up for mood swings, energy crashes, and potential problems regulating insulin.

Cutting out carbs gives your body a big break from this, and a healthy gut microbiome can make this effect even more pronounced. Studies indicate that having a balanced microbiome rich in Lactobacillus acidophilus and Bifidobacterium bifidum can significantly support the way your body deals with glucose, helping you maintain your blood sugar levels already within a normal range.11

How a Keto Diet Benefits Your Microbiome

The great thing about the relationship between your microbiome and a keto diet is that it runs both ways. Your gut microbiota can do wonders for your diet––and being on a keto diet is also really good for your bacterial good guys.

For instance, eating a ketogenic diet means that you're already cutting out some of the foods that feed undesirable bacteria, like sugar and processed foods. This naturally gives your bacterial allies an advantage, letting them stay in the majority and colonize your gut. Similarly, eating keto means that you tend to avoid foods that can damage your intestinal lining, like grains and beans. The gluten and phytic acid they contain can really do a number on your gut lining, making it hard for beneficial bacteria to set up shop—but eating keto deals with that issue before it starts.

And, all those good fats you're getting on the keto diet can be really beneficial to your gut microbiome, since healthy fats are good sources of omega-3s—and omega-3s are not only highly correlated with microbial diversity, but they also help beneficial bacteria adhere to your intestinal lining, giving them a leg up on the bad guys.12,13

Recent research has also been conducted about how a ketogenic diet can both increase the abundance of types of beneficial bacteria in the gut, and decrease some of the problematic strains that can lead to temporary inflammation.14

Keto-Friendly Tips for Maintaining Your Gut Microbiome

Now that you know just how important your gut microbiome is to making the most of your keto diet, taking steps to maintain and nourish your microbial allies is a clear next step. The good news is, there are lots of keto-friendly options for supporting your gut microbiome, so try incorporating a few of these suggestions into your routine.

• Make sure that you're eating high quality foods as part of your keto diet.

If you're following a ketogenic diet, chances are that you're already cognizant of what you're putting in your body...but on the off chance that you've been following the letter of the law instead of its spirit, consider this a wake-up call. Eating technically keto but doing so with a lot of low quality fats and proteins isn't going to give you the results you want, and low quality foods are often full of antibiotics or pollutants, both of which can absolutely devastate your bacterial balance.

• Focus on getting enough magnesium and potassium.

It can be particularly easy to let these two nutrients slide when you're on a keto diet, since they're commonly found in things like beans, potatoes, and bananas, but they're both really important for your gut to work properly. Not having enough magnesium changes the composition of your gut bacteria, and the resulting mix may leave you open to unwanted mood changes; while not having enough potassium shifts the way your digestive system works, creating conditions that allow unwanted bacteria to thrive. Be sure to include keto-friendly foods that are rich in these nutrients in your diet, including spinach, chard, pumpkin seeds, avocados, and salmon.15

• Give your gut microbes the building blocks they crave with a low-carb prebiotic supplement.

There's no way around it: your beneficial gut bacteria really need prebiotics to thrive, and your body needs the SCFAs they ferment to feel good and function properly. It can be difficult to get all the prebiotic fiber you need even in a typical diet––most people on a normal Western diet get far less than the daily recommendation of 30 grams of fiber a day––and eating a ketogenic diet can add another layer of complexity, so you may need to look at other options.

One easy way to get plenty of prebiotic fiber with fewer carbs is to supplement with a premium prebiotic powder. Look for a food-based, organic one like Hyperbiotics Prebiotic Powder, which contains a mix of FOS, inulin, and soluble dietary fiber to give your good guys all the nutrition they need without compromising your keto diet. (It's so easy, and much lower in carbs than a serving of prebiotic-rich vegetables or fruits. For instance, one banana has 27 grams of carbs, but Prebiotic Powder has just 6 grams per serving.) If you count net carbs in your keto diet by subtracting dietary fiber while tracking your macros, it’s even more impressive—one serving of Prebiotic Powder equals just one net carb!

• Take a premium probiotic to encourage a diverse gut microbiome.

There are so many factors in our modern lifestyle that can throw your microbiome out of whack, that even if you are eating a healthy diet, it's helpful to replenish your gut with beneficial bacteria to keep it in balance. To make sure you have a wide variety of strains to support your dietary efforts, look for a premium probiotic supplement like Hyperbiotics Better Body. This multi-strain formula designed for weight management is a keto dieter’s dream, with the perfect combination of beneficial bacteria, along with white kidney bean extract to help discourage the absorption of carbohydrates. Better Body can be especially helpful during the sometimes rough initial phase of the keto diet (when many people experience digestive distress due to the sudden cutback of sugar and carbs) by supporting healthy digestive function.

Even though keto's not the simplest diet out there, the results are more than worth it, so don’t give up! With a little targeted probiotic support, your efforts will be rewarded with healthy days for years to come.


