BiotiQuest® Gut Health & Probiotics Blog with Martha Carlin

How To Level Up Your Keto Diet With Probiotics?

Martha Carlin | Dec 19, 2022 | 8 minutes read

The connection between your gut microbiome and well-being cannot be denied.

The last few decades have opened the door to understanding how truly we are what we eat. Whether you’re on keto, a carb lover, or a green smoothie pro, every meal you eat alters and shapes your gut microbiome.

Studies reveal that a diverse gut microbiome is a healthy gut microbiome. The more types of microbes you have in your gut, the better your body is equipped to deal with unexpected health events.

Keto, by design, limits the number of carbohydrates you have in a day, reducing the presence of carbohydrate-consuming bacteria in your gut. Some carb-loving bacteria, like Bifidobacteria, are key to a healthy immune system.

Keeping to a long-term keto-only diet — without periodic carbohydrate exposure or a prebiotic and probiotic supplementation — can reduce beneficial bacteria like Bifidobacteria and potentially harm your gut health.

However, a high carbohydrate diet feeds many types of bacteria, including those that are not beneficial and can lead to the overgrowth of pathogens.

Some believe a persistent keto diet will negatively Impact the balance of your gut, and some claim that it can have a protective effect on your brain and keep your immune system healthy. A better approach is something called Keto Flexing. You can learn more about this approach from Ben Azadi, author of Keto Flex.

Let’s dive into all things Keto to better inform your health journey!


Keto and Gut Health

Your gut microbiota consists of trillions of bacteria, fungi, and viruses. It plays an essential role in nutrient metabolism, pathogen protection, production of bioactive compounds such as butyrate and bacteriocins, conversion of simple sugars such as fructose and glucose to mannitol, maintaining the energy balance in the body, and enhancing your immunity.

A diet rich in non-digestible carbohydrates or fiber can support the growth of microbes that specialize in producing short-chain fatty acids (SCFAs) such as butyrate, acetate, propionate, and valerate.

Butyrate is the primary source of energy for colonocytes — intestinal wall cells — and plays a vital role in maintaining a healthy gut barrier and intestinal motility, suppressing and preventing colorectal cancer, and reducing mucosal inflammation and oxidative stress.

The classic western diet is already low in fiber but high in simple carbohydrates. A diet lacking in more complex fiber can quickly derail the delicate balance of your gut, whether it is the classic western diet or 100% keto with no flexing.

Supplementing your low-carb, high-fat diet with a keto probiotic supplement can support your overall gut health and let you continue to take advantage of ketosis.

What is a ketogenic diet?

A ketogenic diet comprises healthy fats, moderate proteins, and low carbs. A 2000 kcal keto diet will consist of:

  • 55-60% good quality fat (olive oil, ghee, animal fat)
  • 30-35% protein (grass-fed, pasture-raised, wild-caught), and
  • 5-10% carbohydrates (leafy fibrous greens, low glycemic index fruit, and veg)

The objective of the ketogenic lifestyle is to induce ketogenesis, which has closely related benefits to a fasting state. Ketones are an alternate and cleaner burning fuel source for the body.

Intermittent fasting leads to a lack of simple sugars in the blood and induces the body to break down fats for energy (ketosis). Entering a ketogenic state during fasting has been associated with weight loss, improved insulin sensitivity, increased good cholesterol, and healthy gene expression.

How does a ketogenic diet work?

If you’re new to keto, your body primarily uses carbohydrates as its energy source. In a keto diet, your carbohydrate intake is greatly reduced, and it will induce your body to enter a catabolic state — breaking down complex molecules such as lipids (fat cells) and protein for energy.

Once your body runs out of its available sources of glucose and glycogen (a form of glucose stored in the liver), it flips to ketogenesis. Ketogenesis is the breakdown of fat (triglycerides) molecules into ketone bodies (acetoacetate and 3-d-hydroxybutyrate) and glycerol. Recall we noted above that butyrate is important for a healthy gut lining.

A low-carb diet results in lowered insulin levels in the blood and the presence of insulin inhibits ketogenesis.


An environment lacking carbohydrates will decrease the need to produce insulin and allow the body to enter a ketogenic state. Ketone bodies supply energy to the heart, kidneys, muscle tissue, and brain.

ATP (adenosine triphosphate) is the primary energy source, also known as the “energy currency” of the cells. As it happens, ketones are a much more efficient source of energy (ATP) when compared to glucose. For every 100 gm of glucose, you get roughly 7,800 gm of ATP, whereas for every 100 gm of beta-hydroxybutyrate and acetoacetate (ketones), you get around 10,500 and 9,400 gm of ATP, respectively.

Since keto stimulates the breakdown of fat and suppresses fat storage, if practiced longer term, it can lead to rapid weight loss. It takes about 3-4 months to become fat adapted, after which it is important to add back some carb flexing to maintain your metabolic flexibility.

