Gut Bacteria: The Good, The Bad and Keeping It Balanced

Not all bacteria is bad for you—and your gut needs it to help you feel your best.

It was the Father of Medicine, Hippocrates, who reportedly first said, “all disease begins in the gut.”

While it seems that the medical community forgot that important lesson for a period of time, we are finally back to appreciating and actively working towards a healthy balance in the human body.

Repeat after me: not all bacteria is bad.

In fact, in recent years we’ve truly been able to hone in on the importance of understanding the trillions of bacteria—or microorganisms—living in our intestines. We now know that it’s possible to have too much bacteria—both good and bad—and that the everyday probiotic likely isn’t enough to help keep our intestines balanced and healthy.

How Bacteria Works

When a patient has “bad” bacteria growing in the large intestine, it isn’t always a case of harmful pathogens; sometimes it simply refers to an overgrowth of normal bacteria. That said, certain bacterias such as Helicobacter Pylori, Clostridium difficile, Salmonella or Klebsiella pneumoniae DO deserve the bad reputation they get.

They work to confuse the immune system, potentially causing autoimmunity, and release toxins that cause brain fog and fatigue. Toxins (called LPS) from bacteria also jam up methylation, which can be a real issue for those of us with MTHFR and other methylation genetic SNPs.

Additionally, there are conditions that are directly linked to the disruption or imbalance in the gut, such as:

  • Fibromyalgia
  • Anxiety
  • Weight gain
  • SIBO
  • IBS
  • Bloating, Constipation and Diarrhea
  • Depression and anxiety
  • Headaches
  • Allergies and Histamine Intolerances
  • PCOS and PMS
  • ALS
  • Leaky Gut
  • Skin Rashes and Acne
  • Heart, Liver, and Kidney Diseases
  • Diabetes
  • Osteoporosis
  • Alzheimer’s Disease
  • Autoimmune Conditions

As for the healthy, good-for-you gut flora, you’re probably aware of the usual suspects: Lactobacillus Acidophilus and Bifidobacteria. The key to a balanced gut, however, is our diet—and a healthy diet is the answer to feeling our best.

Every single day we are feeding the microorganisms inside our intestines by way of the food choices we make. What we consume determines the population inside our guts. So it begs the question: Are you feeding the bacteria to promote a healthy or unhealthy gut?

The Solution to a Balanced Gut

If feeding determines what happens inside of us—and balance is the goal—then simple, balanced meals are a must. Aim for small meals containing a little bit of everything: carbs, vegetables, proteins, and fats, at consistent intervals throughout the day.

Foods that are high in fiber such as fruit, vegetables, nuts and seeds, feed bacteria. Some is a good thing, but too much can lead to overfeeding. That’s right—eating too much healthy food can cause an overgrowth of bacteria. Fermented foods have been popular, and can be a good thing in small amounts, but too much, and you could actually be adding in too many bacteria. Sugar and high starch foods also overfeed bacteria.

Food that is not well digested also feeds bacteria. And we tend to not digest well when we are stressed and when we eat too much food at once.

To avoid overfeeding, keep your serving sizes to an amount you are sure to digest and allow (at least) a 10-hour break overnight while you sleep. It can also help to take digestive enzymes with meals, to be sure your food is being digested.

On the other hand, we are exposed to many things that decrease our good bacteria – so are also always at risk of having too few bacteria. If you’ve had to take antibiotics, you may have killed off some of your good bacteria (and allowed others to overgrow). Stress itself is known to cause lower good bacteria. And so does gluten.

That’s part of why the Stress Remedy Program is so successful at helping people recover their health – because I guide you to eat in a way that supports your good bacteria to be perfectly balanced, while also helping you to recover from stress.

For those that are already experiencing gut-related issues… and we already determined that almost everything is gut-related… then starting with a stool panel is the obvious first step. Today’s advanced DNA stool tests allow us to identify all of the bacteria in the large intestine, rather than just what shows up with a LIVE culture.

Isn’t that awesome?! We can actually KNOW who is living in our intestines, and then make changes if needed to keep them on track.

Once we determine the bacteria we can start you on a customized protocol for rebalancing your gut. Two things that should immediately jump out at you in that last sentence are: customized and rebalancing.

My approach to gut health is to never kill off all of the bacteria in your body.

Therefore, when treating patients, I do not use antibiotics which only address certain bacteria or often kill too much inside. It’s also not effective to simply pour in a whole bunch of “good” bacteria with a high dose probiotic product.

Not all probiotic products are equal. Some contain dairy, or other unwanted ingredients. Some never make it to your intestines. Some have too much or too little Lactobacillus and Bifidobacteria – two good bacteria that we are able to get from a product.

Instead, I take a herbal approach, using herbs* that effectively address the overgrowth (and other microbes like yeast) while preserving the good guys. I also use traffic-directing bacteria that help to encourage bad to leave and the good bacteria to stay. We take it slow with dosing herbs in order to avoid the die-off response of the bacteria that can result in digestive pain, headaches, and fatigue.

We should never have to make you feel worse, to make you better.

Additionally, we work on healing leaky gut because good bacteria needs healthy intestinal cells in order to flourish.

Then, once we have the bacteria back in balance, we can use a high quality probiotic to keep it that way. I’ve tried many probiotic products over the years, and my patients reported the most benefit from one particular product – so I brought it into the Nature Empowered product line for you to access here.

After helping thousands of patients find a new balance in their guts, I can confidently say that it is possible. With trillions of bacteria, what one person may lack, another may have a surplus of. But when we see follow up stool results that show that the bacteria are on track, and the inflammation and leaky gut are resolving, it is so exciting. Autoimmune conditions go into remission, bone densities improve, extra weight comes off, rashes go away, and bloating disappears. It takes time to address each patient’s specific needs—but there’s no denying that the results are worth it.

For help finding out who is living in your intestines, and whether they are out of balance and needing attention, learn more about my Leaky Gut and Digestive Solutions Program.

–Dr. Doni
11th March 2019

*Please keep in mind that any and all supplements—nutrients, herbs, enzymes, or other—should be used with caution. My recommendation is that you seek the care of a naturopathic doctor (with a doctorate degree from a federally-accredited program) and that you have a primary care physician or practitioner whom you can contact to help you with individual dosing and protocols. If you ever experience negative symptoms after taking a product, stop taking it immediately and contact your doctor right away.