Important: 5 Most Dangerous Side Effects of Low Carb Diet

Written By

Rhea Dali

Expert Reviewed By

Dr. Lauryn Lax, OTD, MS

Dr. Lauryn, OTD, MS is a doctor of occupational therapy, clinical nutritionists and functional medicine expert with 25 years of clinical and personal experience in healing from complex chronic health issues and helping others do the same.

Low Carb Diet, Pen, Note, Tape Measure And Vegetable Salad

Low Carb is So Hot Right Now…Until You Ask Your Gut

Low carb is the new black—all the rage, at least at the time of this writing.

The premise: Cut the carbs. Bring on the fat. Lose the weight, body fat, fatigue and brain fog.

Sounds too good to be true; yet with nearly 1 in 3 millennial adopters and counting according to a 2019 Business Insider poll of over 1000 people between ages 18 and 29, it doesn’t look like the low carb movement is going anywhere soon.

Despite the hype and before-and-after underwear photos on Infomercials, however a key issue no one is talking about in the low carb movement is what happens to the gut biome—and perhaps why trending data and research is showing, for the long-term at least, low carb diets are not pretty.

What Is Low Carb Diet?

Low Carb Diet Plan, Vegetable Salad On The Table

Low carb is nothing new, dating back to 1972 when Dr. Robert Atkins challenged the “status quo” to America’s “Basic 4” lower-fat food guide pyramid at the time,  rolling out his first iteration of the Atkins’ diet with his book “Dr. AtkinsDiet Revolution”. The work was inspired by his own medical research and experimentation using carbohydrate restriction, as opposed to calorie restriction, for weight loss results without significant hunger. In the book, he explained his findings on balancing blood sugar and shedding pounds via low-carb dieting, suggesting people eat under 20 grams of carbs per day, paired with high protein, high fat and low carb, low fiber veggies like leafy greens.

At the time, The Atkins Diet seemed scandalous—too good to be true. Seriously “I can eat butter and bacon and lose weight?” Nevertheless, it got a few early adopters; until, a few years into it, America’s heart disease and underlying obesity epidemic began to really slowly pick up, paving way for the low fat era to take center stage.

In 1977, the U.S. Senate’s Select Committee on Nutrition and Human Needs, chaired by George McGovern, put the diet-heart hypothesis on the national agenda with its publication of the “Dietary Goals in the United States.”  This report was spurred by an increased record number of deaths and heart disease within the Senate and House committee members themselves within a two year time frame, and it was the first comprehensive statement by any branch of government on risk factors in the American diet.  Not knowing what had truly caused several heart attacks to occur to close political members, Senator McGovern stated: “Too much fat, too much sugar or salt, can be and are directly linked to heart disease, cancer, obesity and stroke,”—poising fat as the “enemy” that all dieters of the 80’s and 90’s know all too well. The publication of the Senate’s report led to an updated publication every five years of the U.S. Dietary Guidelines. For the first time, the federal government told Americans to eat more fruits, vegetables, whole grains, poultry, and fish, and to cut the fat.

Even though no valid study to date has actually found that a significant amount of heart attack patients actually have high cholesterol as the Senate committee claimed, this was overshadowed by the belief that eating fat, must cause us to get fat.

Never mind that the real culprit—a disrupted gut microbiome from the growing refined foods and processed foods industry, sugar and high-fructose corn syrup explosion and Atkins’ revolution was also at play in the background.

The low fat era had “a moment”, characterized by Slim Fast shakes, 100 calorie snack packs, low-fat and fat free versions of everything, from Skippy peanut butter to fat free Kraft singles, Parkay “I Can’t Believe it’s Not Butter”, and 40-calories Nature’s Own wheat bread, Taebo infommercials, and images of Suzanne Sommers and Richard Simmons in tights and sweat bands still dancing in our heads. Until, Americans woke up again in the late 1990’s and early 2000’s that something still was not working. Americans’ waistlines were still growing.

Enter: Dr. AtkinsNew Diet Revolution, a New York Time’s bestseller in 1997—the perfect opportunity for another stab at the low carb, high fat diet propaganda. Atkins’ was followed by the Zone, South Beach and most recently keto—seemingly simple solutions that promised incredible results.

