Keto diet may increase 'bad' cholesterol, reduce bacterial diversity in the gut

• The ketogenic diet may help with short-term weight loss, but there are concerns about its long-term effects on gut and cardiovascular health.
• A recent 12-week study involving 53 healthy adults adds to these concerns, suggesting that the ketogenic diet may support weight loss but not improve heart health markers and could negatively impact gut microbiome diversity.
• In contrast, a low-sugar diet appears to contribute to weight loss and lower cholesterol without affecting the gut microbiome.
• Health experts have differing opinions on the ketogenic diet, but they unanimously recommend low-sugar intake along with healthy eating patterns for better overall health.

A new randomized control trial published in Cell Reports Medicine involved 53 healthy adult volunteers following one of three diets — ketogenic, low-sugar, or moderate-sugar — for 12 weeks.

Ketogenic (keto) diets significantly reduce carbohydrate intake, often at the expense of high-fiber, plant-based foods, while emphasizing high-fat options.

In contrast, low-sugar diets only limit added sugars and naturally occurring “free” sugars like those present in honey, syrups, and juices, allowing for more flexibility and the inclusion of all healthy food groups.

Results showed that both ketogenic and low-sugar diets both led to weight loss. However, the ketogenic diet adversely affected the gut microbiome diversity and did not improve cardiovascular health markers, while the low-sugar diet showed improved cholesterol with no adverse effects on the gut microbiome.

These preliminary findings suggest that while both ketogenic and low-sugar diets may aid in weight management, low-sugar diets appear to be a healthier option for maintaining cardiovascular health and supporting a healthy gut microbiome —important factors in overall well-being.

Keto vs low-sugar diet: Impact on healthy adults

A collaborative study led by health and nutrition specialists at the University of Bath, United Kingdom, alongside researchers from several institutions, explored the effects of ketogenic and low-sugar diets on gut microbiota, cardiovascular health, and overall wellness in a generally healthy adult population.

Sixty participants aged 18 to 65, with a body mass index (BMI) between 18.5 and 29.9 (classified as normal to overweight), were recruited from the Bath area.

The selected participants met strict inclusion criteria, which required them to have no diagnosed metabolic diseases, such as diabetes, and no recent use of antibiotics , prebiotic or probiotic supplements, or any other substances that could influence the study outcomes.

Out of the recruited participants, 53 completed the full 12-week diet intervention, with slightly more females (classified by sex chromosomes ).

They were randomized into three diet groups:

1. a ketogenic diet group that reported less than 8% of daily calories from carbohydrates
2. a low-sugar diet group that reported less than 5% of daily calories from free sugars
3. a control group that reported a moderate carbohydrate and sugar intake, consuming approximately 18% of their calories from free sugars

The researchers gathered baseline data on various body measurements — including fat mass, bone mineral density , and waist circumference — as well as information on regular dietary habits, calorie expenditure, and blood pressure. They also assessed blood biochemical profiles, which included cholesterol and blood sugar levels.

Participants’ total nutrient intake was self-reported through weighted food diaries maintained throughout the study. There were no calorie restrictions.

The research was primarily conducted in natural living conditions to explore how diet affects health markers and gut microbiome composition outside of a controlled environment.

Keto diet promoted fat loss but reduced gut bacteria diversity

While the ketogenic diet successfully reduced body fat, at four weeks, the researchers observed a slight increase in LDL cholesterol and a notable increase in apolipoprotein B levels, which can contribute to the buildup of plaque in the arteries and increase the risk of heart disease.

By week 12, there were no significant differences in these markers between the ketogenic and control groups, indicating that the ketogenic diet had no substantial impact on cardiovascular health during the study period.

However, consistent with previous research , the ketogenic diet group experienced a significant decrease in gut microbiome diversity after just four weeks, which persisted at 12 weeks.

Specifically, participants following the ketogenic diet experienced largely reduced levels of Bifidobacteria , a bacteria commonly taken as a probiotic and known for supporting digestion and immune function .