Just as it's not good to be a carb-burning machine all the time, the same is true for fat. It is important to keep your microbiome and body flexible to benefit from both fuel sources.

What are the health benefits of Keto?

A keto diet has been shown to improve symptoms of metabolic syndrome. Metabolic syndrome is a collection of health conditions such as:

  • Obesity
  • High fasting blood sugar levels due to insulin resistance (prediabetes or type 2 diabetes)
  • Low HDL (good cholesterol)
  • High triglycerides
  • Hypertension (high blood pressure)

Lowering the consumption of carbohydrates - a basic keto requirement - has been shown to enhance insulin sensitivity. With lower insulin levels, the stored fat in adipose tissues is broken down in the liver as a source of energy in the form of ketones - acetoacetate, beta-hydroxybutyrate (BHB), and acetone.

Research shows that as your body adapts to keto, your insulin levels and blood sugar will stabilize at lower levels, and the presence of ketones will provide a satiety (feeling full) effect for longer periods, which can further reduce calorie intake.

A systemic review of 13 randomized controlled trials that compared VLCKD (very low carbohydrate ketogenic diet) and LFD (low-fat diet) in 1569 overweight and obese subjects found that VLCKD subjects had greater long-term weight loss.

Benefits of Keto diet besides weight loss include:

  • Lower total triglycerides (cholesterol)
  • Increase in HDL (good cholesterol)
  • Lower diastolic blood pressure
  • Reduces blood glucose (HbA1c) and insulin levels
  • Increased insulin sensitivity

Does Keto improve gut health?

One of the best ways to stay healthy is to keep your gut microbiome healthy. A keto diet will alter your gut microbiome. It can lead to both the growth of helpful bacteria such as A. muciniphila and the loss of some harmful microbes that depend on carbs for survival.

A diet rich in MUFAs and PUFAs decreased the gut populations of pro-inflammatory microbes (bad microbes) such as Desulfovibrio and Turicibacter.

In a study of mice, a ketogenic diet made up of monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA) was found to have increased the numbers of A. Muciniphila and Lactobacillus — both of which can produce SCFAs, which have positive health effects.

This study found that a keto diet improves the Firmicutes (such as Lactobacillus) to Bacteroidetes (such as Prevotella) ratio, which can have a positive effect on Autism Spectrum Disorder (ASD) behavioral symptoms.

Possible disadvantages of the Keto diet

  • Keto Flu
  • As your body adapts to using ketones as its primary energy source, you may go through some of the following side effects, collectively known as the keto flu:

    • Bad breath
    • Fatigue
    • Headache
    • Dizziness
    • Nausea
    • Vomiting
    • Constipation&
    • A low exercise tolerance

    Keto flu symptoms generally resolve within a few days to weeks as your body adapts to the ketogenic state. As your body breaks down stored fat cells, it releases environmental toxins stored in these fat cells into the bloodstream. This may potentially cause some of these flu-like symptoms. You begin to feel better as your body eliminates these toxins from your bloodstream.

    1. Risk of nutrient deficiency (nothing a little planning won’t take care of!)

    A common concern while following a ketogenic diet is getting the full range of nutrients that your body needs to function at its best. Micronutrients and minerals such as folate, vitamin K1, vitamin C, molybdenum, selenium, and manganese can be particularly concerning for people new to the diet.

    Proper planning and prioritizing nutrient-dense eating such as nuts and seeds, low glycemic vitamin c rich fruits (lime, lemon, avocado, and star fruit) and vegetables for fiber and folate (fibrous leafy greens), organ meats, pasture-raised meats, and wild-caught fish can address these concerns. & &

    1. A shift in your intestinal microbiome

    Studies like this suggest that adding prebiotic fiber while on a ketogenic diet, such as inulin — found in chicory root, and prebiotic and probiotic supplements — can help increase the diversity of your gut microbiome.



    Keto and Probiotics

    Your diet determines which microbes will thrive in your gut. Keto promotes the growth of bacteria such A. muciniphila, which has been credited with strengthening gut integrity, modulating insulin resistance, and protecting the host from metabolic inflammation.

    But there are some complex carb-loving bacteria, such as Bifidobacteria, whose populations may decrease due to a limited amount of carbs in your diet.

    One of the simplest ways to address this concern is by using prebiotic and probiotic supplements such as Sugar Shift

    . Rich in probiotics such as B. bifidum,& B. longum, L. plantarum, and L. reuteri, as well as inulin, a prebiotic that encourages the growth of beneficial bacteria in your gut.

    Want to learn more? Listen to Ken Kubota talk about his health goals and experience with Sugar Shift!

    Can probiotics make keto better?

    Adding a probiotic to your routine may improve your ability to sustain ketosis.

