"My doctor wants me to take another antibiotic for this cold that won't quit, but I've read antibiotics damage the gut and even can make me fat," a patient recently asked me. "I've read mixed reviews and I know you've given them the thumbs down in the past, but really, how bad are antibiotics?"

Firstly, let's not totally dismiss antibiotics. After all, they can be life saving and in certain situations, become absolutely necessary. They've saved millions of lives. Trust me, we do not want to live without antibiotics in the twenty-first century.

That being said, antibiotics today are over-prescribed and often unnecessary. Developments to prevent and treat infectious diseases—like sanitation, early vaccines and best-use of antibiotics—have dramatically reduced deaths from infectious disease. But there is a cost.

Take sanitation ... hyper-focusing on hygiene and sterilization using hand sanitizers and overusing vaccines and antibiotics has dramatically altered our gut ecosystem, spiking autoimmune and allergic diseases and contributing to things like obesity, diabetes, heart disease, depression and autism.

While western medicine has greatly advanced with acute disease, we've failed miserably addressing chronic disease.

Louis Pasteur discovered the bug or microbe causing infections and Alexander Fleming discovered antibiotics to cure them. This simple cause-effect "cure"—single bug, single disease and single drug—might work for infection, but not so much for chronic disease.

Ever since, we have been searching for "cures" for chronic diseases (including cancer and dementia), yet we can't find them! Medicine's history has become the pursuit of a holy grail—a pill for every ill. This failed approach will continue to fail because chronic disease results from the complex interaction of our genes, lifestyle and environment. A magic pill or other "miracle cure" just isn't going to cure us. We need a well rounded, permanent lifestyle approach.

So back to the original question: Antibiotics can become detrimental because they damage your gut ecosystem, what we collectively call our microbiome, which is made up of 100 trillion bugs that live inside you and outnumber your cells an astounding 10 to 1.

True, antibiotics wipe out the bad stuff that is causing the infection; but they are like napalm—they take out everything in their path—including the good bacteria.

That becomes a real problem because while your gut has trillions of bacteria, they collectively contain at least 100 times as many genes as you do. That bacterial DNA in your gut outnumbers your own DNA by a very large margin.

That's important, because among its functions, this bacterial DNA controls immunity, regulates digestion and intestinal function, protects against infections and even produces vitamins and nutrients.

Antibiotics destroy these beneficial bacteria, which creates a wide open field for the overgrowth of bad bugs, yeast and candida, leading to numerous problems including mood disorders, food allergies, fatigue, skin issues and of course, digestive issues.

Overgrowth of bad bugs can also encourage cravings for sugary, processed junk foods, leading to weight gain and other problems that eating junk foods creates. So it is clear that antibiotics can potentially make you fat.

When a patient comes to see me, I ask if they have a history of taking antibiotics. More often than not, I've learned overuse has led to their gut issues, including leaky gut.

I recently had a patient born by C-section, who was then bottle fed and as a child suffered recurrent ear infections. Conventional doctors—doing what they felt was best—overprescribed antibiotics, eventually leading to irritable bowel syndrome during the patient's teen years and then an autoimmune disease as a young adult. I hear this story repeatedly, and much of this stems from not honoring, respecting and tending to your inner garden.

More often than not, the antibiotics children receive for viral infections, colds, sore throats and other ailments, for which they likely would have gotten better on their own, have damaged their delicate gut flora starting at an early age.

One Centers for Disease Control and Prevention (CDC) study found 71 percent of children who suffered C. diff infections (inflammation of the colon caused by a specific bacteria called clostridium difficile) received numerous courses of antibiotics for respiratory, ear and nose illnesses 12 weeks before infection.

Another study published in the American Society for Microbiology found a one-week course of antibiotics could negatively affect your microbiome for long periods of time, potentially even for a whole year.

Other studies link long-term antibiotic use to diverse problems including depressed immunity, higher stress levels, behavior problems and obesity.

While antibiotics can sometimes be absolutely necessary, I highly recommend conferring with a Functional Medicine practitioner to discuss alternatives (including allowing infections to heal on their own).

If you must use antibiotics, I recommend a few things before and after using them.

First, add in the good stuff. Eat a low-glycemic, whole-foods diet and take quality probiotics and prebiotics. A high-quality, multi-strain probiotic helps populate your gut with beneficial bacteria. Prebiotics, a form of soluble fiber, which also helps feed good bugs, which can be found in onions, garlic, resistant starch, sweet potatoes, dandelion greens and jicama.

Unlike regular starch, your small intestine doesn't absorb potato starch. Instead, your gut bacteria process it, creating molecules that help balance blood sugar and healthy gut flora. In other words, when you consume resistant starch, it "resists" digestion and does not spike blood sugar or insulin.

I like to supplement with my favorite resistant starch found in Bob's Red Mill Unmodified Potato Starch. I suggest adding about 1 teaspoon to a glass of water.

Then, focus on gut repair—especially after you're finished using antibiotics. Utilize gut-healing nutrients including L-glutamine, omega-3 fats, vitamin A and zinc to repair your gut lining so it can resume its normal, natural functions. The use of digestive enzymes can help you digest your food better.

That's it … pretty simple but with amazing results.