Yet…the overweight and obesity epidemic that both these diets—low carb and low fat—claim to fight has only continued to get worse, not better. Jumping from practically non in the 1960s and 70’s—when Dr. Atkins first proposed we cut the carbs; then to 13% in 1980 to over 34% in 2008 to nearly 70% in 2020 where roughly 2 out of 3 U.S. adults are overweight or obese, and 1 in 5 kids—the little creatures who should be the most vibrant and healthiest versions of themselves. Obesity aside, the chronic disease epidemic—autoimmune disease, cancer, heart disease, mental health illness like anxiety is at an all time high, with over 60% of Americans also having a lifestyle and nutrition induced disease.

Is it because American’s aren’t eating fat and they are eating too many carbs still?

Nope. Many are watching their carbs and actually making peace with fat. [In fact, of all developed nations, Americans eat the least amount of fiber! People in traditional hunter gatherer tribes and non-westernized societies intake 50 to120  grams of fiber per day, whereas we only get about 15 grams.

Is it because Americans have no willpower and don’t know anything about “healthy eating”?

Nope again. According to a poll by the Food Industry Executive 93-percent of consumers want to eat healthy and want all-natural and organic foods, and over 60% report trying to make healthy choices most or all of the time—about the same amount of people who are actually overweight.  And because of the COVID-19 pandemic alone, the Industry also saw a 30% uptick in consumers taking more supplements and eating more “functional foods”—such as paleo-approved bars and chips, keto shakes, and foods with added vitamins and minerals.

Couple Eating Low Carb Diet

But something is clearly still not working.

Oh yes, never mind us also mentioning that Dr. Robert Atkins later died of a heart attack in 2004…from his own diet? His wife, Mrs. Atkins, initially refused an autopsy be performed on her husband. However, a couple years later, both she and his physician shared that he did have health complications in a New York magazine article that leaked, “Of course, Atkins did have blockage. In 2001, his coronary arteries were perhaps 30 to 40 percent blocked, according to Patrick Fratellone, his cardiologist and employee.”

Disclaimer: We will all die from something. No one is immune from death or unfortunate circumstances in our health. Additionally, not all low carb diets are “bad”; just like not all low fat diets are “bad”. However, the bigger piece to the puzzle here that has been missing the entire time has do the gut microbiome!

As a refresher: When we speak of ‘the gut microbiome’, we’re primarily talking about the trillions of microorganisms that inhabit the large intestine, or colon that influence our total health. Their collective genome is enormous (about 3 million genes versus 23000 genes in a human being) and they produce thousands of substances that can positively or negatively affect our energy, hormones, blood sugar, digestion, immune system, brain function, and everything in between, depending on what we feed them.

Regardless of what diet you prescribe to—low carb, low fat, vegan, vegetarian, fruititarian, and beyond—the “results” you see and how you feel at the end of the day all come down to what the diet does to and for your gut microbiome.


Meet Katie. 37. Die hard keto follower. She does an excellent job of keeping her net carbs under 20 each day. She also has severe constipation, low T3 hypothyroidism, slowly progressing inflammatory bowel disease, occasional stomach pains under her right and left rib cage, low energy—needing her butter coffee plus MCT oil every morning to function, only gets about 5 hours of solid sleep, and she hasn’t had a period in 4 years.

The one key theme behind her health history? Her symptoms started about a year after cutting the carbs.

There are many reasons why balance—not restriction—does a body and biome good; especially when we are talking about carbs.

These are facts that no keto book, or even low fat diet advertisement, is really sharing with you either. Some side effects I’ve seen several patients experience on a LONGER-TERM super low carb, high fat diet.

Side Effects of LONGER-TERM Super Low Carb, High Fat Diet

Side Effects Of Low Carb Diet

#1. Gut Dysbiosis & Leaky Gut.

