Researchers compared how two different diets affected the gut bacteria of people with obesity and prediabetes. One group ate a ketogenic (keto) diet—low in carbs, high in fat—while another group ate a regular balanced diet with the same calories. After just 2 weeks, the keto diet made significant changes to the types and functions of gut bacteria, while the regular diet didn’t. The keto diet reduced certain beneficial bacteria but increased others, and changed how genes in the gut work, particularly those involved in energy use and vitamin production. These changes might explain why keto diets can help some people lose weight and improve their health.

The Quick Take

  • What they studied: Whether a keto diet changes gut bacteria differently than a regular diet when both diets have the same number of calories
  • Who participated: People with severe obesity (BMI over 35) who had prediabetes—meaning their blood sugar was higher than normal but not yet diabetic. The study also included healthy people as a comparison group.
  • Key finding: The keto diet caused rapid and significant changes to gut bacteria composition and function within just 2 weeks, independent of calorie reduction. The regular diet did not produce these same changes, even though both diets had equal calories.
  • What it means for you: If you’re considering a keto diet for weight loss or blood sugar control, know that it works partly by changing your gut bacteria in ways a regular calorie-restricted diet doesn’t. However, this is a short-term study, so we don’t yet know if these changes are beneficial long-term or if they help with sustained weight loss.

The Research Details

This was a randomized controlled trial, which is considered one of the strongest types of research. Researchers randomly assigned people with obesity and prediabetes to follow either a keto diet or a standard balanced diet for 2 weeks. Both diets reduced calories by 30% to make them fair comparisons. Before and after the diets, researchers collected stool samples and analyzed them using advanced genetic sequencing to identify all the bacteria present and what genes those bacteria contained. They also collected samples from healthy people to see how their gut bacteria compared.

The researchers used whole-genome metagenomic sequencing, which is a fancy way of saying they read the complete genetic code of all the bacteria in the stool samples. This allowed them to identify not just which bacteria were present, but also what functions those bacteria could perform in the gut.

This research approach is important because it goes beyond just counting bacteria—it shows what those bacteria actually do. By comparing the keto diet to a calorie-matched regular diet, researchers could prove that keto’s effects on gut bacteria aren’t just from eating fewer calories. This helps us understand the specific mechanisms of how keto works, which could lead to better treatments for obesity and prediabetes.

This study has several strengths: it’s a randomized controlled trial (the gold standard for research), it used advanced genetic analysis rather than simple bacterial counting, and it included a healthy control group for comparison. However, the study was very short (only 2 weeks), and the exact number of participants wasn’t specified in the abstract. Longer studies would be needed to determine if these changes persist and whether they actually lead to better health outcomes.

What the Results Show

At the start of the study, people with obesity and prediabetes had less diverse gut bacteria compared to healthy people—meaning they had fewer different types of bacteria. After 2 weeks on the keto diet, this diversity decreased even further. Specifically, bacteria called Lachnospiraceae (which are generally considered beneficial) decreased significantly, while Bacteroidaceae increased.

The keto diet also changed the functional capabilities of the gut bacteria. Genes involved in energy metabolism, amino acid synthesis (building blocks for proteins), and vitamin production were altered. These changes didn’t happen in the group eating the regular calorie-restricted diet, even though they ate the same number of calories.

Another important finding was that acetate—a short-chain fatty acid produced by gut bacteria—increased significantly in people on the keto diet. Acetate is thought to be beneficial for metabolism and may help explain some of keto’s health effects.

The study found that the changes in gut bacteria happened quickly—within just 2 weeks. The fact that these changes occurred independently of calorie restriction suggests that the specific composition of the keto diet (high fat, low carbs) directly influences gut bacteria, rather than weight loss alone causing the changes. The researchers also noted that genes related to RNA modification and nucleic acid activity changed, though the practical significance of these changes isn’t yet clear.

Previous research has suggested that keto diets affect gut bacteria, but this study provides more detailed evidence by using advanced genetic analysis. It confirms that keto’s effects on the microbiome are distinct from simple calorie restriction. The findings align with other research showing that diet composition—not just calories—shapes which bacteria thrive in our gut.

This study only lasted 2 weeks, so we don’t know if these bacterial changes persist over months or years. The abstract doesn’t specify the exact number of participants, making it hard to assess the study’s statistical power. We also don’t know if these bacterial changes actually lead to better health outcomes or sustained weight loss. Additionally, the study only looked at people with obesity and prediabetes, so results may not apply to people of normal weight or those without blood sugar problems. Finally, individual responses to diet vary greatly, so some people might experience different changes than what was observed on average.

The Bottom Line

If you have obesity and prediabetes and are considering a keto diet, this research suggests it may work through mechanisms beyond simple calorie reduction—specifically by changing your gut bacteria. However, this is early-stage research, and we need longer studies to confirm whether these bacterial changes lead to lasting health benefits. Talk to your doctor before starting any restrictive diet, especially if you take medications for blood sugar or other conditions. A moderate confidence level is appropriate here—the research is solid but limited to a 2-week timeframe.

This research is most relevant to people with obesity and prediabetes who are interested in understanding how keto diets work. It may also interest people with type 2 diabetes, though this study didn’t include diabetic patients. Healthcare providers treating metabolic disorders should be aware of these findings. People without weight or blood sugar problems probably don’t need to change their diet based on this single study. Pregnant women, people with certain medical conditions, and those taking specific medications should consult their doctor before trying keto.

This study shows changes happen within 2 weeks, but that doesn’t mean health benefits appear that quickly. Weight loss typically takes several weeks to become noticeable, and improvements in blood sugar control may take 4-12 weeks or longer. The long-term sustainability and health benefits of these bacterial changes remain unknown and require further research.

Want to Apply This Research?

  • Track daily macronutrient ratios (percentage of carbs, fats, and proteins) and correlate them with weekly measurements of energy levels, digestion quality (bloating, regularity), and blood sugar readings if available. This helps users see if their specific diet composition affects how they feel.
  • If trying a keto diet, use the app to log meals and monitor the carb-to-fat ratio daily. Set reminders to track digestive symptoms and energy levels to identify personal patterns. Users can also log any blood sugar readings if they have a glucose monitor.
  • Establish a baseline of current gut health markers (digestion quality, energy, bloating) before dietary changes. Then track weekly for at least 8-12 weeks to see if changes in diet composition correlate with improvements in these markers. Compare results between different diet approaches to find what works best individually.

This research describes what happened in a 2-week study and should not be considered medical advice. The ketogenic diet is a significant dietary change that may not be appropriate for everyone, especially people taking medications for blood sugar, heart conditions, or kidney disease. Before starting a keto diet or any restrictive diet, consult with your doctor or registered dietitian, particularly if you have prediabetes, diabetes, or other medical conditions. Individual responses to dietary changes vary widely. This study shows correlation between diet type and bacterial changes, but does not prove that these changes cause health improvements. Long-term safety and effectiveness of ketogenic diets for weight loss and metabolic health require additional research.