13 Signs Your Bad Gut Bacteria Are Making You Sick, Part 1

bad gut bacteria

It could be that your bad gut bacteria have overwhelmed the good guys and are behind some chronic health issues that you can’t explain. Thirteen common ills that bacteria affect are examined. Do a self-check and determine if the bad gut bacteria in you might be the culprit.

bad gut bacteria

IF YOU have been experience some chronic health issue and are perplexed about what is causing it, consider that you may have too many bad gut bacteria. We all all some bad gut bacteria, and when they overwhelm the good critters, we can get sick as a result.

This post looks at the following 13 signs that indicate you have bad gut bacteria that’s making you sick:

Your Diet Is Dominated by Processed Foods and Sugar
You Get Sick. A Lot
Your Body Weight Is A Yo-yo
Your Skin Is Blemished and Unhealthy Looking
You Have GI Problems or Leaky Gut
Your Sinuses Make You Suffer
You Experience Food Intolerance
You Have An Autoimmune Disease
You’re Depressed, Anxious or Often In A Foul Mood
You’re Often Tired
You Get Yeast Infections
Your Joints Ache
You’re Allergic. To Everything, It Seems.

How can a bunch of microscopic microflora (as the gut bacteria are sometime called) have such a huge impact on our health? Well, for starters, there’s lots of them, they have their own DNA, and they interact with just about every biological system in our body.

There are more of these microbes in our gut than there are human cells in our body! That means that you have many trillions of bacteria on and in you. Each of these microbes carries genetic material in the form of DNA. The whole collection of this community’s DNA is called the microbiome.

“The microbiome of your digestive system, or the gut microbiome, contains perhaps 5,000 to 10,000 different species of bacteria that provide essential services of nutrition and protection,” says biochemist Erika Angle, PhD, the CEO and co-founder of Ixcela, a microbiome testing company. “The makeup of your gut microbiome is determined by your genes—however, it is the organ that can be most influenced by your actions, for example diet, exercise, and stress management.”

As Dr. Angles suggests, your lifestyle choices matter to the health of those critters that inhabit your microbiome. And he’s not alone in that assessment. Among many others, renown doctors like Mark Hyman, Josh Axe and Michael Greger and Justin Sonnenburg, namesake of Stanford University’s microbiome-focused Sonnenburg Lab, work to delineate the capacity of the bacteria in your gut to help make you healthy, or ill.

Let’s set the stage for the rest of this post with a five minute video by Michael Greger, MD:


The two big takeaways from Dr. Greger’s video are:

  1. The bacterial strains in your gut have a very significant role in determining if you’re well or sick; and
  2. Dietary interventions can tip the scale in your favor.

Next up, I’m going to provide some information to help you assess if your microbiota may be behind some common health issues. In Part 2, various dietary interventions and specific probiotic strains will be explored that can improve populations of the beneficial bacteria in your gut.


13 Signs You Have Bad Gut Bacteria (and your microbiome is in trouble)

Without benefit of getting your microbiota tested in order to assess whether it’s beneficial or detrimental to your health, how can you tell if yours is predominately beneficial to your health? One way is to get a sense if your gut bacteria might be the culprit behind any chronic health issue you might have, such as the 13 listed below.

Healthline and Reader’s Digest outline various indications that your microbiome may be unhealthy, which I’ll summarize, beginning with perhaps the one most of us have experienced — a poor diet.

1. Your Diet Is Dominated by Processed Foods and Sugar

A diet high in processed foods and added sugars can decrease the amount of good bacteria in your gut. This imbalance can cause increased sugar cravings, which can damage your gut still further. High amounts of refined sugars, particularly high-fructose corn syrup, have been linked to increased inflammation in the body. Chronic inflammation can be the precursor to a number of diseases and even cancers, and that’s why it’s often termed, “inflammaging“.

Guess what happens as sugar, processed food loving bacteria begin to occupy a disproportionate amount of your gut microbiome? They demand more of it. Your gut bacteria has been found in studies to actually influence the foods you desire.

