Gut Health and Immunity are Intertwined

You are not just a human being, but a super-organism made up of trillions of microbiomes which live on and inside your body, whose numbers outstrip the number of human cells you’re made up of. This symbiotic and sometimes antagonistic relationship with our microbes has a big influence on our overall health and our immunity.

This relationship with our microbiome has evolved over thousands our years, from the eating of a variety of preserved and fermented foods which have created a colorful diversity of bacteria, fungi and protozoa which live within us.

In our guts, these microbes act as a signaling mechanism to tell the immune system how to respond to things we eat and pathogens we encounter. This is especially important in the development stages of our being and matures to create a balanced immune response – not overreacting creating auto-immunity and not underreacting as so to allow infections to take hold. The bacteria create a variety of by-products from their growth in our guts, including amino acid type products, short chain fatty acids (butyrate and propionate) which enhance the gut barrier, and promote T-cell regulation, stopping over-reactive responses of the immune system. T-cells are a type of white blood cell which controls the immune response. Specific species have been identified such as Bacteroides fragilis which have anti-inflammatory effects and enhancing T-cell activity.

Conversely aberrations in gut integrity with pathogenic bacteria like clostridia, E.Coli, H Pylori, Prevotella have been known in clinical studies to create a ‘leaky gut’ which allows for compounds created by these pathogens to migrate into general circulation and initiate a continued low grade inflammatory response which can target specific organs creating damage and sometime discomfort.

In relation the lungs, recent research has shown they have their own microbiome. They are exposed to several thousand litres of microbiome ridden air daily. The upper respiratory tract is where you can find microbes in abundance and thus the lungs are constantly exposed microbe ingestion and egestion through muscoal defense and mucociliary clearance. The gut biome dwarfs that of the lung biome, however there are indications that the two are interlinked, whereby lung diseases are influenced by shifts by the gut microbiome. Additional research has shown that susceptibility to pulmonary infections, like listeria and viruses, are influenced by the absence of normal gut flora.1 When the lungs are burdened by the presence of streptococcus and staphylococcus species, there’s an increased likelihood of Idiopathic pulmonary fibrosis.2

Research is specifically indicating that it’s the loss of microbiome diversity either from anti-biotic use or gut infection, which causes dysregulation in the immune response or bacterial killing mechanisms systemically, affecting the alveolar macrophage (white blood cell) function in the lungs. The inflammatory signaling pathways are altered creating a more heightened immune response called a cytokine storm, whereby tissues are flooded with immunological insults which the body cannot deal with and clear from the of the lungs.

It appears that the influence is not just one way, the lung microbiome affects the gut microbiome too. When there is infection to the lungs, such as influenza, it has been shown to alter microbiome of the gut reducing the levels of lactobacillus and lactococci (the good guys)and increasing Enterobacter.3 (bad bacteria)

Lifestyle factors like exposure to air pollution and smoking has microbiome changing effects in the lungs worsening the innate immune response. Smoking in particular or exposure to 2nd hand smoke increases the development of pathogenic bacteria in the lungs like bacillus, staphylococcus and Acinetobacter which subsequently increases inflammatory markers like CRP and IL-6.4 Pre-loading the body with an inflammatory burden will weaken it further whenever an infection is present like from a virus or bacterium.

This vital link or cross-talk between the gut and lung microbiome seems to be confirmed by the latest research and the connections are established either through blood or lymphatics, or alterations in the systemic cytokine profiles – that is the general inflammatory responses in the body.

So, how do we protect our lungs for optimal health? Maintaining your gut and lung microbiome environments seems to be the optimal way forward. This can be done by eating a variety of fermented foods to support the gut microbiome, and stopping smoking and exposure to 2nd hand smoke, as well as limiting your exposure to air pollution when it gets bad outside. Another good therapy for lung health is inhaling minute salt crystals through an inhaler. Salt helps to lower mucus production, killing or removing pathogens, and reducing inflammation in the lungs, by lowering IgE levels.


For more information regarding gut health and immunity, please contact Functional Medicine Practioner, Miles Price at 2881 8131 or


  1. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Abt MC, Osborne LC, Monticelli LA, Doering TA, Alenghat T, Sonnenberg GF, Paley MA, Antenus M, Williams KL, Erikson J, Wherry EJ, Artis D Immunity. 2012 Jul 27; 37(1):158-70.
  2. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity.Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser J Nat Med. 2010 Feb; 16(2):228-31
  3. Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation. Wang J, Li F, Wei H, Lian ZX, Sun R, Tian Z J Exp Med. 2014 Nov 17; 211(12):2397-410.
  4. Li, K., Chen, Z., Huang, Y. et al.Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety. Respir Res 20, 272 (2019).

Written by Miles Price

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