Gut Bacteria: Drivers of health and disease

Gut Bacteria. Hidden from view and silently thriving within your body, they play an important role in maintaining your gut and your body’s health.


Your body’s health depends on many factors, some are external, like the type of diet you eat, your exposure to environmental toxins or drugs, or the lifestyle you follow. But there are also important factors that occur deep within your body, like the makeup and function of your genes, which determine how your body works.

Another important intrinsic factor buried deep within your body, which has a huge impact on your health, are gut bacteria.

Your gut, which represents the largest organ system in your body, starts in your mouth and works its way down to your stomach and intestines. In all these body locations, bacteria thrive, making up the gut microbiome. However, most of the gut bacteria is located within the large intestine, where they are in charge of digesting fermentable fibre and producing important chemicals that affect your health.

Intestinal Gut Bacteria


What species are there?


Within the gut’s large intestine, where the vast majority of gut bacteria live, a normal healthy microbiome is composed of a large number of different bacterial species. Studies have shown that these healthy bacterial communities mostly belong to the Firmicutes and Bacteroidetes phyla1. Other phyla of gut bacteria, found in lesser abundance, include members of the Proteobacteria, Fusobacteria, Actinobacteria and Tenericutes groups.


However, it has been established that there is no ideal combination of gut bacteria that define a healthy gut. Research has shown that the gut microbiome of healthy people varies significantly. In other words, different healthy people harbour different combinations of gut bacteria. This was one of the key findings of the Human Microbiome Project, which analysed the gut microbiome of hundreds of healthy participants2.


What do they do?


The intestinal microbiome has three basic roles. First, it protects our body against invading pathogens, and during our first days out of the womb, it helps with the development of our immune system. Second, it produces vitamins and amino acids that are essential for the optimal functioning of our body. Finally, the intestinal microbiome is the primary processing agent of complex polysaccharides, such as fermentable fibre, found in the food we eat3-4.


Without the gut bacteria, we would not be able to process these food components. Through the fermentation of dietary fibre and carbohydrates, gut bacteria produce special chemicals called metabolites, including:

  • Short-chain and medium-chain fatty acids, produced from the fermentation of dietary fibre
  • Secondary bile acids converted from primary bile acids
  • Metabolites generated from meat-derived choline and l-carnitine
  • Vitamins K and B12, and folate as well as antimicrobial compounds


These compounds serve various purposes in your body, from feeding the cells lining your colon to modulating the function of the immune and nervous systems and protecting our body from pathogens.


Gut Bacteria: the good and the “relatively good”


Despite the wide-spread variation in microbial “species formulas” found in healthy people, some specific gut bacteria species have been associated with beneficial roles, whereas others have a more context-dependent role.


For example, some bacteria are innocuous, unless they overgrow. This is the case of Fusobacterium nucleatum, a bacterium commonly found in the mouth, and nowhere else, under healthy conditions. However, when this species overgrows and expands to other body sites, like the gut, it has been associated with colorectal cancer, inflammatory bowel disease and appendicitis, among many other diseases5. These bacterial species are called pathobionts. They are defined as bacteria that may be common residents of our body and innocuous under normal conditions but have the potential of becoming pathogenic and cause inflammatory conditions. In Table 1 we list some examples of pathobionts reported in the human gut.


Bacterial strain Conditions Promoting Pathogenesis
Segmented Filamentous Bacteria Found to cause colitis in mice with deficient immune systems
Promotes disease in animal models of rheumatoid arthritis and multiple sclerosis
Helicobacter hepaticus Induces colitis and large bowel carcinoma in certain mice models
Helicobacter pylori Associated with increased risk of gastric cancer in mice carrying certain mutations
Proteus mirabilis & Klebsiella pneumonia Responsible for inducing colitis and colorectal cancer in immune-deficient mouse models
PrevotellaceaeTM7 Associated with colitis in mutant mice with an altered immune system
Clostridium difficile May lead to pseudomembranous colitis in people who follow a long-term antibiotic treatment
Vancomycin-resistant Enterococcus May invade the bloodstream in people receiving broad-spectrum antibiotics



Other bacterial species have been consistently associated with beneficial functions and are considered as part of the normal or commensal flora living in the gut. These can be considered “good bacteria” (as long as dysbiosis does not occur). These include:


      • Akkermansia municiphila

        This is one of the most abundant species of the human gut, representing between 0.5-5% of the total gut bacteria. This species can produce sugars from the degradation of mucus, which are used as a food source by other bacteria7. Benefits: It helps maintain mucosal health and promotes mucus production. Dysbiosis: Low levels of this bacterium are associated with obesity and metabolic dysfunction, whereas overgrowth has been linked to multiple sclerosis8.


