Protecting Your Microbes

by | Jul 20, 2021 |

A common misconception is that all bacteria are the bad guys, enemies to be vanquished at all costs. Humans clean like we’ve never cleaned before, harnessing antibacterial hand-soaps and disinfecting sprays in the hope of avoiding bugs, the winter lurgy or worse. Paradoxically, the strategies we thought were keeping us safe may in fact be putting us at risk. This suggests a need to reframe the way we think about microbes and be aware of the negative impact our hypervigilance can have on our well-being. With this in mind, let’s explore strategies that protect the beneficial microbes living inside of us in order to bolster our health.

Prioritise Sleep and Relaxation

It’s no secret that our health suffers when we experience too much stress and too little sleep. What is interesting is that both stress (1) and sleep loss (2) can disrupt the balance of bacteria that naturally live in the gut, a condition known as dysbiosis which has been shown to have deleterious effects on health (3).

Practicing good sleep habits such as reducing blue light exposure in the evening, not consuming caffeine late in the day, going to bed at consistent times and implementing relaxation techniques before lights out have been shown to aid sleep quality and therefore potentially your gut health. Incorporating exercise, yoga and/or mediation into your daily routine can do wonders for relaxation and supporting your microbes too.

Eat for your microbes

What we eat on a daily basis can modify the delicate balance of microbes residing in our gut. Research has indicted that our microbiome is in part shaped by our diet, with experiments showing that dietary changes can induce large, temporary microbial shifts within 24 hours (8).

Our microbiome and health are inextricably linked. Since diet can modify the types and abundance of bacterial populations living within us, the food we eat can either positively or negatively impact our overall health. For example, Lactobacillus, a probiotic linked to reduced inflammation in sufferers of inflammatory bowel disease, was shown to be present in increased levels in the guts of mice which were fed fish oil (9). Conversely, studies have shown that diets rich in saturated animal fats increase the levels of Bilophila in the guts of mice and humans, an undesirable effect for those genetically susceptible to colitis as the bacteria has been known to exacerbate the condition (9).

While further research needs to be done in order to understand how specific foods and bacterial species affect the microbiome, there are ways we can eat in order to generally support this area of our health.

Microbial diversity is king when it comes to benefiting our guts and science is starting to reveal that the types of food we eat can have a marked influence on the variety of our microbes inhabitions. Fermented foods in their raw, unpasteurized form, boost healthy bacterial strains in our body and have been shown to provide beneficial health effects (10) (11). Non-soluble fibre, a popular choice on the microbial menu, helps our microbes thrive. Processed foods and reduced fibre intake, in contrast, are thought to decrease microbial diversity, dietary features all too common in western societies.

The main takeaway is this: aim to eat foods that make your microbes happy, because if they’re in good knick, you will be too.

Ease up on the cleaning

With all the advertisements blaring on our TV screens, you would be forgiven for thinking you have to drown your hands in alcohol every time you leave your seat. In truth, many pathogens are more effectively removed by soap and water, and what’s more, antibacterial hand sanitizers are in fact causing some pathogens to develop immunity to the products that are designed to kill them.

Your skin’s microbes are soldiers defending against attack by opportunistic pathogens. Wiping the good guys out with antibacterial products leaves you vulnerable to lingering enemies who are ready to sweep in at a moment’s notice, creating an imbalance requiring treatment (usually in the form of antibiotics).

Microbes are vital to the body’s infection-fighting immune system, they’re not something you want to willingly remove. So Instead of buying into advertisers’ fear-mongering, remind yourself of the beneficial nature of your microbes; don’t be scared of these tiny guys, most are there to help you.

It might sound counterintuitive in today’s pandemic world, but getting your hands dirty can do a world of good for your health. There are some common soil microbes that are essential to our gut flora. However, over the decades, hyper cleanliness and city lifestyles mean a vast portion of the population miss out on these wonderful organisms. Gardening is a great way to expose yourself to clean dirt and a fun way for your body to become acquainted with nature’s tiny helpers.

Use antibiotics only when required

The introduction of modern interventions such as antibiotics has not only changed the way in which humans acquire ancient microbes, but also the composition of these microbes. According to Dr Martin Blaser’s disappearing microbes hypothesis (4), our microbiota have been dwindling over generations, the consequences of which aren’t looking pretty.

