Microbe Spotlight: Klebsiella
Understanding Klebsiella in the Microbiome
As you may already know, the human gut microbiome (aka microbiota) is a diverse community of microorganisms residing in the gut. The microbiota plays a crucial role in our overall health and wellbeing. Among these many microorganisms is Klebsiella, a genus of bacteria that, while often benign, can sometimes become pathogenic, leading to various health issues. Chances are, if you are reading this article, you have tested positive for Klebsiella in a stool test.
Klebsiella: A Pathobiont in the Microbiome
Klebsiella species, such as Klebsiella pneumoniae and Klebsiella oxytoca, are considered commensal microorganisms which means they are naturally present in the gut. They are classified as pathobionts, a term used to describe organisms that can exist as part of the normal flora without causing harm but have the potential to become pathogenic under certain conditions. These conditions include a weakened immune system or disruptions in the gut microbiome balance (dysbiosis). When Klebsiella proliferates excessively, it can lead to infections, including respiratory issues, urinary tract infections, and even sepsis.
Klebsiella pneumoniae is particularly challenging to treat due to its ability to develop resistance to multiple antibiotics. This resistance makes infections caused by this bacterium difficult to manage and control. Additionally, the bacterium's capability to form biofilms - protective layers that shield it from the immune system and antibiotics - further complicates treatment efforts.
What about carbohydrates “feeding” klebsiella growth?
It’s a misconception that carbohydrates “feed” Klebsiella, therefore strengthening colonies. Carbohydrate intake does not directly influence the growth of Klebsiella bacteria in the human body. Klebsiella, belonging to the Proteobacteria phylum, primarily metabolises proteins and peptides rather than carbohydrates. Its ability to thrive in the gut or other environments is more influenced by factors such as immune status, underlying health conditions, and the local microenvironment rather than specific types of carbohydrates consumed. While diet can indirectly impact the gut microbiome overall, changes in carbohydrate intake alone are unlikely to significantly promote or inhibit Klebsiella growth. Therefore, when it comes to managing Klebsiella infections, focusing on a healthy balanced diet is crucial, as other factors beyond diet play pivotal roles in bacterial colonisation and pathogenicity.
Histamine Production, Klebsiella and the Microbiome
If you are reading this article it’s highly likely you believe you have histamine intolerance or MCAS (mast cell activation syndrome) and you have identified Klebsiella in your microbiome as the possible culprit to your health issues and food intolerance.
Histamine is a compound involved in local immune responses and regulating physiological function in the gut. Certain gut microbes can produce histamine, which in excessive amounts, can lead to histamine intolerance, manifesting in symptoms like headaches, hives, abdominal pain, and flushing. Klebsiella spp, along with other microbes like E.coli and some species of bacteroides, can cause an overproduction of histamine in the gut and exacerbate symptoms in individuals with histamine intolerance or mast cell activation disorders.
Endotoxemia and Lipopolysaccharides (LPS)
Klebsiella and other Gram-negative bacteria contain lipopolysaccharides (LPS) in their outer membrane. LPS, also known as endotoxin, can trigger a strong immune response when it enters the bloodstream. This condition, known as endotoxemia, can lead to systemic inflammation and is associated with various chronic diseases, including metabolic disorders, cardiovascular diseases, and autoimmune conditions. Managing Klebsiella overgrowth is crucial in preventing endotoxemia and maintaining overall health.
Chronic endotoxemia can result in a range of symptoms, including:
Fatigue: Persistent tiredness and lack of energy due to ongoing immune system activation.
Brain Fog: Difficulty concentrating, memory problems, and a general feeling of mental cloudiness.
Inflammation: Chronic inflammation manifesting as joint pain, muscle aches, and overall body discomfort.
Gastrointestinal Issues: Bloating, abdominal pain, diarrhea, and other digestive disturbances.
Mood Disorders: Increased risk of anxiety, depression, and irritability.