High fat, low carb diets can be excellent for “starving” out unhealthy pathogenic bacteria that have resulted from a former life of antibiotic therapy, artificial sweeteners, refined and processed foods and other dietary imbalances. However, just like a long-term low FODMAP diet results in insufficiency dysbiosis—killing off healthy bacteria as well—the same thing can happen with a high fat, carb-restricted approach. A high-fat diet has been found to reduce healthy colonic bacteria overall while boosting total anaerobic microflora and Bacteroides counts. Bacteroides are normally beneficial organisms, but overgrowth is associated with inflammatory bowel disease, constipation and bloating, SIBO, impaired GI motility and autoimmune disease.  Under no-carb feeding conditions, immune cells actually have a diminished ability to generate an immune response at all, making you more susceptible for the early stages of autoimmune conditions like irritable bowel disease, Hashimoto’s and blood sugar and insulin production resistance (type 1 diabetes). A high fat, low fiber diet also increases intestinal permeability – that is, it causes leaky gut, by turning off the genes that code for proteins that comprise tight junctions, the ‘seals’ between neighboring intestinal cells. Tight junctions in our intestines are intended to stop unwanted or dangerous gut contents – such as undigested proteins and bacterial toxins – from leaking through the gut wall and into the bloodstream. One of those toxins is endotoxin or LPS”, a component of the cell walls of gram negative bacteria. Saturated fat intake, in particular, increases the absorption of endotoxin from the gut into the bloodstream and the resulting endotoxemia triggers inflammation associated with blood sugar intolerance, weight gain and oxidative stress.

#2. High Cholesterol.

Contrary to popular belief, high cholesterol does not necessarily mean you’ll have a heart attack. Instead, if you see this marker, high cholesterol means your body is inflamed, stressed and both your gut bacteria and gallbladder are not metabolizing your fats well—your gallbladder is congested and not working appropriately (remember: the gallbladder helps breakdown fat). Additionally, your gut bacteria can’t break down the fats you eat fast enough—dysbiosis is at play. One patient came to me with a total cholesterol of 600 after adopting a high fat, moderate protein, low carb diet for just one month! We later discovered the real culprit underneath: Candida, SIBO and no gallbladder. On a side note, if you’ve had dysbiosis from too much sugar, too many carbs and an obese lifestyle, some of these patients actually see decreases in cholesterol initially as the body and biome also comes back to balance. (Again, it’s all about what your gut bacteria are doing).

#3. Right Sided Abdominal Pain.

If your right side, under your rib cage, hurts when you eat, that’s your gallbladder speaking. Additionally, weight loss resistance, needing coffee to “poo”, skin problems, hormone imbalances, a yellow cast to your eyes or reddened skin—especially your palms, recurrent SIBO, fish oil burps, nausea or queasy stomach when you eat fats or a bitter metallic taste in your mouth are also indicators a high fat, lower carb diet is probably not for you.

#4. Hypoglycemia, Low Energy & Mental Fatigue.

High fat, low carb can balance blood sugar, spark energy and ignite brain power for some—after all your brain is made up of 60% fat itself. However, if your body is not digesting or absorbing fats well, your HPA axis is stressed or you’re not eating enough overall (because fats fill you up and blunt your hunger), then you’ll experience the opposite. 

#5. Constipation.

Simply put: healthy poo and waste is created by fiber and “bulk” in your stool. No fiber to help push food through and help your bacteria and wastes get excreted out the back door, you’ll more than likely feel stuck (or feel like you also need to rely on your butter coffee to go #2). 

Ketosis and the fasting/intermittent fasting lifestyle that often goes hand-in-hand with it are often touted on Instagram or Facebook forums like a badge of honor with people bragging about how they broke through the “keto flu” alive; went a total of 11 days just drinking water and bone broth; or only got 8 net carbs today—however, beyond a short-term reset, what are you really gaining?

Don’t let these facts stop you. Low carb really great for some people—especially epilepsy brain injured patients and people with mental health disorders — who’s gut microbiomes are a wreck—needing a reset from a neurological disease connected to extreme dysbiosis itself—keto helps their gut biome go one extreme to another. Likewise, the low carb approach can be really great kickstart for the “typical” American who actually does have a lot of dysbiosis, associated with blood sugar problems, extra body fat and weight to lose, sugar addiction.

However, once more, after the short-term reset, say past a year’s time, you can risk sending your body—and your biome—to the other extreme, eradicating healthy gut bacteria and the foods that feed them if you don’t integrate a fiber-focus and pre-biotic mindfulness to your lower carb mix.