      • Bacteroides fragilis

        This is a member of the common Bacteroidetes phylum, one of the two most common phyla found in the human gut. Benefits: This species has been shown to be an important modulator of immune functions, microbial balance, intestinal barrier function and neuro-immune health in animal models9. Dysbiosis: Low levels of this gut bacteria has been associated with reduced anti-inflammatory capacity in the intestine10.


      • Bifidobacterium

        Species of this bacterial genus are found in breast milk, and in the gut of infants fed breast milk. This bacterium is also found in some probiotic supplements. Benefits: Presence of this gut bacteria has been associated with various health benefits11, including increased protection from infections. A study transferring this bacterium from infants into animal models has shown that species like B. bifidum, B. dentium, and B. longumstimulate systemic and intestinal immunity12.


      • Clostridia (class) 

        This is a broad group of bacteria belongs to the phylum Firmicutes (next to Bacteroidetes, one of the most common bacterial phyla in the gut). Some members of this class are highly pathogenic, like Clostridium difficile. However, most species are commensal and live peacefully in the gut13. Benefits: Commensal Clostridium species are important producers of short-chain fatty acids like butyrate, which is an essential source of energy for colonocytes (cells from the colon) and play important roles in health. Members of the Clostridia have also been associated with improved gut barrier function, immune regulation, and protection against infections13. Dysbiosis: Reduced levels of this bacterial group have been associated with autoimmune diseases, immune dysfunction, and inflammatory alterations. Patients suffering from IBD, for example, have been shown to host reduced levels of specific Clostridia species14-16.


      • Enterococcus

        A member of the Firmicutes phylum, some species within this lactate-producing genus are commensal, like Enterococcus faecalis. Benefits: Early colonization by species of this genus has been associated with improved colonic homeostasis and increased protection from infectious pathogens17. Dysbiosis: During events of dysbiosis, E. faecalis has been shown to expand and increase its relative abundance and invade the bloodstream and organs, causing disease17-18.


      • Escherichia

        This bacterial genus includes the well-known bacterium E. coli, which is a common inhabitant of the gut. Most strains of this species are non-pathogenic, but some are highly dangerous and can cause serious diseases. Benefits: Commensal E. coli help with the breakdown of foods in the gut and are important producers of Vitamin K19. They also have an important role in protecting our body from infections, especially from pathogenic strains of this species. Dysbiosis: high levels of this bacterium have been linked to inflammation whereas low levels may lead to decreased protection from pathogenic E. coli strains.


      • Faecalibacterium prausnitzii

        Another member of the Clostridia group of bacteria, this species is the most abundant bacteria found in the large intestine, representing up to 5% of the intestinal population of gut bacteria. This species is an important producer of the SFCA butyrate and is linked to healthy guts20. Benefits: This bacterial species is associated with anti-inflammatory responses, and with the maintenance of mucosal homeostasis. Dysbiosis: Alterations to the normal levels of this bacteria in the large intestine is associated with IBS, coeliac disease, colitis, chronic idiopathic diarrhea, and some cancers20.


      • Lactobacillus

        Well known as the predominant bacterial species of the vaginal microbiome, species of this genera are also present in the gut. They are also commonly found in probiotic products. Benefits: members of this genus are important producers of lactate and the SCFAs acetate and butyrate. These chemicals are important energy sources of intestinal epithelial cells. This species is also known to produce important antimicrobial chemicals that help fight off pathogens and chemicals that improve immune function21-22.


      • Enterobacter

        These members of the Proteobacteria phylum are a diverse group of bacteria that include both pathogenic and commensal species. Benefits: along with other intestinal commensal species, Enterobacter species help maintain homeostasis and influence inflammatory responses. Dysbiosis: some species of this genus are important nosocomial pathogens (acquired in hospitals), linked to conditions like bacteremia, endocarditis, septic arthritis, osteomyelitis, skin/soft tissue infections, as well as lower respiratory tract- urinary tract and intra-abdominal infections23. Altered levels of commensal species have been linked to inflammatory responses and to intestinal mucosal health24. High levels of this bacteria have also been associated with the development of diverticulosis25.



