Morganella Overgrowth: Symptoms and Natural Treatment
If your gut has felt “off” for a while (with bloating, food reactions, stubborn UTIs, or unexplained histamine-type symptoms), the bacteria Morganella might be part of the picture.
While best known for hospital-acquired infections and urinary tract infections, Morganella spp. can also show up on stool tests and contribute to gut dysfunction and inflammation.
This is a research-informed article to what Morganella is, why it can be tricky to treat (antibiotic resistance is real!), and how to approach it with practical, gut-friendly strategies.
What is Morganella?
Morganella spp. are gram-negative and facultative anaerobic bacteria of the Enterobacteriaceae family. It can be a common inhabitant of the gastrointestinal tract (your intestines), but not necessarily always present. Its transmission is mainly through contact with contaminated persons or objects — think healthcare settings, shared surfaces, or cross-contamination.
Some strains are ESBL (extended-spectrum beta-lactamase) producers, which makes them resistant to many beta-lactam antibiotics. That complicates standard treatment choices if infection truly takes hold.
Morganella in the gut
In a healthy microbiome, problematic organisms are kept in check by competition (from your “good guys”; or probiotics), your immune system, and gut motility. But when the terrain shifts, for example after antibiotics, with low stomach acid, slowed motility, chronic stress, or a high-inflammatory diet, Morganella can overgrow. This can increase endotoxin burden (LPS) , histamine reactivity and intolerance, and intestinal inflammation.
Morganella spp. is also linked to SIBO, being a common Hydrogen and Histamine producer.
Common symptoms of Morganella spp.
Symptoms overlap with other dysbiotic patterns and are not exclusive to Morganella overgroth. It’s important to confirm with appropriate testing (like a GI-MAP), rather than self-diagnosing.
Digestive
Bloating, excess gas, abdominal discomfort
Irregular stools (typically loose stools, or alternating with constipation)
Foul-smelling gas or stools
Food intolerances (especially higher histamine or high-fat meals)
Systemic
Brain fog, fatigue, headaches
Histamine flares: flushing, hives, nasal congestion, itchy skin
Joint or muscle aches after meals
Urinary and pelvic
Recurrent UTIs or urinary urgency/frequency (Morganella is a known UTI pathogen)
Strong ammonia-like urine odor
Risk factors of Morganella overgrowth
There are several risk factors that can contribute to morganella overgrowth in the gut:
Recent or frequent antibiotics
Long-term PPI use and low stomach acid
Slow motility (constipation, hypothyroidism, EDS/hypermobility, vagal dysfunction)
Hospitalization or exposure to healthcare settings
High refined sugar/ultra-processed diet
Alcohol consumption
Poor sleep
By looking into and/or addressing these risk factors, you greatly reduce the likelihood of developing a Morganella overgrowth and SIBO.
Antibiotic resistance
Some ESBL-producing strains carry ESBL enzymes, providing resistance to many antibiotics such as penicillins and cephalosporins. In serious infections, culture and sensitivity testing can guide therapy.
One important thing to know is that broad-spectrum antibiotics can worsen dysbiosis by killing beneficial bacteria and creating resistant organisms upon exposure, making gut symptoms worse after short-term relief.
For gut colonization and overgrowth without systemic infection, a terrain-first approach (working on the microbiome and its balance) often helps reduce burden and symptoms while supporting resilience.
When to consider antibiotics
Acute, red-flag infections (fever, flank pain, rising inflammatory markers) or complicated UTIs require medical care, and often time the use of antibiotics.
For gut overgrowth, if antibiotics are used: insist on culture and sensitivities (a test can tell us beforehand if the strain you have will be resistant to certain antibiotics or not), and plan for microbiome repair afterward.
Testing options
Chances are, you have found this article because your stool test came back showing Morganella spp. overgrowth. No need to panic! See below for natural treatment strategies.
The best way to detect overgrowths is through comprehensive stool testing, such as microbiome mapping (GI-MAP and similar PCR-based test options). These tests can detect Morganella spp. (amongst other bacteria, parasites and viruses), estimate relative abundance, and even provide antimicrobial susceptibility in some panels.
They typically also include markers of inflammation (calprotectin), digestion (elastase, steatocrit), short-chain fatty acids, and beta-glucuronidase.
In case of UTIs and when urinary symptoms are present, a urine culture with sensitivities is key.
If morganella is present, you can also consider a SIBO breath test if bloat (also called distention) is important and/or painful.
Natural treatment strategies
I highly recommend you work with a practitioner, especially if you have recurrent UTIs, chronic symptoms, diagnosed conditions, or are on any medication. The following are general educational guidelines and should not be construed as medical advice.
Calm inflammation and support the mucosa
This can be done in multiple ways, typically some (but not all) of these will be necessary:
Demulcents: DGL, slippery elm, marshmallow root, and aloe vera inner fillet (not the whole leaf) can soothe the lining and reduce reflux-type symptoms during die-off.
Zinc L-carnosine: Supports mucosal repair and tight junction integrity.
Omega-3s (EPA/DHA): Helps temper LPS-driven inflammation.
Vitamin D : Supports antimicrobial peptides and immune balance.