Metabolic Dysfunction: Insulin resistance, weight gain, and difficulty losing weight.
Cardiovascular Problems: Increased risk of heart disease, high blood pressure, and atherosclerosis due to systemic inflammation.
Immune System Dysregulation: Increased susceptibility to infections and autoimmune conditions.
Skin Issues: Eczema, psoriasis, and other inflammatory skin conditions.
Sleep Disturbances: Difficulty falling or staying asleep, leading to poor sleep quality.
Testing Methods for Klebsiella in the Microbiome
How to Test for Klebsiella in the Microbiome:
There are a lot of gut tests and microbiome tests out there. If you are wanting to know if klebsiella overgrowth is playing a role in your health The most accurate test for detecting Klebsiella in the microbiome is metagenomic sequencing, also known as shotgun sequencing. This advanced technique allows for the comprehensive analysis of all microbial DNA present in a sample, providing detailed information about the bacterial composition, including the presence and abundance of Klebsiella species. Here is a brief overview of the different testing methods available:
Metagenomic Sequencing (aka Shotgun Sequencing)
Comprehensive Analysis: Unlike 16S rRNA gene sequencing, metagenomic sequencing looks at all DNA in a sample, giving a complete picture of the microbial community, including bacteria, viruses, and fungi.
Species-Level Identification: It can accurately identify specific Klebsiella species.
Functional Insights: This method also shows what the microbes can do, like antibiotic resistance and metabolic activities.
Alternative Testing Methods
16S rRNA Gene Sequencing: Focuses on a specific region of bacterial DNA. Useful but less detailed than metagenomic sequencing and may not identify all bacteria at the species level.
Culture-Based Methods: Traditional method of growing bacteria in a lab. Effective but may miss some bacteria that don't grow well in lab conditions. Does not give an overall picture of the microbial community.
PCR (Polymerase Chain Reaction): Detects specific Klebsiella species by targeting unique genetic markers. Highly specific but doesn't give an overall picture of the microbial community.
For the most accurate and detailed analysis of Klebsiella and the microbiome, metagenomic sequencing is the best choice. It provides a full view of all microbes present and their functions, offering deeper insights into the microbiome.
Labs Offering Different Types of Microbiome Testing and Reporting on Klebsiella
Metagenomic Sequencing (Shotgun Sequencing)
USA
NirvanaBiome: Specializes in shotgun metagenomic sequencing for detailed insights into the gut microbiome, including Klebsiella. Kit’s available globally.
Australia
Microba: Utilises shotgun metagenomic sequencing for detailed gut microbiome analysis, including Klebsiella. Kit’s available globally upon request.
Europe
Both Microba and NirvanaBiome can ship to Europe upon request.
16S rRNA Gene Sequencing
USA
Viome: Uses metatranscriptomic sequencing but does not use shotgun sequencing. It covers a wide range of microbes, including Klebsiella, full list of microbes may not be available to the consumer or practitioner.
Ombre (previously Thryve): Uses 16S rRNA sequencing for microbiome analysis, which includes Klebsiella.
UK/Europe
ScreenMe: (UK) Offers 16S rRNA sequencing for microbiome analysis, including Klebsiella.
Atlas Biomed: Uses 16S rRNA sequencing for microbiome analysis, including Klebsiella.
Biomesight: Uses 16S rRNA sequencing and can detect Klebsiella.
YourGutMap (UK): Uses 16S rRNA sequencing for comprehensive gut microbiome analysis, may report on Klebsiella.
Biomes (Germany): Uses 16S rRNA sequencing for gut health analysis, including Klebsiella.
Targeted PCR and Culture-Based Methods
USA
GI-MAP by Diagnostic Solutions Laboratory primarily uses qPCR technology to assess microbial DNA, focusing on the identification and quantification of specific pathogens, including bacteria like Klebsiella.
