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Magical Microbes & The Marvellous Microbiota

Updated: Dec 8, 2022

Key Definitions:

Microbiota - are the microorganisms that live on and inside the human body

Microbiome - is the genetic material of all the microorganisms including bacteria, archaea and fungi that live on and inside the human body

12 killed by rare bacterial infection in Essex – Independent

MRSA 'kills 10,000' – Daily Mail

Antibiotic resistant superbugs 'will kill 90,000 Britons by 2050' – The Gaurdian

We have all heard the headlines. No wonder we are so scared of microbes and are quick to label them as ‘bad’, ‘pathogenic’ and even ‘deadly’. Well in this next blog post I am making it my absolute mission to change your mind. I hope very soon you will be giving your microbes the love they deserve.

From the moment we enter this world our very own colonisation journey begins. Naturally our rite of passage out of the womb through the vagina inoculates us with bacteria from our mother’s gut. Setting us up to process a lifetime of energy intake from the food we eat. In fact, it has been shown that vaginally born babies get most of their gut bacteria from their mother, whereas caesarean born babies have more bacteria within their guts associated with hospital environments [1]. Wowza!

This human microbiota community as it is known consists mainly of bacteria. However, we host other single celled organisms too, including archaea, fungi, viruses and other microbes. Research carried out in 2016 suggested that there are 1.3 microbial cells for every cell in the human body [2]. Some of these microbes are useful and have essential processes in our bodies such as breaking down sugars in breast milk. Some are pathogenic. Others only become pathogenic when they inhabit the wrong place or have a significant boom in numbers.

Once we have entered this world the next challenge is consuming energy to aid in growth, development and ultimately our survival. Thus, comes the choice that faces all parents, breast or bottle? Breast milk contains prebiotics known as indigestible oligosaccharides that promote the growth of specific microbial communities. The breast milk also contains viable bacteria present in low concentrations including Bifidobacteria. These bacteria are important for inhibiting the growth of pathogenic organisms, modulating mucosal barrier function, and promoting immunological and inflammatory responses [3]. Research has shown that breast fed babies appear to have stable and relatively uniform gut microbiome compared with formula-fed babies [4].

As we grow, we require more energy and nutrients than we can source from our mother’s milk alone. The introduction of solid foods results in a dramatic shift of the infant microbiome. One study comparing the microbiota of young European children from Italy with children from a rural African farming community in Burkina Faso found that the microbiome of the European children was dramatically less diverse [5]. The European children were breast fed for a shorter time, ate more calories, more fat and animal protein, and less fibre when compared with those from Burkina Faso. Another study on infants and adults from the United States, Amerindians from Venezuela and individuals from rural Malawi showed differences in gene expression in the microbiome reflect a striking adaptation of the microbiota to the different diets in these populations [6].

Our diet is not the only thing that affects our microbiome. In 1928 a scientist named Alexander Fleming accidently discovered penicillin. For years we abused this new discovery, seeing antibiotics as a wonder drug to cure pathogenic bacterial infections in ourselves and our food chain. It is only later down the line that we are starting to understand that there are fact consequences to such abuse. These include eventual antibiotic resistance and unsettling of the composition of the gut microbiota. In fact, broad spectrum antibiotics can affect 30% of the abundance of bacteria in gut communities [7]. This can take months or even years to restore [8].

All hope is not lost as research has developed, we have discovered the wonders of pre- and pro-biotics. These marvellous magical foods have the power to re-ignite and re-establish our gut microbiomes. Prebiotics are types of non-digestible dietary fibre that feed the friendly bacteria in your gut helping them to produce nutrients for your colon cells leading to a healthier digestive system. Some sources include breast milk, chicory root, Jerusalem artichoke, dandelion greens, garlic, leek, onion and asparagus [9]. Probiotics on the other hand are live microorganisms that when consumed or applied to the body have health benefits. Some products include tempeh, miso, soya sauce, pickled vegetables, kimchi, kefir and butter milk.

As you may have gathered these microscopic little creatures in fact live in symbiosis with us. By reducing abnormal microbial exposures, maintaining a good microbial diet and reducing antibiotic usage and other medications we can prevent dysbiosis and keep our microbiota in balance and happy. Now please take all you have learnt and go and show some respect for you microbial inhabitants.



1. Shao, Y., et al., Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature, 2019. 574(7776): p. 117-121.

2. Sender, R., S. Fuchs, and R. Milo, Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol, 2016. 14(8): p. e1002533.

3. Sudo, N., et al., The requirement of intestinal bacterial flora for the development of an IgE produ ction system fully susceptible to oral tolerance induction. J Immunol, 1997. 159(4): p. 1739-45.

4. Bezirtzoglou, E., A. Tsiotsias, and G.W. Welling, Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe, 2011. 17(6): p. 478-82.

5. De Filippo, C., et al., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A, 2010. 107(33): p. 14691-6.

6. Yatsunenko, T., et al., Human gut microbiome viewed across age and geography. Nature, 2012. 486(7402): p. 222-7.

7. Dethlefsen, L., et al., The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol, 2008. 6(11): p. e280.

8. De La Cochetiere, M.F., et al., Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol, 2005. 43(11): p. 5588-92.

9. Moshfegh, A.J., et al., Presence of inulin and oligofructose in the diets of Americans. J Nutr, 1999. 129(7 Suppl): p. 1407S-11S.


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