srch srch

Hygiene and gut health

Sunday September 13, 2020
Hygiene and gut health

In the current COVID-19 pandemic regular disinfection is essential.  In the short term it is so important to ensure that hands are washed regularly with antibacterial soaps, and that viral transfer is minimised.  Subsequently, the workplace, favourite café and supermarket are exceptionally clean, but beyond COVID-19 should a long-term disinfection strategy be implemented?  And what are the potential repercussions of excessive hygiene?


What is the microbiome?

The microbiome is the collective term for the bacterial colonies that live in the gastrointestinal tract.  Chances are you have read or heard on several occasions that humans have a greater number of bacterial cells than human cells.  What makes these bacteria so important is the relationship they have with us and the interaction with the food we eat.


For instance, the microbiome ferments resistant fibres from food into signalling agents called short chain fatty acids, which further provide a fuel for the microbiome, but also initiate a cascade of events that influence circulating levels of fats and glucose.


The microbiome and immune system 

Healthy microbiome healthy you
Bacterial colonies living in the gastrointestinal tract (the microbiome) support the immune system.

Excitingly, we have learned that the microbiome produces antibiotic-like substances which support the immune system.  Subsequently, research has shown a whole array of benefits from the supplementation of beneficial bacteria that include, cholesterol reduction, improved mood, improved digestion, the reduction of pathogenic (infection-causing) colonies and improvement of digestive symptoms.  


In fact, evidence shows that the microbiome develops during gestation, primarily from the maternal microbiome and is further influenced by the method of childbirth, medication, method of feeding such as breastfed vs formula-fed, plus illnesses and exposure to pollution.  And what cannot be ignored, is the potential for a reduced risk against infection and disease by maintaining a healthy and diverse microbiome.


Hygiene - can too much cleaniness work against us? 

In terms of antibacterial and antiviral strategies, it is well established that internal and topical antibiotic therapy wipes out all bacteria, irrelevant if they are infection causing or beneficial.  These effects may take months to re-inoculate and expand the microbial diversity back to pre-treatment levels.  


This effect has been associated with the increased risk of allergies, atopic allergies, besides gastrointestinal conditions, and the development of autoimmune conditions. However, a careful balance is required for the selective use of antibiotic medication on a necessary-need basis, so that a balance is maintained between the bacteria that should be reduced and those that can be tolerated.   Furthermore, researchers acknowledge the need for targeted microbiome interventions as a future addition to disease control.

Investigation into antibacterial topical formulas for hand hygiene show that regular short-term use does not affect the skin microbiome diversity, yet investigation into long term regimens are necessary to understand the effects on not only skin bacteria but also the gastrointestinal microbiome.  



Finding the clean balanceHand sanitiser can be accidentally transferred from the hands to the lips via cutlery, plates and snacks


Studies investigating the microbial effects of eczema have found that topical emollients that have antioxidant and antimicrobial properties may improve skin microbiome diversity and reduce pathogenic Staphylococcus species. However, it can be easy to inadvertently consume hand sanitiser, for example, via transfer on to cutlery, plates, eating with hands or even applying lip balm with fingers.

To address the question this article started with, what are the potential repercussions.  This article is by no means saying that the current hygiene strategies that are underway to minimise viral transfer should be boycotted.  Not at all, hygiene is extremely important.  However, the message lies in preserving microbiome diversity.

Six top tips to preserving the microbiome while maintaining an antibacterial and antiviral regimen:

  1. Eat organic wholefoods.  These foods have been raised or grown without the use of antibiotics and pesticides and therefore will help to preserve the microbiome and gut health in general.

  2. Include several portions daily of resistant fibre-rich foods, such as, leafy green vegetables, Jerusalem artichoke, chicory, and unripe bananas.  Resistant fibres are often termed prebiotics and are also available in food supplements.  These foods will provide the essential fibres that the microbiome love to ferment.

  3. Consider a beneficial bacteria formulation that provides several strains of bacteria and includes saccharomyces boulardii, plus prebiotic fibres.  Saccharomyces boulardii has been shown to support an antiseptic compound called secretory IgA (sIgA).

    sIgA lines the gastrointestinal tract to stop pathogenic bacteria and viruses from taking hold onto the cells that line the tract.  This stops the pathogen from entering the body where it could exert an infection.

  4. Start each meal with bitter tasting leaves, herbal bitters, or apple cider vinegar to stimulate gastric secretions.  Gastric secretions not only help digest the meal but are also protective from infection as they are naturally antibacterial and antiseptic.

  5. If you are feeling stressed, try implementing some stress management techniques.  Stress turns ‘off’ non-essential processes of which includes the immune function.  This makes the stressed individual more likely to contract an infection. Stress management may stall this process and reduce the risk of infection through normal immune responses.

  6. Wash hands frequently with antibacterial soap and water.  It is essential to rinse the soap thoroughly from the hands so as not to inadvertently consume it.



Improved sanitation, hygiene and antibiotic development have been essential throughout the 20th century to reduce communicable disease.  Yet little emphasis has been given to the preservation of a healthy microbiome.

Antibiotic and antiseptic therapy can alter the microbiome, yet there are simple steps that can be taken to minimise the disruption and promote its rapid recovery.  


A healthy microbiome can be invaluable in health and it is considered essential for minimising the severity of contracted infections.


Author: Jenny Carson is a Nutritional Practitioner and Technical Services Manager at Viridian Nutrition. She holds a BSc honours degree in Nutritional Science and is a Master of Research (MRes) in Public Health.


Collado MC, Rautava S, Isolauri E, Salminen S. Gut microbiota: a source of novel tools to reduce the risk of human disease?. Pediatr Res. 2015;77(1-2):182-188.

Lynde CW, Andriessen A, Bertucci V, et al. The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients. J Cutan Med Surg. 2016;20(1):21-28.

Scudellari, M., Cleaning up the hygiene hypothesis. Proceedings of the National Academy of Sciences Feb 2017, 114 (7) 1433-6.

Two AM, Nakatsuji T, Kotol PF, et al. The Cutaneous Microbiome and Aspects of Skin Antimicrobial Defense System Resist Acute Treatment with Topical Skin Cleansers. J Invest Dermatol. 2016;136(10):1950-1954.


The information contained in this article is not intended to treat, diagnose or replace the advice of a health practitioner. Please consult a qualified health practitioner if you have a pre-existing health condition or are currently taking medication. Food supplements should not be used as a substitute for a varied and balanced diet.


TAGS: DigestionMicrobiome, Friendly Bacteria


Back To Top

The Leading Brand of ethical vitamins