Genova Diagnostics GI Effects Comprehensive Stool Profile, uses a combination of PCR, culture, and microscopy to evaluate gut health and identify imbalances in the gastrointestinal microbiome, including Klebsiella.
Doctor's Data: Provides culture-based and PCR testing for various gastrointestinal pathogens, including Klebsiella.
Australia
Nutripath partners with Diagnostic Solutions Laboratory in the USA to offer the GI-MAP test. Primarily uses qPCR technology to assess microbial DNA, focusing on the identification and quantification of specific pathogens, including bacteria like Klebsiella.
UK/Europe
Medichecks: Provides PCR and culture-based tests that can detect Klebsiella.
The Doctor's Laboratory: Offers a range of microbiological testing, including Klebsiella.
Eurofins (Multiple Locations): Offers targeted PCR and culture-based microbiological testing that can detect Klebsiella.
*Note: the majority of this information is based on web searches. Please confirm with the company directly if they report on Klebsiella prior to purchasing your kit. I can vouch for Biomesight, Microba and NirvanaBiome.
Naturopathic and Herbal Medicine Approaches
Addressing Klebsiella overgrowth and managing histamine production can be a daunting process. I recommend working with skilled microbiome expert with a naturopathic and herbal medicine approach. This approach generally emphasises restoring balance and supporting the body's natural healing processes as well as reducing the potential damaging impact of many “eradication” style approaches.
Dietary Interventions:
Low-Histamine Diet: Reducing the intake of histamine-rich foods (e.g., aged cheeses, fermented products, and processed meats) can help manage symptoms. This approach should only be used short term for some symptom relief. It is useful for symptom management only; the food is not the problem!
Probiotics and Prebiotics:
Probiotics: Specific strains of probiotics, like Lactobacillus and Bifidobacterium, have been shown to help restore gut balance and inhibit the growth of pathobionts like Klebsiella through mechanisms such as competitive inhibition and immunomodulation. Some probiotics contain species of bacteria that produce histamine, so it is best to consult a practitioner before self-prescribing.
Prebiotic Fibres: Prebiotic fibres, found in foods like garlic, onions, and bananas, feed beneficial gut bacteria and support a healthy microbiome. Fructans, including inulin and fructooligosaccharides (FOS), specifically feed beneficial bacteria such as Lactobacillus. This process reduces Klebsiella abundance in the gut by promoting the growth of lactic acid-producing species, which outcompete pathogenic bacteria and enhance overall gut health. Lactulose syrup, a prebiotic, helps reduce Klebsiella by promoting the growth of beneficial bacteria, inhibiting pathogenic bacteria and restoring the colonic pH. Lactulose also encourages the growth of lactic acid-producing lactobacilli species, which helps to reduce Klebsiella numbers.
Herbal Antimicrobials To Consider for Klebsiella Overgrowth:
Herbal Clove (Syzygium aromaticum): Clove has demonstrated antimicrobial properties that can target harmful bacteria like Klebsiella. The herbal extract is a safe and effective choice (not the essential oil).
Pomegranate Husk (Punica granatum): Rich in tannins and polyphenols, pomegranate husk exhibits antibacterial activity, particularly against antibiotic-resistant pathogens like Klebsiella pneumoniae, making it a potential natural alternative for controlling such infections.
Propolis: A resinous mixture produced by bees, propolis has been found to possess antimicrobial properties that can help manage bacterial infections. There is some evidence to support its use against klebsiella. It’s important to source humanely harvested propolis.
Baical Skullcap (Scutellaria baicalensis): This herb contains baicalin, a flavonoid with antibacterial properties that can aid in controlling bacterial overgrowth, including klebsiella. This herb contains compounds such as baicalin, baicalein, and wogonin, which have shown broad-spectrum antimicrobial and biofilm disrupting properties.
