If you met me 30 years ago, I would have been the last person to promote loving germs. I was a sickly child making recurrent visits to the doctor's office for antibiotics and continually the victim of a variety of illnesses. Essentially, I was the poster boy for the war on germs and wanted to kill them all.

That mindset changed the moment I walked into my first microbiology lab in 1988. As my professor, Donn Kushner, pointed out to me, most of the germs out there could be our friends if only we let them. From that moment on, I worked not to kill, but ultimately love microbes.

I admit that it's not easy to associate the word "love" with germs. But when you think about how involved they are in our everyday lives, you can appreciate their importance. They are with us before we are born and long after we pass. Every external action we take in this world exposes us to them. On our insides, every biological function – metabolism, fat storage, cholesterol levels and even our psychological state – is affected by their presence. We are destined to either live closer than any loved one or family member.

This reality isn't new. For close to 50 years, we've known microbes are more than just microscopic villains out to kill us. But over the past decade, researchers have explored this bond in-depth and inadvertently become relationship therapists. They are discovering how we can make the best of this microbial marriage and reverse some of the damage we've done that requires immediate change.

None is more relevant than the crisis of antibiotic resistance. By misusing and abusing these drugs, we have forced some species to turn into unstoppable enemies. It's time to embrace the good microbial species to help us keep pathogens at bay.

We've also learned how a lack of harmony may influence some of our greatest chronic disease challenges, such diabetes, obesity, cardiovascular disease and cancer. We are even learning that there may be links to such enigmas as Alzheimer's disease, psychological disorders and autism.

But it's not all bad, as most relationships have ups and downs; it's a long-term dynamic process.

Take, for example, your diet. What you choose to eat directly affects the microbes living inside your intestines. If you choose simple sugars and saturated fats, you're doing them and yourself no favours. The food may taste good, but farther down the gastrointestinal tract, bacterial species known to trigger inflammation rise in number while those responsible for keeping your body balanced lose ground.

Keep this up and you'll end up with a host of problems, from the expected weight gain to a higher risk of depression and cardiovascular disease. Replace the sugar with fibre and the saturated fats with polyunsaturated versions such as omega-3-fatty acids, and you reverse the trend, as beneficial bacteria become more populous while those inflammatory species are kept in line.

The influence of microbes goes beyond what you eat. Your skin is a prime spot for bacterial growth and certain species contribute to a healthy glow. But others take advantage of the oils, dirt and pollutants to cause a variety of troubles, including acne, rashes, eye infections and dandruff – even tanning can leave you vulnerable to these unwanted invaders. But don't fret – research is showing us how we can avoid these problems by adding in some good species to balance the scales. Applying bacteria similar to probiotics (just don't eat them) can improve the situation. Soon you'll be seeing a variety of options on drug store shelves in which you are not removing bacteria, but instead spreading them on your face and gums.

There are hundreds of ways our everyday activities affect our bond with microbes. Much like my journey, we can all learn how to live well with germs. Granted, it may be too late to change avowed germophobes. But for those still open to the idea of benefits from microbes, there is the opportunity to look away from war and find peace.

I believe this is particularly important for children. By learning how to love germs instead of fear or hate them, we may finally achieve a goal once thought to be impossible. They may become the first generation of germphiles.

Jason Tetro is a Toronto-based microbiologist with more than 25 years experience in research. His latest book, The Germ Files, published by Doubleday Canada, is out on Feb. 2.