When you starve the gut bacteria of their #1 fuel source, they have no need to live or work for you. Healthy guys can’t multiply. Short chain fatty acids—their pathogen and toxin defeating chemicals can’t be produced. And you’re left with a dysbiotic gut biome that becomes so accustomed to digesting fats and proteins, that even if you do want to try to eat carbs again, it may feel like a rocky road with some unpleasant symptoms like constipation, bloating, blood sugar spikes. Your bacterial landscape has been in a drought and needs to be regrown in order to not die if the apocalypse happens and your Perfect Keto bars and test strips are nowhere in sight. These are facts Healthy Eating Culture is not telling you—what happens to your gut biome on any restricted, “clean eating” or fad diet.

Just some food for thought.

Balance (with some carbs included) do a body and biome good. Microbiota-accessible carbohydrates (MACs) in particular are the main source of carbon for colonic bacteria and favor an increase in beneficial bacteria.  Some “gut loving” carbs to consider adding back in your diet to increase beneficial bacteria like Bifidobacteria, Lactobacilli and Akkermansia muciniphila include:

Prebiotics & MACs”

Veggies For Low Carb Diet

Most fruits and veggies will give you a benefit, but here are some of the top hitters:

  • Apples
  • Asparagus
  • Artichoke
  • Berries
  • Carrots
  • Cooked and cooled sweet potatoes, red potatoes and fingerling potatoes
  • Cooked and cooled rice, gluten free oats and lentils/legumes
  • Cruciferous Veggies (broccoli, cauliflower, brussels, cabbage)
  • Dark leafy greens
  • Garlic
  • Green tipped bananas and plantains
  • Leeks
  • Pears
  • Winter Squash

*Cook, sautée and/or lightly roast veggies to aid in better digestion if you tend to bloat or constipate easily.

Additionally, probiotics—found in foods and supplements—can help. My top recommended probiotic at the moment is actually a “synbiotic”—probiotic and pre-biotic combined, called Seed Probiotic. Additionally, some popular types or fermented foods include the following.

Sauerkraut: Made from finely chopped cabbage fermented by several lactic-acid-producing bacteria.

Kimchi: Traditional Korean dish made from fermented cabbage, radish, scallion and cucumber combined with a variety of other seasonings.

Kombucha: A fermented drink usually a combination of sweetened black or green tea and a symbiotic colony of bacteria and yeast (a ‘SCOBY’).

Kefir: Fermented drink traditionally made with a base liquid of milk (but can be made with water and coconut water too) and grains of bacteria and yeast.

Protocol for Gradually Reintroducing Carbs + Building Up Your Biome (if you are carb sensitive”)

What to do if you want to increase carbs, but you feel bloated after just one bite of a potato or banana?

Prebiotics and MACs can be problematic for people with lactose intolerance, IBS, SIBO or other gut conditions (this is probably the reason why you were avoiding them in the first place!). That said, the key here is actually two fold: #1. Actually work with a practitioner to identify your gut pathology (bacterial overgrowth, not enough probiotic rich bacteria, etc.) and “clean up” shop inside with a targeted dysbiosis-restoration approach using probiotics, prebiotics, short chain fatty acids and possibly some antimicrobial herbs (everyone is different); and #2.  The “go low and slow” method can work wonders, as well as therapeutic use of supplemental fibers and probiotics to boost your biome.

A general slow-fiber introduction protocol I will utilize for most folks in conjunction with some deeper digging entails two steps – the first step entails bringing in probiotics (about 15 Billion of diverse strains), and even various botanicals designed for bacterial overgrowth (like those with berberine), in addition to introducing a high-potency, broad-spectrum enzyme (lipases, cellulases, amylases, proteases) to take with the meal and again 60-90 min after the meal. The next step: After a 3-4 week regimen of getting the basics of the gut in order, bringing in more high-fiber foods within a mixed meal gradually to gauge response. Sometimes, people respond poorly to fibers due to lack of an adequate mucin layer, so the husks of fibers become irritating for the gut lining. In that case, focusing on aloe, glutamine, and zinc, to name a few. Eugenol, a compound from a variety of plants, especially herbs/spices (e.g., tulsi, oregano, thyme, dill) may even help stimulate formulation of that mucin layer as shown in some studies.

Here’s to carb freedom.


Ann F. La Berge, How the Ideology of Low Fat Conquered America, Journal of the History of Medicine and Allied Sciences, Volume 63, Issue 2, April 2008, Pages 139–177,

Wiley, C. 2019. Consumers Say They Want to Eat Healthy. Food Industry Executive.