Says Dr. Angle from Ixcela:

“Changes in microbiome composition have been shown to send signals to the brain, both direct nervous signals and biochemical signals, resulting in cravings for certain foods.”

An unhealthy, sugar-loving microbiome might crave sugar, suggests research from Switzerland, and like an artful puppet master, it will make you crave sugar as well. In a vicious circle, sugar feeds bad bacteria and yeast in the body, leading to an overgrowth of harmful bacteria and yeast, which will compromise gut function.

Sugar is a Toxin, say Three Celebrity Doctors. Watch the Interviews.

2. Your Body Weight Is A Yo-Yo

Have you ever been in a cycle of gaining and losing weight without having a clue as to why that is happening? Your gut bacteria might be the culprit. Gaining or losing weight for no obvious reason may be a sign of an unhealthy gut.

An imbalanced gut can diminish your body’s ability to absorb nutrients, regulate blood sugar and store fat. Weight loss may be caused by small intestinal bacterial overgrowth (SIBO), while weight gain may be caused by insulin resistance or the urge to overeat due to decreased nutrient absorption.

Not surprisingly, if you have sugar or other unhealthy cravings, you’ll be more likely to gain weight. But in addition, research indicates that certain bacteria in your gut predisposes you to obesity to begin. A study with mice showed that altering gut bacteria made the mice more likely to lose or gain weight depending on the strain populations dominate in the gut.

100 Trillion Reasons You’re Fat, Sick and Depressed (Part 1)

3. You Have GI Problems or Leaky Gut

Bloating, gas, indigestion, heartburn, diarrhea and constipation can be can all be signs of an unhealthy gut. A balanced gut will have less difficulty processing food and eliminating waste. “These types of digestive issues often indicate a microbial imbalance in the gut,” says Frank Lipman, MD, bestselling author and founder of Be Well and the Eleven Eleven Wellness Center in New York City.

Doctors believe that one cause of chronic inflammation is bacteria that penetrate the gut wall, leading to leaky gut syndrome. Intestinal permeability, sometimes referred to as ‘leaky gut,’ is a broad term reflecting the loss of some connectivity in the cells of the gut wall that then enables various harmful compounds and organisms to breach this gut lining and distress the rest of the body.

4. You Experience Food Intolerance

Food intolerance is the result of difficulty digesting certain foods (this is different than a food allergy, which is caused by an immune system reaction to certain foods). It’s thought that food intolerance may be caused by poor quality of bacteria in the gut. This can lead to difficulty digesting the trigger foods and unpleasant symptoms such as bloating, gas, diarrhea, abdominal pain, and nausea. There is some evidence that food allergies may also be related to gut health.

5. You’re Depressed, Anxious or Often In A Foul Mood

If you consistently feel “out of it”, irritable, or have other mental issues, your microbiome could be to blame, according to the American Psychological Association. “Most neurotransmitters are actually made in the gut, so brain function is often a result of the health of our gut,” Dr. Lipman says. “If there is an imbalance of beneficial and harmful bacteria, it can manifest as problems with mental clarity and memory, along with signs of depression and anxiety.” One study from the UK found people that were given prebiotics, which feeds good gut bacteria, had lower anxiety.

Dr. Weil’s Four Alternatives to Antidepressant Drugs

6. You Get Yeast Infections

Yeast and similar infections are often a result of systemic yeast, or fungal overgrowth in the gut. This is why you’re more likely to get infections when you take antibiotics, because they are indiscriminate bacteria killers, destroying the bad along with the good bacteria that help keep yeast populations in check. Too much sugar in your diet can also feed the fungus. “The infections are quite common in our society as we are overexposed to antibiotics, environmental toxins, a diet in refined carbs and sugar, stress, and lack of sleep—the standard American way!” Dr. Lipman says.

7. You Get Sick. A Lot

A healthy gut microbiome could add years to your life, according to some research. The opposite is also true—an unhealthy microbiome could mean you get sick more often. Approximately 70% of our immune system is centered in the gut. An unbalanced microbiome can lead to compromised immune function and greater vulnerability to disease and infection.

