e.g., headaches, palpitations, insomnia, exertional fatigue, photophobia, and dizziness.^4,5 Dysbiosis has been directly linked with a number of disorders including IBS, IBD, SIBO,^6–8 fatigue, and autoimmune conditions.9 Dysbiosis caused by an infection or antibiotic use, often results in infectious diarrhoea (also known as gastroenteritis). In all cases, the state of dysbiosis leaves the gut much more vulnerable to external pathogens (as found in contaminated food, for example), easily overwhelming the immune responses and leading to symptoms of varying severity, from diarrhoea to sepsis.

Dysbiosis – What’s Causing It?
There is rarely one single ‘root cause’ to dysbiosis and putting the pieces of the puzzle together can provide us with a more comprehensive picture. So, what can drive dysbiosis?Poor digestion, including low stomach acid and reduced digestive enzymes, accompanied by overeating, may predispose us to a high number of pathogenic bacteria.10 Poor bile production and flow (e.g. due to gallstones, cholecystectomy, poor methylation) may also play a role since bile acids have antimicrobial properties.¹¹Prolonged physical or mental stress can increase the risk of low stomach acid. High cortisol is associated with reduced levels of sIgA,¹² therefore, lower immune surveillance at the gut lining level.Low dietary fibre – Important to cleanse the gut and remove foods which otherwise encourage proliferation of pathogens.¹³Altered mucus production – Mucus is essential to mediating the host–microbiota relationship. Alterations in mucin structure due to FUT2 polymorphisms may affect microbial adhesion,¹⁴ and potentially lead to dysbiosis¹⁵ and reduced microbial diversity,¹⁶ in particular of Bifidobacterium species.¹⁷Food poisoning/exposure to contaminated food and water when travelling¹⁸ – The most common pathogens include Vibrio cholerae, Clostridium difficile, Shigella, Shiga toxin-producing E. coli (STEC), rotavirus, norovirus, and the parasite Giardia lamblia.Medication – Over-prescription of antibiotics can affect the microflora in the short-¹⁹ and long-term,²⁰ and may result in pathogenic colonisation, commonly with Salmonella and C. difficile.21 Proton-pump inhibitors (PPIs) can also increase the risk of developing bacterial overgrowth if taken long-term.^22,23Slow motility or diverticulitis can lead to stasis and faecal entrapment, which can drive an overgrowth of bacteria, and contribute to small intestinal bacterial overgrowth (SIBO).^{24,25, 26} Decreased motility can be caused by excess dietary sugar, chronic stress, and conditions such as diabetes, hypothyroidism, and scleroderma. In particular, disturbed Motor Migrating Complex (MMC) activity has been associated with SIBO.²⁷Structural issues caused by gastric bypass surgery, small intestinal diverticula, intestinal obstruction, and fistulas in Crohn’s disease.²⁸ Teeth loss also needs to be considered as this can affect one’s ability to chew properly, leading to undigested food particles and microbial fermentation in the small or large intestines. Adding to this, poor oral hygiene and use of antibacterial mouth washes or chlorinated water can lead further to dysbiosis.²⁹Compromised immune system can reduce our resilience to intestinal parasitic infections. Depletion of stomach acid, low levels of sIgA,30,12 and use of immunosuppressive medications (e.g. steroids) can also play a role by weakening our defences.³¹