Baicalin and Baicalein: These compounds exhibit antimicrobial effects and have been shown to inhibit the growth of various bacteria, including Klebsiella pneumoniae. (Qin et al)
Research: Studies have indicated that extracts from Baical Skullcap can inhibit the growth of Klebsiella and other pathogenic bacteria, suggesting its potential as part of a treatment strategy for bacterial infections. (Chen et al)
Baicalein has been shown to re-sensitise antibiotic resistant Klebsiella to antibiotics (doxycycline). It works by disrupting the bacterial membranes, which helps doxycycline enter the bacteria more effectively. Baicalein also boosts the production of harmful molecules that damage bacteria, reduces the bacteria’s ability to pump out antibiotics, and prevents the formation of bacterial biofilms. Additionally, it helps reduce inflammation caused by bacterial toxins. (Wang et al)
Rock Rose (Cistus spp): Cistus monspeliensis & Cistus salviifolius (Montpellier Rockrose & Sageleaf Rockrose): These herbs have shown strong antibacterial activity against multidrug-resistant Klebsiella pneumoniae. Extracts, particularly from the maceration process, demonstrated significant inhibition of the bacteria, indicating their potential use as alternative treatments. Cistus ladanifer (Gum Rockrose): This herb's extracts have been effective in inhibiting the growth of Klebsiella pneumoniae in vitro, supporting its potential role in herbal remedies against this resistant pathogen.
Oregano (Origanum vulgare): Oregano contains compounds such as carvacrol and thymol, which have shown antimicrobial properties against a variety of pathogens, including Klebsiella species. These compounds can inhibit bacterial growth and disrupt bacterial cell membranes. While oregano extract can be very effective against Klebsiella, it is important to avoid using oregano oil as it can be quite potent and cause inflammation to the lining of the gut, as well as contribute to dysbiosis by “killing” beneficial microbes as well as harmful ones.
Thyme (Thymus vulgaris): Thyme has antimicrobial properties that can be effective against Klebsiella when used as an herbal extract (not essential oil).
Garlic (Allium sativum): Known for its broad-spectrum antimicrobial effects, high allicin garlic can help reduce pathogenic bacteria such as e.coli and Pseudomonas in the gut. While allicin has broad-spectrum antimicrobial properties, direct evidence of its effectiveness against Klebsiella is lacking. Further research is required to explore its potential in treating infections caused by this pathogen. High allicin garlic should not be used long term as an herbal antimicrobial.
Berberine: An alkaloid found in plants like Goldenseal and Oregon Grape, berberine has antimicrobial properties that can help control bacterial overgrowth. However, berberine is strongly antimicrobial and can reduce the numbers of beneficial microbes. Berberine has the potential to do harm; therefore, it should be used cautiously and under the supervision of a trained herbalist and microbiome specialist.
Oregano Oil: While oregano oil (and other essential oils) contains potent antimicrobial compounds like carvacrol and thymol, its use should be limited due to its strength and potential to cause collateral damage to beneficial microbes in the gut. It is best avoided or used in a very diluted form and for short durations, preferably under the guidance of a healthcare professional.
Supportive Supplements:
Vitamin C: An antihistamine vitamin and immune booster.
Quercetin: A natural flavonoid that has antihistamine and anti-inflammatory properties.
DAO Enzyme: Supplements containing diamine oxidase (DAO) enzyme can help break down histamine in the gut, alleviating symptoms of histamine intolerance.
Lifestyle Factors:
Stress Management: Chronic stress can negatively impact gut health and the immune system. Practices like yoga, meditation, and mindfulness can help manage stress.
Adequate Sleep: Ensure sufficient and quality sleep to support overall health and immune function.
Understanding the role of Klebsiella in the microbiome and its potential to impact histamine production and endotoxemia is crucial for those managing histamine intolerance or related health conditions. Through accurate testing, dietary interventions, and naturopathic approaches, it's possible to restore balance in the gut microbiome and improve overall health. It’s best to consult with a healthcare professional before making significant changes to your diet or starting new treatments.