8. You’re Skin Is Blemished and Unhealthy Looking

A Russian study found that over half of acne sufferers they examined had impaired intestinal microflora (bacteria).  Skin problems such as psoriasis or rosacea can be related to changes in the relative activity and levels of different bacterial species.

Skin conditions like eczema may be related to a damaged gut. Inflammation in the gut caused by a poor diet or food allergies may cause increased “leaking” of certain proteins out into the body, which can in turn irritate the skin and cause conditions such as eczema.

Your Battleplan To Combat Aging Skin, Part 1/3

9. Your Sinuses Make You Suffer

Is it possible that your gut is to blame for your insufferable sinuses? A study from the University of California San Francisco found that chronic sinus infections were linked with a lack of bacterial diversity, as well as a lack of certain bacteria, in the sinus microbiome (the bacteria that inhabit the sinus cavity) ; however, the gut microbiome likely influences it as well. The study author, Susan Lynch, told NPR: “… the gastrointestinal tract is a prime target for, perhaps, altering immune responses at sites remote from that niche.”

10. You Have An Autoimmune Disease

Autoimmunity occurs when your body’s immune system attacks what it thinks are pathogens, but are really parts of you. Because of your gut’s connections to the immune system, autoimmune disease has been linked to an unhealthy microbiome. Research has indicated that abnormal population levels and/or species of gut microbiota may cause or contribute to some autoimmune diseases, for instance to Type 1 diabetes, multiple sclerosis, and lupus.

A possible mechanism suggested for multiple sclerosis is that certain species of bacteria produce biochemicals that directly affect the T-cells of the immune system (so-called “killer cells”), perhaps triggering demyelination (the loss of the insulation around the nerves).

11. You’re Often Tired

An unhealthy gut may contribute to sleep disturbances such as insomnia or poor sleep, and therefore lead to chronic fatigue. The majority of the body’s serotonin, a hormone that affects mood and sleep, is produced in the gut. So gut damage can impair your ability to sleep well. Some sleep disturbances have also been linked to risk for fibromyalgia.

12. Your Joints Ache

Your joint pain may be affected by the type of bacteria living in your gut. Gut dysbiosis (imbalance) is implicated in the development of chronic inflammatory diseases that cause joint pain. Different specific changes in the microbiome have been linked to rheumatoid arthritis and spondyloarthritis, as well as psoriatic arthritis.

Causality has not been determined; meaning, it’s not clear if these changes are present before the diseases manifest or as a result of the disease. Nonetheless, they make a good case for maintaining optimal gut function as a long-term preventative measure.

14 Ways to Wipe Out Chronic Inflammation (and why you need to)

13. Your Allergic. To Everything, It Seems

One theory behind why so many more of us are prone to allergies and asthma is that our gut microbiomes have been altered in the past couple of generations, likely due to diet changes and antibiotic use, according to the University of Utah.  Surprisingly, this increased likelihood of allergies and asthma starts from birth. Research from the University of California San Francisco found that specific microbes in babies’ guts predicted a threefold risk in allergies by age two and asthma by age four.

Why The Right Gut Bacteria Is Essential To Good Health and How Antibiotics Kills It All

Your Takeaway

The type of bacterial strains in your gut matter a lot. The winner of the incessant battle between beneficial and harmful microbes will substantially influence whether or not you’re healthy.

As Dr. Michael Greger said in this video above, the bacterial strains in your gut have a very significant role in determining if you’re well or sick.

Try to get a sense if any of the long-term health issues you may be experiencing could be, at least in part, due to the harmful bacteria in your gut. If that’s likely, be sure to read Part 2 of this two-part series on how to transform bad gut bacteria into the good critters, and why you need to if you’re to have a long healthspan.


Read Part 2



Last Updated on July 7, 2023 by Joe Garma

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Joe Garma

I help people live with more vitality and strength. I'm a big believer in sustainability, and am a bit nutty about optimizing my diet, supplements, hormones and exercise. To get exclusive Updates, tips and be on your way to a stronger, more youthful body, join my weekly Newsletter. You can also find me on LinkedIn, Twitter and Instagram.

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