Belly bugs: the aliens that live in our gut

By Lily McCann

Though we may not have solved the question of whether we are alone in this universe we do know that we are not alone on Earth. Every one of us carry billions of microbes in and upon our bodies. In this issue we explore how these little aliens influence our health and emotions, and what this means for our concept of identity.

Edited by Andrew Lim and Zhiyou Low

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Illustrated by Helena Pantsis

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Figure 1 (1):  "Animalcules"

The figures above may look exceedingly simple to you. Beautifully drawn, yes, but nothing particularly complicated —mere ovals and lines of black ink. If I told you that the drawings were 350 years old, your interest might be piqued by that fascination we hold for all historical relics. You might wonder what the images are attempting to portray. You would only be more confused, however, were I to describe them to you using the name they were known by to the artist: “animalcules”. (2)

These drawings, penned by a Dutch draughtsman in the early 1680s, are the first known depictions of bacteria from inside a human body (2). They were discovered by a man called Anthonie van Leeuwenhoek in a sample taken from between his teeth. Leeuwenhoek had examined “animalcules” in various water samples before turning to saliva, analysing the shape and movements of the little cells beneath his microscope, which he made from hand-crafted glass mounted between plates of brass. It is now known that these “animalcules” are in fact bacteria, and that they are avid colonisers not only of our mouths but every other body surface, too.

These single-celled organisms parted ways with animals some 2.7 billion years ago in evolution and could not appear any more alien to ourselves (3). Though simple in structure and function, they are capable of populating the most inhospitable and extraterrestrial of environments. In fact, Deinococcus radiodurans (pictured below) can survive for years in the harsh vacuum of space (4).

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Figure 2 (5): Deinococcus radiodurans

Freaky, right?

The evolutionary distance between bacteria and ourselves does not seem to deter them from entering into the most intimate of symbiotic relationships with us. Despite their alien-ness, despite billions of years of divergent evolution, we have not lost the ability to communicate with these distant relatives of ours. In fact, communication with bacteria is a daily and essential part of our lives. 

The reason we can still chat with these creatures is that they are made up of the same basic “stuff” that we are: genetic material made of sugars, phosphates and nitrogen bases to dictate our functions; proteins to carry out our cellular processes; membranes to hold us together. All these aspects form a common basis for language. Just as human languages consist of orally transmitted units of sounds that can be translated and understood, bacteria can impart signals in the form of particles that can be decoded and acted upon by our own cells. 

One example of this kind of dialogue is the production of molecules called short chain fatty acids by bacteria that digest plant materials in our gut. These bacteria impart their gratitude to us for supplying them with suitable foods by releasing short chain fatty acids, which in turn tell our gut not to worry, signalling our cells and instructing them to reduce inflammation, build up our gut wall and even help fix our blood pressure. These molecules can also travel to the brain, where they are thought to influence the release of various signals including that of the “feel-good” hormone serotonin. (6)

There’s a whole world of dialogue beyond this often referred to as the gut-brain axis of health. Research into the area has revealed that signals produced by gut bacteria are extremely influential in a number of conditions including anxiety and Parkinson’s disease. These relationships often work both ways, giving rise to a strange “chicken-and-egg” situation: those who demonstrate symptoms of such conditions are found to carry altered gut bacterial populations, and altering gut bacteria can in turn change symptoms. For example, in a cruel experiment involving the separation of infant monkeys from their mothers, the stress caused by separation changed the distribution of bacteria colonies in the infants’ guts, whilst administering a certain bacteria often imparted to infants by their mothers was found to reverse the symptoms of this stress (7).

The way that bacteria can change our very emotions has significant implications for our idea of personhood. What are we, if how we act depends on the alien cells we carry in our digestive tracts? Perhaps we ought to extend our definition of identity to include these little cells that are truly, it seems, a part of how we are—another organ of our body, even. 

Happily (for those of you who support the philosophy of a ‘growth mindset’), the way our gut influences our minds is subject to manipulation. And we do not need a scientist to isolate and administer a certain bacterial species to us in order to change it; evidence suggests that simply altering what we eat can have a profound influence.

Dietary change is known to directly alter bacterial gut colonies, and the change shown to bring about the most harmonious of conversations with our gut is increasing our intake of dietary fibre. Flooding our gut community with plentiful fibre causes a rush of signals from bacteria that promote gut health, mental health and healthy ageing. In contrast, a low fibre diet can promote diabetes, cardiovascular problems and, for pregnant mothers, may compromise the neural functioning of a developing child (8). 

What does this mean for medicine? Can we harness the billion-year old dialogue between our cells and the aliens that colonise our gut for our own benefit? Can we coax these residents into a mutually beneficial relationship by approaching them in the right tone? These questions are gradually gaining popularity among the scientific community as trials of probiotic administration are explored in the context of treating illnesses from depression to gastrointestinal disorders (9). We are yet to see where such studies will lead us.

When the outside world seems increasingly bleak, I find comfort in the fact that within us rumbles on the activity of an intricate and disinterested universe, completely alien to and yet an integral part of ourselves. Like farmers of a garden in times of shortage, we exist in a state of codependency with the world we nurture inside our bodies. If we foster a good relationship with its inhabitants, they can protect us from the afflictions of illness, sadness and madness that threaten our species day by day.




1. The Royal Society. Bacteria from Leeuwenhoek's mouth [Internet]. 2022 [cited 17 March 2022]. Available from:

2. Lane N. The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’ | Philosophical Transactions of the Royal Society B: Biological Sciences [Internet]. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022 [cited 17 April 2022]. Available from:

3. Cooper G. The Origin and Evolution of Cells [Internet]. 2022 [cited 17 April 2022]. Available from:,is%20from%20present%2Dday%20eukaryotes.

4. Cox M, Battista J. Deinococcus radiodurans — the consummate survivor. Nature Reviews Microbiology. 2005;3(11):882-892.

5. 5. The European Synchroton. Deinococcus radiodurans [Internet]. 2022 [cited 5 May 2022]. Available from:

6. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti D et al. Fecal Microbiota and Metabolome of Children with Autism and Pervasive Developmental Disorder Not Otherwise Specified. PLoS ONE. 2013;8(10):e76993.

7. Bailey M, Coe C. Maternal separation disrupts the integrity of the intestinal microflora in infant rhesus monkeys. Developmental Psychobiology. 1999;35(2):146-155.

8. Buffington S, Di Prisco G, Auchtung T, Ajami N, Petrosino J, Costa-Mattioli M. Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring. Cell. 2016;165(7):1762-1775.

9. Kazemi A, Noorbala A, Azam K, Eskandari M, Djafarian K. Effect of probiotic and prebiotic vs placebo on psychological outcomes in patients with major depressive disorder: A randomized clinical trial. Clinical Nutrition. 2019;38(2):522-528.

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