Whilst antibiotics are essential for health care, their ill-considered use may pose more of a risk to the future health of patients than previously thought. For example, In a perturbed microbiota – as occurs through antibiotic use (5) – the signals ancestral microbes use to talk to body cells are abnormal which can lead to negative long-term physiology outcomes such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity and type 2 diabetes, just to name a few. Another example of how antibiotics can put our health at risk is the increased risk of developing antibiotic-resistant; a problem at both the individual and societal level (6).

Misunderstandings about the role antibiotics play in common health conditions such as upper respiratory and ear infections may be perpetuating the overuse of antibiotics. Most of these conditions are caused by viruses which don’t respond to antibiotics. Alas, patients continue to pressure doctors for prescriptions and doctors continue to overprescribe them (7).

So when a doctor says that you don’t require antibiotics, instead of pushing for a prescription, listen to their advice and breathe a sigh of relief; your precious microbes will live to see another day.

Consider probiotics

Probiotics are the type of live bacteria and yeasts we want residing in our body; they have positive benefits for our health. These microorganisms can be found in the form of supplements and in fermented foods such as yoghurt, sauerkraut and kefir. Whilst it’s not fully understood how they work, it’s believed probiotics can help those who require them by replacing “good” bacteria when they’re lost, such as is the case when we take antibiotics, as well as helping to restore balance when dysbiosis occurs.

Lots of research has been carried out about the benefits of probiotics on human health including how they help alienate mental health conditions and chronic diseases such as IBS, Crohn’s and migraine. Each strain of probiotic has its own unique properties and thus contribute different health benefits; something to be mindful of when selecting a probiotic.

Whilst experts aren’t yet able to make recommendations on which specific probiotics can improve a particular health condition, it’s an exciting area of research with a promising outlook for future disease treatment and management.


Microbes undeservedly get a bad wrap. Often we fear these tiny creatures instead of acknowledging them for the superheroes they can be. Keeping your microbes healthy is essential for your health, so in future, when looking at ways to protect against illness and disease, consider the pampering of your microbes. It may just be the ultimate in self-care.

Brigid xx



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(2) Benedict C, Vogel H, Jonas W, Woting A, Blaut M, Schürmann A, Cedernaes J. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol Metab. 2016 Oct 24;5(12):1175-1186. doi: 10.1016/j.molmet.2016.10.003. PMID: 27900260; PMCID: PMC5123208.

(3) Carding, Simon et al. “Dysbiosis of the gut microbiota in disease.” Microbial ecology in health and disease vol. 26 26191. 2 Feb. 2015, doi:10.3402/mehd.v26.26191

(4) Blaser, Martin J. Missing Microbes. HarperCollins Publishers, 2014.

(5) Langdon, A., Crook, N. & Dantas, G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med 8, 39 (2016).

(6) Llor, Carl, and Lars Bjerrum. “Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem.” Therapeutic advances in drug safety vol. 5,6 (2014): 229-41. doi:10.1177/2042098614554919

(7) Infectious Diseases Society of America. “Outpatient antibiotic overprescribing rampant: Nearly half written without infection diagnosis, suggests study of 500,000-plus prescriptions.” ScienceDaily. ScienceDaily, 5 October 2018.

(8) Singh, Rasnik K et al. “Influence of diet on the gut microbiome and implications for human health.” Journal of translational medicine vol. 15,1 73. 8 Apr. 2017, doi:10.1186/s12967-017-1175-y

(9) Caesar, Robert. “Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.” Cell, vol. 22, no. 4, 2015, pp. 658-668,

(10) Veiga, P., Pons, N., Agrawal, A. et al. Changes of the human gut microbiome induced by a fermented milk product. Sci Rep 4, 6328 (2014).

(11) Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Jul 6:S0092-8674(21)00754-6. doi: 10.1016/j.cell.2021.06.019. Epub ahead of print. PMID: 34256014.


DISCLAIMER: This article is for informational purposes only. It is not intended to constitute or be a substitute for professional medical advice, diagnosis, or treatment. 


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