BioManufacturing

Modern food processing has drastically altered our microbiomes in ways previously unseen, contributing to the rise of chronic diseases such as cardiovascular disease, neurodegenerative diseases like Parkinson's and Alzheimer's, nonalcoholic fatty liver disease, and colon cancer, all of which have become more prevalent in younger populations over the past 75 years. While medications for conditions like high blood pressure, high cholesterol, and hyperlipidemia are commonly prescribed, they do not address the root cause of these issues.
Processed foods are essentially reassembled products made from purified food components, losing vital elements found in whole foods. These foods are designed to have a long shelf life, requiring the addition of chemicals that inhibit microbial growth, which negatively impacts the microbiome. Research has shown that poor diets lead to unhealthy microbiomes.

Moderate coffee consumption is beneficial for the gut biome due to polyphenols, which are important for the brain-gut connection. Another good source of polyphenols, vitamins, and protein with low calorie density are mushrooms, which provide unique carbohydrates and make a hearty meat substitute. Additionally, naturally fermented cheeses are rich in microbes that support gut health, though the benefits are concentrated in the rind, which is often discarded.

For adults, plant-based diets are advisable, with occasional meat consumption being manageable for the gut. Red wine, as a fermented food, may offer some benefits, whereas beer does not contribute much besides social enjoyment. Water is crucial for maintaining proper gut function, as dehydration can lead to constipation and an unhealthy gut microbiome. Sugar, on the other hand, is detrimental, especially when consumed in response to stress or anxiety, leading to a cycle of poor dietary habits that exacerbate health issues.
Food companies have modified foods to improve taste and extend shelf life, but these changes have stripped away the health benefits, making processed foods less satisfying and more calorie-dense. 

The gut microbiome plays a crucial role in training the immune system to distinguish between beneficial and harmful bacteria, yet the rise of chronic diseases in the Western world is linked to gut dysbiosis—a state where the microbiome's composition or function is altered, driving disease. Once the gut ecosystem is disrupted, opportunistic species can take over, contributing to inflammatory diseases.
A healthy gut microbiome produces molecules that reduce inflammation, keeping the immune system calm. Despite the growing understanding of microbes, harmful bacteria represent only a small fraction of our microbial environment. The spread of Western lifestyles has led to an increase in chronic illnesses worldwide, highlighting the need to rethink how we care for our gut microbiomes.
Remarkably, humans host more microbial cells than human cells, making us more microbial than human. The gut is densely populated with diverse microbes, and fostering this diversity is key to better health. Our microbes rely on dietary fiber, found in plant-based foods, as their preferred energy source. A diet rich in whole grains, beans, vegetables, nuts, and fruits supports a diverse and healthy microbiome. In contrast, a diet low in fiber forces gut microbes to consume the mucus layer lining the gut, leading to inflammation and a breakdown of the gut barrier.
Promoting a healthy diet also involves considering what we drink. In North America, sugary sodas are prevalent, but healthier alternatives exist, particularly fermented drinks, which are simple to make and offer numerous health benefits. Sauerkraut and kimchi are two of the most accessible fermented foods available in grocery stores.