These are just a sample of some bacterial species that have important roles in our body’s function, but many more thrive in your gut. Hence, it pays to keep them healthy and in optimal balance. One of the most effective ways to keep a healthy gut microbiome is by feeding it the right foods.


Feeding your gut bacteria


Gut bacteria living in the large intestine are strongly affected by the amount and the type of food you eat. The type of food, in particular, can directly affect the composition of the gut microbiome, potentially leading to gut dysbiosis and the associated overgrowth of pathogenic species. The most important source of nourishment for the gut bacteria living in your colon is fibre.

      • Types of fibre

        Our body produces a vast number of enzymes, each with specific roles. However, no enzyme produced by our body can process glycans, a type of indigestible carbohydrate found in some foods26. Glycans include resistant starch, inulin, lignin, pectin, cellulose and fructooligosaccharides (FOS), which can only be metabolised by bacteria that produce a special type of enzymes called CAZymes26. Bacteroides, Bifidobacteriumand and Ruminococcus are some of the gut bacteria known to produce these enzymes and being able to degrade glycans in our body.


      • Sources of Gut-friendly Fibre

        The best sources of fibre include whole food plant sources, such as green bananas (try green banana flour), potatoes, rice, cereals, legumes, yams and sweet potatoes, green leafy vegetables, carrots, as well as some fruits with edible peel, like apple and pears27. For a good guide on plant-based whole foods rich in gut-friendly fibre see this recent overview. Beyond fibre, wholefood animal sources, rich in nutrients, are also important and include foods rich in protein, good fats, collagen and other nutrients.


      • What are whole foods?

        Simply defined, wholefoods include any food that is minimally processed, free of added sugars or any food additives, free of pesticides, or hormones. Think of organic, free-range, fruits, vegetables and meats. Wholefoods meats include organ meats, like liver, kidney, tripe or heart, which are rich in important micronutrients like vitamins, minerals, healthy fats and amino acids. These nutrient-dense wholefoods nourish our body and our gut bacteria, helping us keep healthy. For some good recent overviews on plant and animal wholefoods head on to these two recent articles on paleo-diet and animal proteins. Finally, for a more thorough review on how different foods affect gut bacteria and our health, see this recent Nature review.


Another important source of nourishment for your gut microbiome are probiotics and fermented foods, like cheese, yogurt, kombucha, and sauerkraut, which are rich in beneficial microbes. However, not everyone is able to benefit from these products, due to intolerances or sensitivities against them. Some of the most common reactions against probiotics or fermented foods include:


      • Histamine intolerance

        • Function

          Histamine is an important chemical, commonly released after an injury as part of the body’s immune response. Histamine serves various functions in the body, like helping transmit messages to the brain and triggering the release of stomach acids, helping with digestion.


        • Symptoms

          People suffering from histamine intolerance may experience symptoms that are very similar to allergic reactions, including headaches, nasal congestion, fatigue, hives, skin problems, bloodshot eyes, digestive problems, irregular menstrual cycle, nausea and vomiting. In more extreme cases of intolerance, people can experience heart problems and other serious conditions28.


        • Causes

          Histamine intolerance results from a disequilibrium between the production or accumulation of histamine in our body and our capacity to degrade it. Two mechanisms have been proposed to explain the development of this intolerance, involving an excess of histamine present in the body or/and dysfunction in our body’s ability to degrade histamine29.


          • Excess Histamine – This can happen due to excessive consumption of foods rich in histamine or alcohol. Red wine, for example, is rich in histamines and is a strong inhibitor of diamine oxidase, the main enzyme responsible for histamine metabolism. Some food rich in histamines are included in Table 1.


Table 1. Histamine-rich foods. For a more detailed list, look here.

  • Yoghurt
  • Sour cream
  • Buttermilk
  • Kefir
  • Sauerkraut
  • Kimchi
  • Pickles
  • Pickled Veggies
  • Kombucha
  • Cured of fermented meats
  • Wine
  • Alcohol
  • Champagne
  • Beer
  • Fermented soybean (miso, soy sauce)
  • Fermented grains (sourdough bread)
  • Tomatoes
  • Eggplant
  • Spinach
  • Frozen, salted, or canned fish
  • Vinegar
  • Tomato ketchup



      • Impaired histamine metabolism

        The main cause of histamine intolerance involves malfunctions of the enzyme diamine oxidase or DAO. Another important enzyme is histidine decarboxylase (HDC), which helps immune cells produce histamine30. Genetic or acquired impairments involving these enzymes result in our body’s inability to metabolise histamine28, 31.