Types of Dysbiosis
The most common pathogenic bacteria associated with dysbiosis include Yersinia, Salmonella, pathogenic forms of E. coli, Fusobacterium nucleatum,32 Proteus mirabilis,33 Citrobacter, Salmonella,³⁴ and Clostridium difficile.³⁵
Small Intestinal Bacterial Overgrowth (SIBO) is the presence of an abnormally high number and/or abnormal type of microorganisms in the small intestine. This includes Streptococci, Escherichia coli and Klebsiella,36 which are usually found in the large intestine. The symptoms of SIBO include diarrhoea, flatulence, and upper abdominal pain and distension. Prolonged SIBO may interfere with digestion and absorption of food, increasing the risk of vitamin and mineral deficiencies. It may even lead to damage and hyperpermeability of the gut lining.³⁷ SIBO is also associated with a number of conditions such as IBS,^38,39 acne rosacea40,41 and diabetes.⁴²
SIBO is an increasingly popular diagnosis these days, however the testing methods used often result in either false-positives or false-negatives,^43,44 and arguably, can narrow our view. Unfortunately, in the past, there’s been an exaggerated focus on the overgrowth of microorganisms and an overreliance on antimicrobial supplements, antibiotics, and a low FODMAP diet. However, whilst SIBO can very much be a problem for a person, it is merely a marker, an end result, accompanied by wider digestive dysfunction such as low stomach acid secretion, slow motility, colonic dysbiosis, or decreased secretion of digestive enzymes. Candida albicans is an opportunistic yeast, which, if allowed to proliferate, can contribute to a range of issues, from IBS-symptoms to brain fog and mental health issues. Whilst we know high sugar diet contributes to Candida overgrowth, we now acknowledge that adopting a strict low sugar and yeast diet is not the sole and best answer to the problem. Most individuals have some amount of Candida growing in their gut, but the numbers are kept in check by a robust immune system.⁴⁵ Compromised immunity can lead to Candida evolving into the more aggressive mycelial form, hijacking nutrient supplies, and establishing more dominance over the beneficial microbiota.^45,46,47
Parasitic infections are another major cause of dysbiosis, driven by consumption of contaminated food and water (including undercooked meat and fish, or leafy vegetables), travelling to developing tropical countries, poor hygiene, and regular exposure to small children, animals, and hospitals. Commonly identified parasites include Blastocystis hominis,48 Dientameoba fragilis,49 Cryptosporidium, Giardia, Entamoeba histolytica,⁵⁰ and Schistosoma (water-borne flatworms or blood flukes).The symptomatology significantly overlaps with other types of dysbiosis (e.g., fatigue, bloating, brain fog), but abdominal pain, acute or chronic diarrhoea, and anal itching are particularly diagnostic of parasitic infections.⁵¹ Skin rashes, such as urticaria (hives),⁵² weight loss or difficulty gaining weight, and food sensitivities can also be experienced. However, not all parasites are bad, as is the case with the Blastocystis hominis which has been associated with a reduced risk of GI disease.⁵³ There are in fact many different genotypes of this parasite, some pathogenic and some not, so appropriate testing is required to ensure that we’re not treating something that may in fact be a healthy resident of the microbiome.⁵⁴
Restoring the Gut Microbiome Balance: The gut is an interlinked system; the examples above have illustrated that there is no single root cause, or a single microorganism behind dysbiosis, but rather a dysfunctional internal environment which allows the microbe to replicate, evolve, and sometimes take over.
So how do we restore the balance and create an environment that favours beneficial microorganisms whilst being hospitable to pathogens?Utilising the power of probiotics and prebiotics is the most beneficial approach to nurture a diverse and protective microbiome. Commensal microbiota inhibit the growth of pathogenic bacteria via modulation of gut pH (lactic acid secretion), production of bacteriocins, and competition for binding sites on mucins/epithelial cells.55 In doing so, they confer resistance to infection against many opportunistic bacterial and fungal pathogens.^56,57,58 Certain probiotics can really help with SIBO, because they have an overall effect on rebalancing gut flora.58–60 Lactobacillus and Bifidobacterium have specifically been shown to exhibit antimicrobial actions against Salmonella, Shigella, C. difficile, E. coli, H. pylori, Klebsiella pneumonia, Yersinia pseudotuberculosis and Staphylococcus aureus.⁶¹ While avoiding fibre may be necessary in a severely compromised gut, an extensive and prolonged low FODMAP diet can lead to greater fibre intolerance and further dysbiosis.¹³ In general the goal should always be to get people to tolerate a high soluble fibre diet, containing a breadth of different prebiotics. Slowly increasing intake of probiotics and prebiotics can help to build-up tolerance.Encourage robust digestion by practising mindful eating, reducing stress and snacking. Digestive enzymes can also substantially aid digestion and absorption of nutrients and reduce the amount of undigested food available for pathogenic growth, providing a great relief to a compromised gut. They have also been used to successfully break through biofilms from a large range of bacterial species.⁶²Vagus nerve regulation can also be used to increase gastric acid secretions63 and improve gut motility.64 It can be stimulated by whole body cold exposure,⁶⁵ acupuncture,⁶⁶ probiotics,⁶⁷ yoga, meditation, and deep breathing.^68,69Dietary support should also be recommended to reduce refined carbohydrate intake, increase fibre, polyphenols and nutrient-dense foods. Also, limit alcohol and processed foods as they’ve been shown to promote dysbiosis.Support integrity of the epithelial tissue and healthy mucus production^17,70 to improve bacterial colonisation and survival.
When to be specific – Therapeutic Diets and Antimicrobial Agents
In cases of multiple and severe chronic issues, stubborn or pathogenic infections, or where approaches to support digestion & microbiome have not resulted in significant improvements, you may resort to using a more targeted approach; specific diets (e.g. Specific Carbohydrate or low FODMAP diets), or antimicrobial supplements. However, in most cases, these should be utilised short-term, and always alongside interventions that positively modulate the gut ecology.
When opting for antimicrobial botanicals, using a combination of ingredients may be more effective than single ingredients, and may reduce the likelihood of the microbes developing resistance. Botanicals such as clove,⁷¹ thyme,⁷² oregano,^73,74 and barbery bark^75,76 have broad anti-bacterial, anti-fungal, and anti-parasitic properties, and also inhibit biofilm formation.77 Natural antimicrobials can also confer protection when travelling abroad, and they can be paired up with probiotics for increased efficacy. Freeze-dried oils, for example oregano oil, offer far more potency, but can also reduce irritation to the mucous membranes and promote absorption for systemic support, therefore helpful for respiratory, or other infections. The table below lists some of the most versatile and effective antimicrobial botanicals.
Natural Antimicrobials
All of the below have a range of antimicrobial properties against a lot of common pathogens including Salmonella, Staphylococcus aureus, Candida species, Escherichia coli, Clostridium difficile, Proteus mirabilis, Bacillus cereus, Entamoeba hartmanni, Endolimax nana, Blastocystis hominis, Listeria, Campylobacter jejuni, Klebsiella pneumoniae, Fusobacterium nucleatum, H. pylori, Toxoplasma gondii, Schistosoma spp. etc.

Our gut ecology is more than a simple black and white canvas. It is an ever-evolving environment, continuously being affected by other systems whilst affecting them at the same time. In essence, there’s much that we don’t know about the specifics of the gut ecosystem, and, while we should always be interested in specific details and mechanisms, we must also zoom out and consider the interconnections between all these systems.