1. Neal, E.G., Chaffe, H., Schwartz, R.H., Lawson, M.S. . . . Cross, J.H. (2008). The Ketogenic Diet for the Treatment of Childhood Epilepsy: a Randomised Controlled Trial. The Lancet Neurology, 7(6), 500-6. doi: 10.1016/S1474-4422(08)70092-9

2. Boden, G., Sargrad, K., Homko, C., Mozzoli, M., Stein, T.P. (2005). Effect of a Low-Carbohydrate Diet on Appetite, Blood Glucose Levels, and Insulin Resistance in Obese Patients with Type 2 Diabetes. Annals of Internal Medicine, 142(6), 403-11. doi: 10.7326/0003-4819-142-6-200503150-00006

3. Frassetto, L.A., Schloetter, M. Mietus-Synder, M. . . . Sebastian, A. (2009). Metabolic and Physiologic Improvements From Consuming a Paleolithic, Hunter-Gatherer Type Diet. European Journal of Clinical Nutrition, 63, 947–955. doi:10.1038/ejcn.2009.4

4. Martinez-Guryn, K., Hubert, N., Frazier, K., Urlass, S . . . Chang, E.B. (2018). Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids. Cell Host and Microbe, 23(4), 458–469.e5. doi: 10.1016/j.chom.2018.03.011

5. Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., . . . Gordon, J. I. (2016). Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science, 351(6275). doi:10.1126/science.aad3311

6. LeBlanc, J.G., Laiño, J.E., Juarez del Valle, M. . . . Sesma, F. (2011). B‐Group vitamin production by lactic acid bacteria – current knowledge and potential applications. Journal of Applied Microbiology, 6, 1297-1309. doi: 10.1111/j.1365-2672.2011.05157.x

7. LeBlanc J.G., Chain, F., Martín, R., Bermúdez-Humarán L.G. . . . Langella, P. (2017). Beneficial effects on host energy metabolism of short-chain fatty acids and vitamins produced by commensal and probiotic bacteria. Microbial Cell Factories, 8, 16(1), 79. doi: 10.1186/s12934-017-0691-z.

8. McLoughlin, R.F., Berthon B.S., Jensen, M.E., Baines, K.J., Wood, L.G. (2017). Short-chain fatty acids, prebiotics, synbiotics, and systemic inflammation: a systematic review and meta-analysis. The American Journal of Clinical Nutrition, 106(3), 930-945. doi: 10.3945/ajcn.117.156265.

9. Bahr, S. M., Weidemann, B. J., Castro, A. N., Walsh, J. W., Deleon, O., Burnett, C. M., . . . Kirby, J. R. (2015). Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure. EBioMedicine, 2(11), 1725-1734.

10. Devaraj, S., Hemarajata, P., Versalovic, J. (2013). The Human Gut Microbiome and Body Metabolism: Implications for Obesity and Diabetes. Clinical Chemistry, 59(4), 617–628, doi: 10.1373/clinchem.2012.187617

11. Simon, M., Strassburger, K., Nowotny, B., Kolb, H., Nowotny, P., Burkart, V., . . . Roden, M. (2015). Intake of Lactobacillus reuteri Improves Incretin and Insulin Secretion in Glucose-Tolerant Humans: A Proof of Concept. Diabetes Care, 38(10), 1827-1834. doi:10.2337/dc14-2690

12. Bentley-Hewitt, K. L., Guzman, C. E., Ansell, J., Mandimika, T., Narbad, A., & Lund, E. K. (2015). How fish oils could support our friendly bacteria. Lipid Technology, 27(8), 179-182.

13. Menni, C., Zierer, J., Pallister, T., Jackson, M.A., Long, T. . . . Valdes, A.M. (2017). Omega-3 Fatty Acids Correlate with Gut Microbiome Diversity and Production of N-carbamylglutamate in Middle Aged and Elderly women. Scientific Reports, 7. doi: 10.1038/s41598-017-10382-2

14. Ma, D., Wang, A. C., Parikh, I., Green, S. J., Hoffman, J. D., Chlipala, G., . . . Lin, A. (2018). Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice. Scientific Reports,8(1). doi:10.1038/s41598-018-25190-5

15. Winther G., Jørgensen, P., Elfving B., Nielsen D.S. . . . Wegener, G. (2015). Dietary magnesium deficiency alters gut microbiota and leads to depressive-like behaviour. Acta Neuropsychologica, 27(3),168-76. doi: 10.1017/neu.2015.7


Rachel Allen is a writer at Hyperbiotics who's absolutely obsessed with learning about how our bodies work. She's fascinated by the latest research on bacteria and the role they play in health, and loves to help others learn about how probiotics can help the body get back in balance. For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter. To learn more about how a healthy microbiome can enrich your life, subscribe to our newsletter.