How Your Gut Microbiome Affects Energy Levels and Helps Fight Fatigue

The gut microbiome plays a central role in many aspects of human health, including energy production, metabolism and immune function. Understanding the connection between your gut and energy levels can provide actionable insights into combating fatigue. When the gut is balanced, nutrients are absorbed efficiently, inflammation is kept under control and the body produces energy more effectively. When it is out of balance, fatigue, sluggishness and poor recovery from stress or illness often follow. 

In this article, we explore how your microbiome influences energy, why imbalances are linked to fatigue-related conditions, and practical steps to support vitality. These insights are provided by Vivere's Head of Nutrition, Yusra Serdaroglu Aydin, a registered dietitian with a background in nutrition, food engineering and culinary arts. Her approach is grounded in science and shaped by a strong understanding of personalised nutrition and the human microbiome.

Here are the five biggest takeaways from this article about whether the gut microbiome can affect energy levels:

• The gut microbiome helps regulate energy by supporting nutrient absorption, reducing inflammation and fuelling mitochondria.

• A lack of butyrate-producing bacteria is linked with fatigue, especially in conditions like CFS/ME and long COVID.

• Many people with fatigue disorders also report IBS-type digestive problems, showing a strong gut–energy connection.

• The microbiome produces neuroactive compounds that can influence both brain function and energy levels.

• Supporting gut balance through a balanced diet, lifestyle, and personalised testing can make a meaningful difference in energy and resilience.

The gut microbiome plays a crucial role in converting food into usable energy. Beneficial bacteria break down fibres into short-chain fatty acids like butyrate, which fuel colon cells and support mitochondria, the body’s energy factories [1]. Some microbes also produce B vitamins and other cofactors that are essential for metabolism [2]. When the gut is diverse and balanced, this system runs smoothly, providing stable energy throughout the day.

When the microbiome is disrupted, however, the picture changes. Fewer butyrate-producing species means cells struggle to generate energy efficiently. Low microbial diversity is also linked with inflammation, which drains resources and increases oxidative stress [3].

The gut-brain axis further highlights the connection between energy and microbiome health. This communication network links the central nervous system with gut microbes, regulating mood, stress responses and sleep patterns. Disruptions in this axis can result in low energy and poor cognitive function [4]. 

Together, these changes create the perfect environment for fatigue, brain fog and slower recovery from daily activities.

The connection between gut health and energy becomes clearer in conditions where fatigue is severe and persistent. In Chronic Fatigue Syndrome (CFS), also called myalgic encephalomyelitis (ME), research has shown a core deficit in butyrate-producing bacteria compared to healthy individuals. This lack of butyrate may contribute to the exhaustion, poor recovery and cognitive problems people with CFS experience [5].

Long COVID shows similar patterns. Patients often report lingering tiredness and brain fog, and studies suggest changes in the gut microbiome and its chemical outputs may play a role. Neuroactive metabolites made by gut microbes can influence the nervous system, potentially adding to the fatigue symptoms seen in both CFS/ME and long COVID [6].

These conditions also highlight another link: digestive discomfort. Between 30% and 90% of people with CFS report IBS-like symptoms such as bloating, cramps, diarrhoea or constipation. This overlap suggests that gut disruption is not just a side effect but may be part of the underlying problem [7].

Common signs of CFS include [8]:

• Persistent fatigue despite enough sleep

• Sleep problems, including insomnia and sleeping too much

• Brain fog or difficulty concentrating

• Symptoms getting worse after physical or mental activity,

Optimising your gut to support energy levels involves dietary, lifestyle and supplementation strategies.

• Include a variety of plant-based fibres from vegetables, fruits, legumes and whole grains. Fibre nourishes beneficial bacteria that produce energy-supporting short-chain fatty acids [9].

• Fermented foods such as kefir, yoghurt, kimchi and sauerkraut introduce live bacteria that can enhance microbiome diversity.

• Prioritise micronutrient-rich foods containing iron, magnesium and B vitamins to support metabolic processes.

• Limit highly processed foods and added sugars that can promote the growth of less beneficial bacteria and impair energy production.

• Regular physical activity enhances microbiome diversity and improves mitochondrial efficiency, leading to sustained energy [10].

• Adequate sleep supports circadian rhythms, which influence microbial activity and energy metabolism.

• Stress management techniques such as meditation, deep breathing or gentle movement can reduce inflammation and support gut health.

Certain probiotics, prebiotics and micronutrients can provide additional support when dietary changes are insufficient. Probiotic strains such as Bifidobacterium and Lactobacillus have shown promise in improving energy and reducing fatigue in clinical studies [11]. Prebiotics like inulin and fructooligosaccharides feed beneficial bacteria and enhance their energy-supporting functions [12]. Micronutrient supplements like iron and magnesium may be necessary if dietary intake is inadequate or absorption is impaired due to gut imbalance [13].

While general strategies are helpful, the most effective approach involves understanding your unique microbiome profile. Personalised microbiome testing can identify specific bacterial imbalances, highlight nutrient needs, or specific markers that may affect energy. With this knowledge, nutrition and lifestyle recommendations can be tailored to your needs, helping restore energy more effectively and sustainably.

“Your gut is at the centre of how energised you feel each day. A healthy microbiome fuels your cells with key nutrients, supports stable blood sugar, manages inflammation and communicates directly with your brain to help you feel clear and focused. When the balance shifts, the effects show up quickly as tiredness, poor concentration and reduced resilience. Looking after your microbiome through foods your body needs, lifestyle choices and, where needed, personalised guidance is one of the most effective ways to improve daily energy and overall wellbeing.”

Vivere helps you take control of your health with personalised insights from state-of-the-art gut microbiome testing, nutritional guidance, science-backed supplements and expert support. Sign up today and start living better, for longer.

[1] The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication - Frontiers

[2] Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities - Nature

[3] Gut Microbiota Dysbiosis, Oxidative Stress, Inflammation, and Epigenetic Alterations in Metabolic Diseases - PMC

[4] The Gut-Brain Axis: Influence of Microbiota on Mood and Mental Health - PMC

[5] Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS - ScienceDirect

[6] A Narrative Review on Gut Microbiome Disturbances and Microbial Preparations in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Implications for Long COVID - PubMed

[7] Insights into myalgic encephalomyelitis/chronic fatigue syndrome phenotypes through comprehensive metabolomics - PMC

[8] Myalgic encephalomyelitis or chronic fatigue syndrome (ME/CFS) - NHS

[9] Dietary Fiber Intake and Gut Microbiota in Human Health - PMC

[10] The Crosstalk between the Gut Microbiota and Mitochondria during Exercise - Frontiers

[11] Mechanism of Action and Beneficial Effects of Probiotics in Amateur and Professional Athletes - Wiley

[12] Health Effects and Sources of Prebiotic Dietary Fiber - PMC

[13] Gut microbiome–micronutrient interaction: The key to controlling the bioavailability of minerals and vitamins? - PMC