    A ketogenic diet will reduce the volume of fermentable carbohydrates and may reduce bacteria associated with SCFA production. However, a ketogenic diet induces the liver to produce high levels of beta-hydroxybutyrate, a key SCFA involved in a healthy gut lining.

    SCFAs such as butyrate are a direct energy source for colon cells and play a role in cross-talk between your gut and brain. Butyrate is associated with increased insulin sensitivity, digestive health, and lower levels of obesity.

    Supplementing with the right prebiotics and probiotics may support increased gut microbial diversity by providing support for a broader spectrum of gut bacteria. It’s particularly important to look for probiotics rich in prebiotics, such as inulin, and beneficial species, such as Bifidobacteria, which can suffer in a keto environment.

    Are probiotics OK on a keto diet?

    Probiotics can support you on a& Keto diet but are a “food source” for the microbiome if they include prebiotics and should not be taken on a complete “fasting” day. Ketogenic diets are generally lower in fiber and can benefit from a probiotic supplement.

    This study advises supplementation with prebiotics such as inulin, lactulose, and galacto-oligosaccharides to increase the population of beneficial bacteria such as bifidobacteria and decrease harmful bacteria such as e-coli. XOS is one of the best fibers to support Bifidobacteria.

    A ketogenic diet has many immediate health benefits, such as reduced blood pressure, better insulin sensitivity, increased weight loss, etc.

    But it can& have an inhibitory effect on the health of your gut microbiota if practiced without flexing in complex carbohydrates periodically to maintain metabolic flexibility. & Research suggests that a sustained keto diet can negatively affect gut microbial diversity, which can negatively impact your immune health, digestive health, production of SCFAs, which help brain function, nutrient absorption, gut and host cross-talk, insulin control, etc.

    But the good news is that studies have found that supplementing with a probiotic supplement can positively impact your overall health and add value to the benefits of keto in the long run.


    What are some keto probiotic foods?

    When choosing probiotic foods and supplements for your ketogenic diet, make sure to avoid:

    • Added sugar - Probiotic drinks such as kombucha can be loaded with sugar which isn’t the best thing while trying to maintain ketosis.
    • Pickled foods in synthetic vinegar - Foods that contain synthetic vinegar do not contain live cultures of probiotics.

    Some probiotic-rich foods that you can use to supplement your diet are:

    Dairy-based probiotic foods:

    • Yogurt, low sugar varieties only&
    • Buttermilk
    • Milk kefir
    • Cheeses such as gouda, cheddar, etc.

    Fermented vegetables:

    • Sauerkraut
    • Kimchi
    • Jiang-gua (fermented cucumbers)

    Fermented beans:

    • Tempeh
    • Miso
    • Natto

    Fermented drinks:

    • Beet kvass
    • Coconut water kefir
    • Kombucha (low sugar)

    Keto-friendly probiotic supplements

    One of the main pillars of a keto is eating low amounts of carbohydrates. But controlling sugar cravings can be difficult when you're just starting your keto journey.

    Supporting your keto with probiotics rich in beneficial bacteria such as Leuconostoc mesenteroides and Lactobacillus reuteri can be a great way to get ahead of your cravings.

    1. mesenteroides produces mannitol — a low-calorie sugar alcohol— in the presence of glucose and fructose in your diet. A keto probiotic supplement such as Sugar Shift which contains both& L. mesenteroides and L. reuteri can possibly support your ketosis journey by reducing cravings and converting glucose and fructose.

    One of our customers, Ken Kubota, reported naturally getting into ketosis after regularly taking Sugar Shift, without being on a vegetarian ketogenic diet.

    It is also important to note that a diverse microbiome is associated with lean weight and better health. In contrast, a gut microbiome dominated by large populations of only a few bacterial types is associated with weight gain and metabolic syndrome.

    Sugar Shift has been formulated by studying the interactions between different gut bacteria and their by-products with the help of our Bioflux model. The following microbial strains work together to support your metabolism and immune health.

    Leuconostoc mesenteroides (TBC0037™) and Lactobacillus reuteri can convert simple sugars into mannitol. Mannitol can possibly have a&protective effect on the brain and inhibit alpha-synuclein aggregation, a hallmark of Parkinson’s disease.

    Pediococcus acidilactici (TBC0068™)&produces bacteriocin pediocin A, which is known to have antiviral and anti-listerial properties.

    Lactobacillus plantarum (TBC0036™) helps break down glyphosate, a potent herbicide present in your food, to its&basic components, phosphate, carbon, and water.

    Bacillus subtilis (DE111®), Bifidobacterium longum, and Bifidobacterium bifidum&control pathogen populations and promote the production of butyrate by gut bacteria which assists in essential functions such as digestion and staving off harmful bacteria. It also boosts the immune system.