Restore digestive function
Ensuring digestion is optimal “upstream” helps alleviate the burden and contributes to less undigested food or improperly broken down foods feeding bacterial overgrowths.
Stomach acid: Low acid favors Enterobacteriaceae overgrowth. If no ulcers, gastritis or H. pylori is present, a trial of betaine HCl with protein meals may help. Using bitters pre-meal to stimulate gastric and biliary secretions is also a great option.
Bile flow: Bitter herbs (gentian, artichoke, dandelion) and phosphatidylcholine support fat digestion and have indirect antimicrobial effects in the small intestine. In some people, bile is insufficient and supplementing with ox bile or TUDCA (bile salts) can be appropriate.
Enzymes support: If elastase is low on testing, digestive enzymes with meals can reduce fermentation and gas pressure.
Improve motility and transit
Again, there are different ways to improve motility, and typically some (but not all) of these will be necessary:
Prokinetics: Ginger, artichoke, Iberogast, and prokinetic drugs can reduce overgrowths pressure by moving contents of the small intestine downstream.
Vagal tone: Nasal breathing, extended exhale breathing drills, gargling/humming, and consistent sleep-wake timing can help stimulate the vagus nerve.
Address constipation first: I have a wonderful (and currently free) guide for constipation here. What helps most people is supplementing with magnesium oxide or citrate, select fiber titration, proper hydration, daily movement.
Target microbial overgrowths
Antimicrobial herbs and botanicals with activity against Enterobacteriaceae and biofilms:
Berberine-containing herbs, oil of oregano, thyme, rosemary, clove, garlic extract (allicin), and neem.
Tannins, pomegranate husk & peel, and polyphenols may inhibit Gram-negative growth and quorum sensing.
Biofilm support: N-acetylcysteine (NAC) and lactoferrin can enhance effectiveness; start low to minimize die-off.
Probiotic strains that can be helpful:
Lactobacillus rhamnosus GG, L. plantarum, and Bifidobacterium longum all have data for reducing endotoxin-related symptoms and improving barrier function.
Spore-based probiotics can compete with opportunists and improve diversity in some cases. My favourite product is MegaSporeBiotic by Microbiome Labs. Use code GUTTALK to sign up and access practionner-grade supplements.
Prebiotics and fiber to prioritize:
Start with gentle fibers (partially hydrolyzed guar gum (PHGG), acacia, psyllium husk) to increase butyrate producers and improve bowel regularity — go slow to avoid bloating!
Polyphenol-rich foods (ex: berries, cacao, green tea) feed beneficial microbes without overfeeding Enterobacteriaceae.
Note on die-off: Temporary upticks in gas, fatigue, or brain fog can happen. If so, titrate slowly, prioritize hydration with minerals and bowel regularity.
For recurrent UTIs only:
Seek culture-based testing to inform treatment decisions
Adjuncts you may consider with your clinician: D-mannose, cranberry proanthocyanidins (PACs), methenamine hippurate (urinary antiseptic), adequate hydration, addressing constipation and estrogen status in peri/postmenopause.
Diet foundations
These are general guidelines applicable for most gut health protocols, please consult your nutritionist or dietician for a personnalized plan.
Emphasize: Cooked vegetables, lean proteins, olive oil, low-glycemic fruits, and fermented foods as tolerated.
Reduce: Refined sugar, alcohol, ultra-processed foods and cured meats.
Having protein (ideally animal-based) at each meal stabilizes blood sugar and supports mucosal repair.
If you are very reactive, you could trial a lower-fermentable plan short term (ex: modified low-FODMAP; SIBO Bi-Phasic Diet) while you treat, then re-expand diet and fiber diversity as symptoms calm.
Safety notes
Pregnancy or breastfeeding: Avoid most antimicrobial botanicals unless guided by your clinician.
Check medication interactions: Berberine can interact with many drugs; PPIs change gut ecology; anticoagulants may interact with certain herbs. These are only a few examples.
Timeline for treatment
This is a sample schedule, not everyone responds on the same timeline, nor wish to fit this one. Please consult your practitioner or doctor first before starting a new protocol.
Weeks 1–2: Bowel regularity, reflux reduction, and sleep are prioritized; initial symptom stabilization.
Weeks 3–6: Use of botanicals and/or probiotics in place; bloat and food tolerance often improve, with fewer histamine-type flares.
Weeks 6–12: Rebuild phase - expand fiber diversity, pull back antimicrobials, continue motility/mucosal support.
If you encounter persistent symptoms, it may point to concurrent conditions like SIBO and its co-infections, fungal overgrowth (SIFO), H. pylori, low stomach acid, or pelvic floor dysfunction.
The bottom line
Morganella spp. are opportunistic Enterobacteriaceae that can contribute to gut symptoms and recurrent UTIs, with a reputation for antibiotic resistance. The most sustainable strategy in my opinion is a terrain-first plan:
Soothe the gut lining, restore digestive function and motility, use targeted botanicals and probiotics, and gradually rebuild diet diversity. With a thoughtful, stepwise approach — and guidance from a practitioner — you can calm symptoms, reduce overgrowth pressure, and restore resilience.