Think bacteria, and words like "infection" and "disease" probably spring to mind. But not all bacteria are bad, especially when it comes to the roughly 100 trillion bacteria, viruses, fungi and other microbes our bodies host. Collectively known as our microbiome, these tiny organisms are all over and inside of us. They feed off of our sweat, mucus and undigested food; some even help support our immune system, metabolism and more, explains Jason Tetro, microbiologist and author of The Germ Files. While not all microbes are body-friendly, there are things you can do to make the benign ones benefit you.

On your skin
You might associate bacteria on your skin with blemishes, but, surprisingly, most skin (as well as sweat and oil gland) bacteria are beneficial, says Tetro. Some strains might even help keep skin healthy and prevent acne.

And it's not just bacteria. "There are viruses, fungi and even mites that choose our skin as their habitat," says Dr. Shannon Humphrey, cosmetic dermatologist at Carruthers and Humphrey and clinical assistant professor in dermatology and skin science at The University of British Columbia.

All those microbes keep our immune system on alert for invaders, explains Dr. Humphrey. And since skin is our barrier to the outside world, a strong defence is important. "Having the right balance of pathogens on the skin keeps the immune system primed," she says.

What you can do
Avoid antibiotics whenever possible. Because they kill both good and bad bacteria, antibiotics may lead to a microbe imbalance, with just one or two species taking over.

Keep clean. Eliminating excess sebum will prevent an overgrowth of the bacteria that like to feed off oils, says Tetro. But, Dr. Humphrey cautions, be gentle: "Some of these abrasive, astringent scrubs or exfoliants can break down the skin barrier, and the skin barrier is an important line of immune defence against bacteria."

Move it. Working up a sweat through regular exercise is a good way to dilute the skin secretions that some bacteria thrive on, says Tetro. And since sweat can promote friendly bacteria, it's a good idea to swap antiperspirant for a natural deodorant, such as The Green Beaver Company Wild Rose Deodorant Stick or Weleda Citrus Deodorant.

Wash your hands. Use soap and water, or an alcohol-based hand sanitizer, which can kill bacterial, fungal and viral pathogens. But steer clear of soaps that contain triclosan, which can contribute to antibiotic resistance.

Feed your face. Consider eating live-culture yogurt, which contains bacteria that may help your complexion. Dr. Humphrey says the science is still too early to confirm whether probiotics can benefit the skin, but the research is promising.

In your mouth
Microbes in your mouth are usually linked to gingivitis, tooth decay and bad breath, but, Tetro points out, there's a lot more going on in there. Plaque, for instance, is a community of good and bad bacteria called biofilm. "The community, when it's stable, prevents other organisms from colonizing," says Dennis Cvitkovitch, microbiology professor in the faculty of dentistry at the University of Toronto. But start eating sweets and the bad microbes in the community can multiply. Those bacteria feed off sugar, and then produce lactic acid, which can make your mouth acidic, dissolving enamel and leading to cavities.

Since the mouth is the first stop in the respiratory and digestive tracts, keeping your oral bacteria balanced helps prevent troublesome microbes from invading other areas of the body. Some research has linked unhealthy mouth microbes with a higher risk of sinusitis, says Tetro, while other studies suggest these bacteria can enter the bloodstream, potentially contributing to problems like cardiovascular disease.  

What you can do
Lose the sweets. Reducing dietary sugar helps control cavity-causing bacteria.

Chew on this. Chewing gum is a good short-term strategy for purging unwanted bacteria. Tetro recommends chewing a sugarless variety for about two minutes (after which the gum may lose its stickiness). Xylitol-sweetened gum is a particularly healthy treat for your mouth microbes because the sugar-like molecules feed healthy bacteria and starve harmful bacteria.

Brush up. Regular toothbrushing will help banish smelly microbes and remove the biofilm and the sugars that feed bad bacteria, says Cvitkovitch. Sure, the biofilm will regenerate, but regularly brushing and flossing it away is nevertheless important; bacteria that stick around and mature are more likely to get under the gums, causing gingivitis and periodontal disease.

In your gut
Stomach bugs can be a good thing. "There are things your body cannot break down to digest, so bacteria enjoy doing this for you," explains Tetro. The microbes convert indigestible fibre into beneficial chemicals and help synthesize vitamins. They also help us metabolize food properly and coat the intestinal lining to crowd out unwanted pathogens. Bonus: Certain bacterial species act as mood-boosters by producing the feel-good brain chemical serotonin, explains Tetro.

Of course, not all gut bacteria are friendly. "Poor diets that are high in refined sugars and fats interact with gut bacteria to stimulate the immune system and alter the composition of bacteria in the gut," says Michael Surette, professor and Canada research chair in interdisciplinary microbiome research at McMaster University in Hamilton. All of this can lead to inflammation throughout the body, which has been linked to obesity, chronic disease and mood disorders, such as anxiety and depression.

What you can do
Mix it up. Eating a varied diet with plenty of fibre will help ensure that you're feeding those good microbes.

Boost those bacteria. Consuming fermented foods, which contain healthy bacterial cultures, is a great way to help keep your gut balanced with plenty of friendly microbes. Try live-culture yogurt, kefir, raw sauerkraut, kimchi and kombucha. And don't forget that other common (and delicious) foods such as unpasteurized honey and dark chocolate with probiotics are good choices, too, notes Tetro.

Get your greens. Include lots of plants in your diet. They have natural antimicrobials to help rid your gut of bad microbes.

In your vagina
Millions of microbes keep the vaginal walls healthy by crowding out potentially harmful bacteria and yeast, but that's not their only job: Certain bacteria produce lactic acid and hydrogen peroxide, which help regulate pH balance, allowing friendly microbes to thrive and banishing the bad guys. A lack of good bacteria, meanwhile, leads to an overgrowth of other microbial species and to associated problems, like yeast infections.

What you can do
Pop oral probiotics. These can help create a healthy vaginal microbiome. And contrary to what you may have heard, don't treat a yeast infection by applying yogurt down there; Tetro says it's best to stick to oral supplements.

Avoid antibiotics. Sometimes, of course, you need a round of antibiotics to kill an infection, but if you can avoid them, your yeast-infection-free vagina will thank you.

Shield yourself. While friendly bacteria help protect against pathogens, that doesn't mean you can skip other means of protection during intercourse. Tetro says condoms are important not only to prevent pregnancy and protect against STIs but also to keep bacteria out of your urinary tract.

Read more:
How much of health is hereditary?
What you need to know about cervical cancer

This story was originally titled "Meet Your Microbes" in the May 2016 issue. Subscribe to Canadian Living today and never miss an issue!