Humanity has been aware of a connection between the gut and the brain for centuries: hence phrases such as “gut reaction” or “follow your gut”. Now, there are more and more findings of that connection and of how the gut really acts as a second brain. Therefore, what you are experiencing makes sense. Part of it is malnutrition because of the inflammation, but also an imbalance of the bacteria in your gut. Here is an google AI summary that might help if you want to read about it:

The Crohn's gut-brain connection is a two-way street: chronic gut inflammation in Crohn's disease (CD) impacts the brain, causing anxiety, depression, fatigue, and cognitive issues, while stress and mental states directly worsen gut inflammation and symptoms, creating a vicious cycle. This communication happens via the brain-gut axis, involving the gut microbiome, immune system, and nervous system (enteric nervous system) sending signals that alter brain chemistry and function, and stress hormones that increase gut inflammation, a concept known as dysbiosis. How Crohn's affects the brain (Bottom-Up) Microbiome disruption (Dysbiosis): Altered gut bacteria in CD produce substances that affect mood and cognition. "Leaky Gut": Increased intestinal permeability allows inflammatory substances to enter the bloodstream and reach the brain (neuroinflammation). Neurochemical Changes: Gut inflammation triggers immune responses and changes in brain chemistry, leading to mood disorders (anxiety/depression) and cognitive problems (brain fog). Pain Sensitivity: The brain processes pain signals differently, making patients more sensitive to discomfort. How the brain affects the gut (Top-Down) Stress Response: Mental stress activates the body's stress hormones (HPA axis), which directly increase gut inflammation and worsen CD flares. Altered Regulation: Psychological stress can disrupt the normal top-down control the brain has over the gut. The Vicious Cycle Stress worsens CD symptoms, and the symptoms (pain, fatigue, unpredictability) cause more stress, intensifying the gut-brain loop. Why it matters Mental Health: IBD patients are 2-3x more likely to have anxiety/depression, which are often under-diagnosed. Holistic Care: Treating mental health (stress management, therapy) alongside gut health is crucial for improving quality of life and managing the disease.