    Ben Azadi, the founder of The Keto Kamp, explores how different alternative health approaches, such as a ketogenic diet and intermittent fasting, can help you become the healthiest version of yourself.

    In this episode of The Keto Kamp, How The Gut Microbiome Could Drive Brain Disorders,&I&break down how the unique formula of&Sugar Shift can support you on your Keto journey.

    Is a prebiotic keto-friendly?

    Yes, prebiotics such as inulin, are indigestible fibers that can help the well-being of probiotics such as Bifidobacteria, which can suffer in a ketogenic environment.

    Do probiotic pills have carbs?

    1 gm of inulin (prebiotic) provides roughly 1.5 calories. A probiotic supplement enriched with inulin (50 mg per serving) will roughly have 1/10 of a calorie.

    Can I have probiotic yogurt while on Keto?

    Probiotic yogurt can positively&affect your immune health. But watch out for added sugar, as that can disrupt ketosis. Here is a great recipe for making your own yogurt. Better yet, make your own fermented milk with our probiotic.


    Keto and immune system

    T-cells are white blood cells that are a part of your immune system that help you fight off infections.Research suggests that a ketogenic diet can enhance the response of T-cells in the production of cytokines— signaling molecules that trigger activity in other immune cells.

    How does keto affect your immune system?

    A ketogenic diet leads to increased ketones in the body. Ketone bodies such as BHB (beta‐hydroxybutyrate)&enhance T-cell (immune) response in the production of cytokines and support the formation of memory T-cells.

    Memory T-cells are immune cells that respond faster to encounters with repeat pathogens.

    Can keto help with inflammation?

    Inflammation is your body’s immune response to things that cause it harm. High-sugar diets have been found to&trigger persistent low-grade chronic inflammation in the body.

    BHB (a ketone body) has been found to counteract this immune response and help&subside chronic inflammation.


    The big question: what kind of fat is good for keto?

    Over the last few decades, fat somehow became unanimous with bad. But new research is showing that this isn’t always true. It turns out that cholesterol and saturated fats do not equal heart disease. Avoid all seed oils (corn, soybean, safflower, etc.) as they are highly processed and inflammatory.

    Dietary fat can come in any of these forms:&

    • saturated fatty acids,
    • monounsaturated fatty acids,&
    • polyunsaturated fatty acids, and
    • trans fatty acids (Manmade hydrogenated fats).

    While planning your keto meals, pick:

    • grass-fed or pasture-raised over grain-fed meats (beef, lamb, poultry),
    • animal fats (duck fat, ghee, lard) over highly processed refined oils,
    • wild game,
    • fatty seafood& - salmon, sardines, mackerel
    • eggs and dairy (cheese, yogurt, etc. in moderation),
    • Fatty fruit (avocados), nuts and seeds.

    Keto, gut health, and probiotics

    Your gut microbiome is essential in keeping you in top shape. Its benefits range from maintaining the integrity of your gut barrier, enhancing immune function, fighting off pathogens, producing and supporting the growth of bioactive compounds such as Pediocin A, as well as synthesizing vitamins such as Vitamin K.

    A ketogenic diet has been shown to support the prevention of metabolic conditions such as obesity, type 2 diabetes to neurodegenerative health conditions such as Parkinson’s and Alzheimer’s.

    But long-term exclusive keto has the inherent drawback of lacking indigestible plant fibers such as inulin and lactulose that feed the broader gut flora. This lack of fiber can become an issue if the diet doesn’t have flexible additions of high-fiber foods.

    Probiotics such as&Sugar Shift can help you bridge the gap between reaping the benefits of being in ketosis and keeping your gut microbiome thriving.

    Want to learn more about Keto or Sugar Shift? Check out these episodes at Keto Kamp with Ben Azadi, Life's Best Medicine with Dr. Brian Lenzkes, and Defiant Health Radio!

    With gratitude,

    Martha Carlin photo Martha Carlin, is a “Citizen Scientist”, systems thinker, wife of Parkinson’s warrior, John Carlin, and founder of The BioCollective , a microbiome company expanding the reach of science and BiotiQuest, the first of it’s kind probiotic line. Since John’s diagnosis in 2002, Martha began learning the science of agriculture, nutrition, environment, infectious disease, Parkinson’s pathology and much more. In 2014, when the first research was published showing a connection between the gut bacteria and the two phenotypes of Parkinson’s, Martha quit her former career as a business turnaround expert and founded The BioCollective to accelerate the discovery of the impact of gut health on all human disease. Martha was a speaker at the White House 2016 Microbiome Initiative launch, challenging the scientific community to “think in a broader context”. Her systems thinking background and experience has led to collaborations across the scientific spectrum from neuroscience to engineering to infectious disease. She is a respected out of the box problem solver in the microbiome field and brings a unique perspective to helping others understand the connections from the soil to the food to our guts and our brains.

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