12 Silent Signs Your Microbiome Could Be in Trouble

Updated: Jul. 31, 2023

The microorganisms in your gut have a major impact on your general health. Here are the warning signs your tummy's ecosystem may not be happy.

A healthy gut microbiome could add years to your life. But your digestive system and gut health might not be in the best possible shape if you have most of these signs or symptoms of potential trouble.

You aren’t taking care of your health

“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, the internal fitness 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.”

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You have GI problems

One of the things your bowel movements can reveal about your health is how healthy (or not) your gut microbiome is. Bloating, gas, indigestion, heartburn, diarrhea, and constipation can be caused by your gut flora being off. “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. “I often remedy this with a combination of diet recommendations, targeted supplements, and lifestyle practices.”

Probiotics can also help get you back on track, he says.

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You’ve been in a bad mood

If you feel out of it, irritable, or have other mental health issues, your microbiome could be playing a role, 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.”

A 2019 review of studies published in General Psychiatry found that using probiotic food and supplements may help reduce anxiety symptoms while regulating the gut.

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You get yeast infections

One way to prevent yeast infections is to up your probiotic intake. “These types of infections can often be a result of systemic yeast, or fungal overgrowth in the gut,” Dr. Lipman says. This is why you’re more likely to get the nasty infections when you take antibiotics, which kill the good bacteria that help keep yeast in check along with the bad.

Too much sugar in your diet can also be an issue. (Read A Nutritionist Just Revealed the #1 Worst Food to Eat for Yeast Infections.) “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.

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You have major sugar cravings

Your gut bacteria could actually influence the foods you desire. “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,” Dr. Angle says.

In a vicious circle, says Dr. Lipman, “Sugar feeds bad bacteria and yeast in the body, and therefore, a diet high in sugar and refined carbs will often lead to an overgrowth of harmful bacteria and yeast, which will compromise gut function.” He advises limiting sugar in your diet and eating wholesome, nutrient-dense foods such as leafy greens and other veggies, healthy fats, and good quality animal protein.

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You’ve gained weight

There are many reasons for weight gain. But, in addition to those, research published in Cell suggested that certain bacteria in your gut might make you more predisposed to obesity to begin with. What’s more, “in connection with obesity, low levels of a compound produced only in the gut have been linked to type 2 diabetes as a risk factor,” Dr. Angle says. (Here are the other secrets your gut is trying to tell you.)

You get sick a lot

A healthy gut microbiome could add years to your life, according to research from the American Society of Microbiology. The opposite is also true—an unhealthy microbiome could mean you get sick more often. “Seventy percent of the immune system surrounds the gut,” Dr. Lipman says. “So if the microbiome is in an imbalanced state, it will affect and often compromise immune function.” To support your immune system, he advises a good quality probiotic, a diet full of antioxidant-rich foods, and getting good sleep.

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You have skin problems

Even the condition of our skin could be influenced by our gut microbiome. Research published in the International Journal of Women’s Dermatology and Frontiers in Microbiology, among other journals, points to a connection between probiotics and skin conditions such as acne and psoriasis. “Skin problems such as psoriasis or rosacea have been shown to be related to changes in the relative activity and levels of three different bacterial species,” Dr. Angle says. “Progress in the possible treatment of these conditions has been made by suppressing bacterial overgrowth of one of the species involved.”

You have chronic sinus issues

You have the clear signs you have a sinus infection, but is your gut to blame? Research published in the American Journal of Rhinology & Allergy suggested that chronic sinus infections were linked with a lack of bacterial diversity, as well as a lack of certain bacteria, in the sinus microbiome—but the gut microbiome likely influences it as well, according to the study author. (Watch out for these other signs you need to pay more attention to your gut health.)

You have an autoimmune disease

Because of your gut’s connections to the immune system, autoimmune disease, in which your body attacks itself, has also been linked to an unhealthy microbiome. “Research has indicated that abnormal levels and/or species of gut microbiota are also suspect in causing or contributing to some autoimmune diseases—studies have shown links to type 1 diabetes, multiple sclerosis, and lupus,” Dr. Angle says. “A possible mechanism suggested for MS is that certain species of bacteria produce biochemicals that directly affect the T-cells in the immune system, perhaps triggering demyelination [loss of the insulation around the nerves].”

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You have joint pain

Among the secrets pain doctors won’t tell you: 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, Dr. Angle says. “Different specific changes in the microbiome have been linked to rheumatoid arthritis and spondyloarthritis.” It is not yet clear if these changes are present before the diseases manifest or as a result of the disease, she says. “However, they make a good case for maintaining optimal gut function as a long-term preventative measure.”

You’re allergic to everything

Allergies are on the rise—and you’re likely at risk. 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 2017 research published in the Journal of Immunology. And this increased likelihood of allergies and asthma may start soon after birth—2016 research in Nature Medicine found that specific microbes in babies’ guts predicted a higher risk of allergies by age 2 and asthma by age 4. Next, check out the 50 best foods and recipes for gut health.

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