Have you been hearing a lot about the gut microbiome lately? From podcasts to health blogs, everyone’s talking about gut bacteria, probiotics, and how they impact overall wellness. If you’re dealing with a gastrointestinal (GI) condition like irritable bowel syndrome (IBS), Crohn’s disease, or ulcerative colitis, you likely already understand the importance of a balanced gut.
One of my favorite experts on the gut microbiome is Dr. Emily D’Adamo, ND—a staff physician at the Center for Generative Medicine in Norwalk, Connecticut. In this article, Emily shares her insights on how you can improve digestive function by understanding and supporting your gut microbes.
What is the gut microbiome? 🤔
➡️ Ask Emily:
"The gut microbiome refers to the entire community of organisms in your large intestine."
These microbes create nutrients, protect gut cells, resist infections, regulate immune function, produce anti-inflammatory molecules, and can even influence neuropsychiatric disorders through the gut-brain axis [1].
Key Takeaway
Your gut isn’t just for digestion—it’s a complex ecosystem that can affect everything from immune response to mental well-being.
What are the signs of an unhealthy microbiome? 🚩
When Emily suspects an imbalanced gut microbiome (dysbiosis), she looks for:
GI symptoms unexplained by endoscopy or colonoscopy:
Diarrhea or constipation
Bloating
Discomfort after meals
Irritable bowel syndrome (IBS)
Inflammatory bowel diseases:
Crohn’s disease
Ulcerative colitis
Complaints outside of the GI system:
Skin issues
Emily notes that the GI tract and skin develop from the same type of cells when you're an embryo, so what affects one can appear in the other!
Autoimmune disorders
Rheumatoid arthritis
Psoriatic arthritis [2]
Ankylosing spondylitis [3]
High blood pressure [4]
Chronic Fatigue Syndrome [5]
Obesity [6]
Cardiovascular disease [7]
Metabolic-associated liver disease (formerly NAFLD) [6]
Chronic pain [8]
Why It Matters
If you notice GI trouble and skin flare-ups, joint pain, or fatigue, it’s worth exploring microbiome health as a potential root issue.
What naturally kills bad bacteria in the gut? 🦠
➡️ Ask Emily:
"Natural antimicrobials—like garlic, oregano, olive leaf, and berberine—work well in certain cases, but they might also affect good microbes."
According to Emily, it's important to separate the idea of killing microbes using antimicrobial drugs or supplements, from simply outcompeting them with beneficial bacteria."
Competition vs. Killing
Direct killing: targeted herbal supplements or antimicrobials can reduce specific pathogens if necessary.
Outcompeting: often a gentler, longer-term solution—raising levels of beneficial microbes so they starve out the harmful ones.
Four “Good Gut” Microbes to Know 🌟
Emily shares four of her favorite key bacterial players that help keep your gut balanced by naturally reducing bad bacteria:
Faecalibacterium prausnitzii (pronunciation here) 🔊
Produces butyrate, an anti-inflammatory short-chain fatty acid.
Often low in Crohn’s disease or other inflammatory GI disorders.
Boost it with:
Gold kiwis
Arabinogalactan
Jerusalem artichokes
Chicory
Resistant starches like green bananas, oats, beans.
Lactobacillus (pronunciation here) 🔊
Major species in skin and urogenital areas.
Produces lactic acid to deter harmful microbes.
Get more from:
Yogurt
Kefir
Sauerkraut
Tempeh
Bifidobacterium (pronunciation here) 🔊
Flourishes early in life due to breast milk.
Low levels may be seen in IBS or immune imbalances.
Support it with:
Green tea
Almonds
Jerusalem artichokes
Human milk oligosaccharides (HMOs) like 2'fucosyllactose, which are special sugars found in breast milk (and supplements) that feed Bifidobacterium!
Akkermansia muciniphila (pronunciation here) 🔊
Lives in the mucus lining and encouraging a thick, protective gut barrier.
Often low in overweight or obese individuals.
Boost it with:
Polyphenols (antioxidants)
Pomegranates
Green tea
Dark-colored berries
Kiwis
What’s the fastest way to heal the gut microbiome? ⚡
➡️ Ask Emily
#1 Eat whole foods
Focus on fiber-rich fruits, veggies, and resistant starches.
#2 Eat more fiber
Many people under-consume fiber; its crucial to eat fiber regularly because it feeds good bacteria, but be sure to ramp it up gradually to avoid GI distress.
#3 Strengthen the gut-brain connection
Practicing meditation using apps like Nerva can strengthen the gut-brain connection.
Practice deep breathing before meals.
Try humming or singing, which can stimulate digestion!
“Remember that the gut microbiome is a living ecosystem. A knowledgeable provider understands this and will order testing before making treatment recommendations."
Key Takeaways 💡
The gut microbiome is an ecosystem – healing your gut is not a simple, one-step process; an interconnected network of microbes impact your digestion, immunity, and even your mood.
Dysbiosis can show up in surprising ways – signs of imbalance (bloating, IBS, skin issues, fatigue) aren’t limited to the GI tract alone.
Outcompete instead of destroy – rather than focusing solely on antimicrobials, increasing beneficial bacteria (e.g., Faecalibacterium, Lactobacillus, Bifidobacterium, Akkermansia) often yields better, longer-lasting results.
Practical tips make a difference – whole foods, gradual fiber intake, and mind-body practices (like gut-directed meditation) strengthen your microbiome and the gut-brain connection.
Personalized guidance matters – working with an expert like Dr. Emily D’Adamo ensures targeted, research-backed strategies for your unique gut health concerns.
Meet Dr. Emily D’Adamo, ND 👩⚕️
Dr. Emily D’Adamo is Staff Physician at the Center for Generative Medicine (CGM). If you’re looking to improve digestion or tackle unresolved GI issues, contact her clinic to schedule an appointment.
Dr. D’s current practice at CGM fuses rigorous science with the patient-centered paradigm she inherited in her earlier work. With Dr. D, no two individuals are alike, and the care they receive reflects that.
When she’s not being a physician, Emily is an avid ceramicist, weight lifter and naturalist.
References
Zhang, N., Dong, X. Causal relationship between gut microbiota, lipids, and neuropsychiatric disorders: A Mendelian randomization mediation study. J Affect Disord 379, 19-35 (2025).
Taneja, V. Gut Microbes as the Major Drivers of Rheumatoid Arthritis: Our Microbes Are Our Fortune! Microorganisms 13, (2025).
Kalinkovich, A., Livshits, G. A cross talk between dysbiosis and gut-associated immune system governs the development of inflammatory arthropathies. Semin Arthritis Rheum 49, 474-484 (2019).
Al-Maweri, S. A. et al. The association between the oral microbiome and hypertension: a systematic review. J Oral Microbiol 17, 2459919 (2025).
El-Sehrawy, A. A. M. A. et al. The Microbiota-Gut-Brain Axis in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Narrative Review of an Emerging Field. Eur J Transl Myol, (2025).
Rondanelli, M. et al. Therapeutic Strategies to Modulate Gut Microbial Health: Approaches for Chronic Metabolic Disorder Management. Metabolites 15, (2025).
Okunlola, F. O. et al. Beyond the Gut: Unraveling the Multifaceted Influence of Microbiome on Cardiovascular Health. Clin Nutr ESPEN, (2025).
Gonzalez, E. et al. Altered gut microbiome composition and function in individuals with complex regional pain syndrome. Anesthesiology, (2025).