Notably, those on the ketogenic diet consumed approximately 40% less dietary fiber—about 15 grams per day—compared to the control diet. The researchers suggest the reduced fiber intake likely hindered the survival and functioning of beneficial Bifidobacteria .

In contrast, compared to the control group, individuals on the low-sugar diet achieved reductions in body fat and total cholesterol, especially LDL cholesterol, without negatively impacting their gut microbiota after 12 weeks.

However, the results should be interpreted with caution due to the self-reported nature of dietary intake, the small sample size, the short duration of the study, and limited generalizability to diverse populations, among other potential limitations.

Low-sugar diets might be the healthier, safer option

While the ketogenic diet has consistently been shown to support short-term weight loss , recent studies similarly indicate it may reduce diversity in gut microbiota, particularly leading to a rapid decline in Bifidobacteria .

Studies caution that this reduction in healthy gut bacteria may negatively impact colonic health , and contribute to risks of obesity , type 2 diabetes , and depression . The ketogenic diet also raises concerns about nutrient deficiencies when sustained over the long term.

Alyssa Simpson, RDN, CGN, CLT , a registered dietitian, certified gastrointestinal nutritionist, and owner of Nutrition Resolution in Phoenix, AZ, who was not involved in the study, agreed with the study’s authors that a low-sugar diet might be a more sustainable and appropriate option for long-term weight loss and overall health.

“ Existing recommendations already advise reducing free sugars and added sugars to improve health, particularly to lower the risk of cardiovascular disease and other metabolic issues ,” she told MNT .

She explained that a low-sugar diet reduces LDL cholesterol levels, whereas high saturated fat intake and low fiber consumption associated with low-carbohydrate diets can lead to increased LDL levels and higher cardiovascular risks.

She said that based on what we currently know, “free-sugar restriction is a more heart-healthy option” than a ketogenic diet.

Simpson summarized what a healthy, low-sugar diet could look like in practice:

“A healthy, free-sugar-restricted diet would focus on nutrient-rich whole foods such as fruits, vegetables, lean proteins, and whole grains, while limiting sugary snacks, beverages, and processed foods with added sugars. It can seamlessly integrate with balanced diets like the Mediterranean or plant-based diets , which also limit sugar intake.”

She noted that low-sugar diets are generally more sustainable than “extreme diets like keto,” as they are less restrictive and more balanced and practical to follow long-term.

Keto diets may still benefit cardiometabolic health

Lucia Aronica, PhD , a lecturer and researcher in personalized nutrition and epigenetics at Stanford Prevention and Research Center, Stanford University, in CA, who was not involved in the research, offered a different perspective.

She argued that while free-sugar restriction can be beneficial, claiming it is the best option for cardiometabolic health oversimplifies the issue.

“The key is personalization. What works best can vary greatly between individuals. Some may see significant improvements just by cutting free sugars, while others might benefit more from a broader carbohydrate restriction,” she stated.

Aronica emphasized that a properly structured ketogenic diet—unlike what she observed in the participants of this study—can significantly enhance metabolic health , particularly for individuals with insulin resistance or metabolic syndrome, which were not the subjects of this study.

She also highlighted a decrease in average ketone levels from week 4 to week 12, indicating that participants likely moved out of nutritional ketosis during the ketogenic diet intervention. “This suggests reduced adherence to the ketogenic diet over time, potentially blunting its metabolic benefits,” she said.

Aronica emphasized:

“While [the low-sugar] approach can be beneficial, as I mentioned before, it’s important not to oversimplify nutrition recommendations. Yes, reducing added sugars aligns with current dietary guidelines and can benefit many people. However, focusing solely on free sugars might miss the bigger picture of metabolic health.”

Still, a low-sugar diet is generally considered safe and healthy for most adults, while the potential risks of the ketogenic diet are still under scientific debate. So, before starting any restrictive eating plan, consult with your doctor or a registered dietitian to find the approach that’s best for you.