Hartman Group. 2020. Functional Food & Beverage 2020 Report Highlights.

Barnard, N. (2004). The Controversy Over Dr. Atkins’ Health. Good Medicine, 13(2/3), 6–8.

Gardner CD, Trepanowski JF, Del Gobbo LC, et al. Effect of Low-Fat vs Low-Carbohydrate Diet on 12-Month Weight Loss in Overweight Adults and the Association With Genotype Pattern or Insulin Secretion: The DIETFITS Randomized Clinical Trial [published correction appears in JAMA. 2018 Apr 3;319(13):1386] [published correction appears in JAMA. 2018 Apr 24;319(16):1728]. JAMA. 2018;319(7):667-679. doi:10.1001/jama.2018.0245

Seitz J, Belheouane M, Schulz N, Dempfle A, Baines JF, Herpertz-Dahlmann B. The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa. Front Endocrinol (Lausanne). 2019;10:41. Published 2019 Feb 12. doi:10.3389/fendo.2019.00041

Ang, Qi & Alexander, Margaret & Newman, John & Tian, Yuan & Cai, Jingwei & Upadhyay, Vaibhav & Turnbaugh, Jessie & Verdin, Eric & Hall, Kevin & Leibel, Rudolph & Ravussin, Eric & Rosenbaum, Michael & Patterson, Andrew & Turnbaugh, Peter. (2020). Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells. Cell. 181. 10.1016/j.cell.2020.04.027.

Retterstøl K, Svendsen M, Narverud I, Holven KB. Effect of low carbohydrate high fat diet on LDL cholesterol and gene expression in normal-weight, young adults: A randomized controlled study. Atherosclerosis. 2018;279:52-61. doi:10.1016/j.atherosclerosis.2018.10.013

Paoli, A., Mancin, L., Bianco, A., Thomas, E., Mota, J. F., & Piccini, F. (2019). Ketogenic Diet and Microbiota: Friends or Enemies?. Genes, 10(7), 534.

Grigolon, R. B., Gerchman, F., Schöffel, A. C., Hawken, E. R., Gill, H., Vazquez, G. H., Mansur, R. B., McIntyre, R. S., & Brietzke, E. (2020). Mental, emotional, and behavioral effects of ketogenic diet for non-epileptic neuropsychiatric conditions. Progress in Neuropsychopharmacology & Biological Psychiatry, 102.

Dashti HM, Mathew TC, Hussein T, et al. Long-term effects of a ketogenic diet in obese patients. Exp Clin Cardiol. 2004;9(3):200-205.

Singh, R.K., Chang, H.W., Yan, D., et al. (2017), Influence of diet on the gut microbiome and implications for human health. J Transl Med.;15(1):73.

Fava, F., Gitau, R., Griffin, B.A., Gibson, G.R., et al, (2013), The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’ population. Int J Obes (Lond).;37(2):216-23.

Daïen, C. I., Pinget, G. V., Tan, J. K., & Macia, L. (2017). Detrimental Impact of Microbiota-Accessible Carbohydrate-Deprived Diet on Gut and Immune Homeostasis: An Overview. Frontiers in immunology, 8, 548.

Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 2014;20(5):779-786. doi:10.1016/j.cmet.2014.07.003

Singh, R.K., Chang, H.W., Yan D, et al. (2017). Influence of diet on the gut microbiome and implications for human health. J Transl Med.;15(1):73.

Wexler, H.M. (2007), Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev.;20(4):593-621.

Wu, N., Yang, X., Zhang, R., Li, J. et al, (2013), Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microb Ecol.;66(2):462-70.

Tagliabuea, A., Ferraris, C., Uggeri, F., Trentani, C. et al (2017), Short-term impact of a classical ketogenic diet on gut microbiota in GLUT1 Deficiency Syndrome: A 3-month prospective observational study. Clin Nutr ESPEN;17: 33-37.

Fava, F., Gitau, R., Griffin, B.A., Gibson, G.R. et al (2012), The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’ population. Int J Obes (Lond).;37(2):216-23.

Cani, P.D., Bibilonim R., Knauf, C., Waget, A. et al (2008), Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes;57(6):1470-81. doi: 10.2337/db07-1403.

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