Understanding the Gut Microbiome: Food as Medicine    

Food as Medicine: Understanding the Gut Microbiome

Did you know that your gut is home to around 100 trillion microorganisms?  

These gut microbiome, including bacteria, viruses, and fungi — play a crucial role in your health, from digesting food and absorbing nutrients to boosting your immune system and even affecting your mood.  

Recently, FemmePharma sat down with Dr. Katherine Sherif, professor of internal medicine who specializes in women’s health, to discuss this fascinating part of our bodies and how we can improve it to promote well-being as we age. 

What is the intestinal microbiome?  

First, let’s start with an overview on exactly what the microbiome is. 

The intestinal microbiome refers to the bacteria, viruses, and fungi that live in our digestive tract — making up the areas from our mouth down to our anus.The small intestine, about 20 feet long, hosts numerous bacteria crucial for nutrient absorption and intestinal protection. The colon, or large intestine, houses the majority of gut bacteria, with the bacterial population increasing further down the GI tract. Overall, about 90% of the body’s microbiome resides in the gut, highlighting its importance in our overall health. 

What are the functions of the gut microbiome?  

So what exactly does our gut microbiome do? Let’s explore some of its key functions. 

1. Metabolize nutrients and manufacture vitamins 

The primary functions of the gut microbiome are to metabolize nutrients and manufacture vitamins. When we consume food, our stomach breaks it into smaller pieces, which then move to the small intestine for nutrient absorption, particularly refined carbohydrates.  

Our small intestine easily absorbs processed foods, which is why we gain weight when we consume too many cookies, crackers, and other yummy but non-nutritional foods. To maintain a healthy gut microbiome, it’s best to consume foods high in fiber to promote healthy levels of the “good bacteria” in our intestinal tract. We also want to avoid eating too much meat, as the excess fat creates bile acids in our colon. 

2. Maintain intestinal structure 

Another crucial function of gut bacteria is maintaining a healthy intestinal barrier to prevent harmful bacteria from entering the bloodstream. Healthy intestinal cells have tight junctions that block bacteria, viruses, and fungi. However, poor diet, certain medications, and illnesses can weaken these junctions, leading to “leaky gut,” where harmful organisms slip into the bloodstream, causing systemic issues. 

3. Protect our immune system 

The gut microbiome also plays a pivotal role in our immune system, with 70% of our immune cells residing in the gut. These bacteria train white blood cells to distinguish between harmful invaders and the body’s own cells, preventing autoimmune diseases.  

4. Defend against infections 

Additionally, gut bacteria produce natural antibiotics, protecting us from infections. When harmful bacteria dominate, the functionality of our immune system may be compromised. 

5. Communicate with the brain 

The gut-brain connection is another significant function of our intestinal microbiome. The bacteria in our gut influences our cognitive functioning and vice-versa. This bi-directional communication affects cognition, mood, and anxiety levels.  

If you’re experiencing depression, anxiety, and/or brain fog, you may see an improvement by adjusting your diet. This is particularly relevant for women experiencing brain fog during perimenopause or menopause, where dietary changes can alleviate some cognitive symptoms. 

How can I improve my gut microbiome? 

Fortunately, if we’re noticing symptoms of an unhealthy gut microbiome (gas, bloating, uncomfortable bowel movements), there are steps we can take to improve it.  

1. Avoid the overuse of antibiotics and NSAIDs 

To heal and maintain the gut microbiome, It’s crucial to avoid antibiotics unless absolutely necessary. Antibiotics can disrupt the microbiome, causing long-term harm.  

Prone to taking ibuprofen daily to reduce those tension headaches or other minor ailments? If so, you may want to try to cut back when you can. NSAIDs (non-steroidal anti-inflammatory drugs) like ibuprofen and acid blockers, can damage the intestinal lining and disrupt gut bacteria.  

2. Eat a nutrient-rich diet 

A healthy microbiome thrives on a diet low in meat, fat, refined carbohydrates, and ultra-processed foods. Cold cuts, in particular, are detrimental due to their tendency to rot in the colon and contribute to an unhealthy gut environment. 

Probiotics and prebiotics are especially important for the health of your gut microbiome. Let’s review examples of each and their benefits now. 


Probiotics, primarily from fermented foods like yogurt, cottage cheese, kimchi, sauerkraut, and tofu, are beneficial for gut health. These foods contain a variety of bacteria that support a balanced microbiome. While probiotic supplements can be useful, they often contain high doses of specific bacteria, which may not be as beneficial as the diverse bacterial populations found in fermented foods. 


Even more important than probiotics are prebiotics, which are fibers that nourish the good bacteria in the gut. High-fiber foods such as raspberries, blueberries, pears, broccoli, spinach, and avocados are essential for a healthy microbiome. Women should aim for 25 grams of fiber daily, and men about 40 grams. It’s vital to identify high-fiber foods you enjoy and incorporate them into your daily diet consistently. 

Regular consumption of fiber-rich foods is necessary to sustain a healthy microbiome. This dietary approach requires a conscious effort to select, prepare, and consume these foods daily, reflecting a return to the dietary habits of previous generations. Educating oneself and making informed dietary choices are imperative for maintaining gut health, as it is a foundational aspect of overall well-being. 


Caring for your gut microbiome can transform your health in remarkable ways. From boosting your immune system to improving mood and cognitive function, a healthy gut is foundational to overall well-being.  

Women, in particular, can benefit by making simple dietary changes—incorporating more fiber-rich foods, like berries and avocados, and enjoying fermented foods, such as yogurt and kimchi. By avoiding unnecessary antibiotics and processed foods, you can support a thriving microbiome.  

Start today with small, mindful changes, and you’ll be on the path to a healthier, happier you. Your gut—and your whole body—will thank you! 

About the author
FemmePharma started as a pharmaceutical research and development company more than 20 years ago. We’ve been reinventing women’s healthcare ever since. Please consult your healthcare practitioner to decide which product best meets your needs.
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