      • Histamine and Food Bacteria 

        Some bacteria present in cheese and other dairy products, fish, meat, and vegetables are able to produce histamine, potentially contaminating the food with high levels of this chemical. The best example is histamine fish poisoning, a disease associated with the consumption of fish contaminated with histamine producing bacteria32. Common bacteria associated with histamine contamination of food include Morganella morganii, Escherichia coli, Hafnia alvei, Proteus Vulgaris, Proteus mirabilis, Enterobacter aerogenes, Raoultella planticola, Raoultella ornithinolytica, Citrobacter freundii, Pseudomonas fluorescens and Photobacterium damselae.


      • Histamine and gut bacteria

        The role of gut bacteria in the production or regulation of histamine has not been extensively studied. One study confirmed the presence of the genes coding for the HDC enzyme in asthmatic patients, hinting at the presence of HDC-producing bacteria in their guts33. This study identified the species Morganella morganii, Escherichia coli and Lactobacillus vaginalis as the bacteria responsible for the highest secretion of histamine. Other bacterial species found in the gut have been associated with the degradation of histamine, further supporting the idea that gut bacteria play an important role in the metabolism of histamine34.


      • Small intestinal bacterial overgrowth (SIBO)

        Another potential cause of intolerance to probiotics and fermented foods is SIBO.


        • What is SIBO?

          This is a serious condition affecting the small intestine, characterised by colonization and growth of gut bacteria normally found elsewhere in the gut35.


        • What causes SIBO?

          SIBO has been associated with multiple health problems, including altered intestinal anatomy36, hypochlorhydria37 (low levels of gastric acids), dysfunctional intestinal motility38-39, and immune dysfunctions40.


        • Symptoms 

          People suffering from SIBO can experience bloating, cramps, diarrhea or constipation, and indigestion35.


        • Associated conditions

          Multiple conditions have been associated with SIBO, including obesity41, type II diabetes42, chronic pancreatitis43, liver disease44, Parkinson’s disease45, IBS, increased likelihood of developing certain infections46.


If you are suffering from SIBO, consuming probiotics or fermented foods could worsen your condition and symptoms. The first step in addressing this condition is to determine which bacteria are causing the SIBO and to establish what is the best way to treat your overgrowth.



      • FODMAP intolerance – Another potential underlying cause behind your intolerance to probiotics and fermented foods is a broader intolerance to FODMAPs.


        • What are FODMAPS?

          FODMAP is a term used to describe a group of compounds found in a wide variety of foods. It includes fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP)47.


        • Where are FODMAPS found?

          FODMAPS are found in virtually all foods, but they are more abundant in some groups. FODMAPS are abundant in:


          • Vegetables, like broccoli, garlic, onion, sugar snap peas, cabbage, cauliflower, and leeks.
          • Fruits, like apple, apricot, cherries, mango, peach, pear, watermelon, plums and persimmon.
          • Proteins, like soy-based products (tofu, soy milk), and legumes (lentils, beans, peanuts).
          • Fats, like vegetable oils like canola, sunflower, safflower, grape seed, soybean, cottonseed, and peanut oils.
          • Starches, like those present in legumes.
          • Dairy products, like cheese, yogurt, and milk.
          • Nuts and seeds, like pistachios, almonds, and hazelnuts.
          • Herbs and cooking spices, like ketchup, soy sauce, mayonnaise, salad dressings, and many others.
          • Sweets, like honey, agave syrup, refined sugars, artificial sweeteners, and high-fructose syrup.
          • Beverages, like beer, wine, soda, and fruit juices.


If you suffer from SIBO, FODMAP or histamine intolerance, the first step you need to take is to radically change your eating habits. You may also need to clear your gut from pathogens and make some lifestyle changes.


By becoming a patient at the Australian Centre for Functional Medicine, you will be taking the first step to a life-long improvement in your health. At our centre, we run comprehensive testing to identify your underlying problems. Whether SIBO, dysbiosis, gut infections, FODMAP intolerance or something else altogether, our comprehensive testing approach, which include blood, stool, breath, urine, among other tests, will reveal your underlying problems.


Based on the results of these tests, we will be able to design a personalised treatment using a combination of natural and conventional medicine. With a treatment plan at hand, we will be able to guide you in your path to recovery and health.





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