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Fight Bacteria with Bacteria: Ways to Balance Your Microbiome

Fight Bacteria with Bacteria: Ways to Balance Your Microbiome


Most people have had gut or digestion discomfort at some point or another. Most of the time, tummy troubles, not to mention other issues like acne and hormone imbalances, can be tied back to your microbiome, or the colonies of microbes that live in your digestive tract (and pretty much everywhere else – on your skin, in your eyes, and in your lungs.

A healthy microbiome.

An optimal microbiome has a diverse ecosystem of bacteria, viruses and fungi. Some are beneficial, others are harmful, and the ones in between do not affect your health either way. 

The operative term here is diverse – when many types of microbes inhabit your system, they keep each other in check. We have been taught all of our lives that germs are bad, but in this case, the more types of microbes you have in your digestive tract, the better. When there’s a variety of species, no one (or few) species should take over because there are others defending their own turf.

Any overgrowth of a particular species, good or bad, means your microbiome is out of balance. 

Lots of life events can throw you off balance – a course of antibiotics, a stressful time period, an illness, a few weeks of eating the wrong foods. You can get yourself back into balance, though. Keep reading to find out what goes wrong and how to reintroduce and support healthy bacteria in your gut. 

Things that go wrong with your microbiome.

Fight Bacteria with Bacteria: Ways to Balance Your Microbiome

When one species grows out of control, it can cause problems. There are a few more common types of microbiome imbalances that you may have heard of. One of the most common microbes that tend to take over when the host (that’s you) consumes a lot of sugar is candida albicans. Candida overgrowth goes by many names: candidiasis, yeast infections, thrush, and other manifestations of the same root problem. Another common overgrowth is SIBO, or Small Intestinal Bacterial Overgrowth, which happens when conditions allow an unusual proliferation of troublesome bacteria in the small intestine.

Keeping your gut bacteria in balance (or getting back into balance).

Imbalances are no fun. Annoying at best, and downright debilitating at worst—no matter where you are on the scale of gut health, you know that an intentional plan to get back into balance will make you feel a world better. Here's 5 options available for working back toward a happy microbiome.


Fight Bacteria with Bacteria: Ways to Balance Your Microbiome

Probiotics are actual, living, beneficial microbes that you can consume to increase the proportion of good species in your system. You can get probiotics in raw fermented foods, like yogurt, pickles, and sauerkraut. You can also opt for probiotic supplements, which are typically in capsule form, and less often packaged as drinks or shots. 

If you take probiotic supplements, it’s important to switch it up every few months so that the type you are taking doesn’t throw your biodiversity off-kilter. The goal is to establish a sustainable culture of the strains in your supplement, then switch to another supplement to establish a sustainable culture of those strains, repeating every few months. 

lactobacillus - Fight Bacteria with Bacteria: Ways to Balance Your Microbiome

Two species that have a lot of research behind them are lactobacillus and bifidobacterium. One study even noted beneficial psychological effects of two specific strains of these.


Think of prebiotics as the food your gut bacteria like to eat. Usually, prebiotics are in the form of resistant starch, which is fiber that your stomach does not digest. Friendly microbes step in and help out, breaking the fiber down into compounds that are useful to your body. 

Fruits and vegetables are the best sources of prebiotics, especially:

  • onions
  • leeks
  • asparagus
  • dandelion greens
  • and bananas.

You can double down on your efforts to diversify your microbiome with synbiotics, which are probiotics and the specific strains’ favorite prebiotics in one supplement.  

Fecal transplant

For severe cases, your doctor may do fecal transplants in a clinical setting. This is exactly what it sounds like – a small amount of poop from a healthy donor is transplanted into the colon of the person who needs it. 

As of now, poop transplants are used in the case of extremely severe microbial invasions, such as c. difficile (c. diff). Who knows – it may come to a point where fecal transplants are used for health optimization or maintenance. For now, it doesn’t come without risks, so it is only carried out in a hospital setting under clinical supervision. 

Antimicrobials in conjunction with probiotics and prebiotics.

Sometimes, a doctor can pinpoint exactly what pathogen has taken over and has to be wiped out in order to restore balance in your microbiome. In this case, you may be prescribed antimicrobials in conjunction with probiotics and prebiotics to treat an overgrowth. 

For example, you may see a doctor for a recurring candida infection, and leave with a prescription for antifungal medication. You may receive a SIBO diagnosis and the primary treatment will be antibiotics. Naturopathic doctors and other natural healers may suggest natural herbal antimicrobials such as oregano oil, pau d’arco, goldenseal, and others, along with dietary changes to address an overgrowth. 

Whether natural or pharmaceutical, antimicrobials wipe out your beneficial microbes in addition to the harmful ones, so work with a qualified professional instead of experimenting on your own. In some situations, it’s possible to do more harm than good. 

Diet changes to balance your microbiome.

Fight Bacteria with Bacteria: Ways to Balance Your Microbiome

Research shows that diet affects microbiome diversity more than anything else. Consuming sugar is one of the fastest ways to feed candida and other species that tend to wreak havoc on your system. That doesn’t mean you have to swear off sweets, though. Monk fruit satisfies your sweet tooth without feeding bad gut bacteria. As a bonus, it contains mogrosides, which can can help support a healthy inflammation response. One large international study found that people who ate 30 different vegetables per week had the strongest, most diverse ecosystems of gut microbes. If 30 sounds daunting, add a smoothie a day to your regimen. You’ll be surprised at how fast you’ll get there. 

Your digestion, your skin, and how clearly you think gives you clues as to how your microibiome is doing. The best thing to do to keep your gut in top shape is to take antibiotics only when necessary, keep your sugar low, eat as many vegetables as you can, and focus on the other measures as needed.