How the Microbiome Is Shaping the Philosophical Concept of an Organism

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The microbiome; a term you may have observed plastered over probiotic and health advertisements on the television, yet the microbiome is much more than a simple yoghurt drink for our consumption. The microbiome challenges the concept of what an organism is, thus questioning the definition of one of the most universal terms used in biology. This post will explain what the microbiome is and discuss why is it crucial for our survival. The microbiome is summoning a collaboration between the minds of scientists and philosophers to collectively rethink the definition of an organism. This phenomenon will be explored through an examination into how the microbiome fits into or changes existing definitions of an organism.

What Is the Microbiome?

To understand what the microbiome is, we must first understand what micro-organisms are. Micro-organisms are tiny organisms such as bacteria, archaea, fungi and viruses.

The human body, both inside and externally (on our skin), harbour a vast array of these type of micro-organisms.

The human microbiota (which refers to only the micro-organisms, whilst microbiome refers to the micro-organisms and their genes, but these terms can be used interchangeably) consists of 10-100 trillion microbial cells harboured by each person, predominantly bacteria in the gut. Different parts of the body all have very different communities of micro-organisms. It may make you feel a little squeamish to think that trillions of bacteria are living in and on our bodies, but don’t worry, these micro-organisms are useful to us. They are the ‘good’ micro-organisms, in contrast to other micro-organisms that are harmful and associated with disease yet often are the typical type of micro-organisms we think of first. We have a symbiotic relationship with these micro-organisms, which is defined as any relationship between two dissimilar organisms. Symbiosis can be; mutualistic which is where both organisms benefit, commensal where one organism benefits and the other is unaffected, or parasitic where an organism benefits and the other suffers. These types of symbiosis are not absolute, an organism can exhibit elements of each type of this classification. We will soon explore what type of symbiotic relationship we have with our microbiome.

The genome, which describes all the genetic material of an organism, is different for everyone. This concept is similar to the microbiome, everyone has different microbiomes. Genetic material makes us who we are, it determines our personality, behaviour and our looks, but the question of nature over nurture remains. Is this the same for the microbiome? If everyone’s microbiome is slightly different, how much emphasis can we put on this for it determining who we become, and how far can it be impacted by our environment? Does this mean the microbiome is part of our definition of ‘self’?

What Is the Role of the Microbiome?

The human microbiome has proven to be extremely important for; the proper functioning of our immune system and its ability to defend against disease-causing pathogens, good nutrition via its production of compounds used in the digestion of food and the synthesis of vitamins, the promotion of fat storage, and also influences on human behaviour via its modulation of the nervous system.

The microbiota benefits us, and the micro-organisms have a safe environment to live, which means we have a mutualistic relationship; both of us benefit from this relationship.

The control and maintenance of these mechanisms in the body shows that the microbiome is vital for homeostasis, which is defined as the ability to maintain a stable internal state despite external changes. A classic example of a homeostatic response is the body producing sweat to cool down when placed in a very hot climate. If the person is not able to cool down, there is a risk of heat stroke and a threat of death if the person seriously overheats. Without this ability to regulate our internal environment, we will not survive.

Without the microbiome; our bodies would not function correctly, and we would not survive.

Can We Manipulate the Microbiome?

In recent years, further research into the role of the microbiome has shown links between how individuals respond to certain drugs, and susceptibilities to certain diseases or conditions. For example, could the microbes in the gut be influencing appetite, thus could be they influencing obesity rates?

The manipulation of the microbiota as a therapeutic tool is an increasingly popular field in science.

An example of a potential manipulation method could be targeted antibiotic use. Antibiotics are used against bacterial infections by either killing or inhibiting the growth of bacteria. However, in the process of killing the ‘bad’ bacteria, some of the ‘good’ bacteria may also be killed, this lack of differentiation between the bacteria can cause the microbiome to become slightly out of balance. The long-term, specific effects of killing the ‘good’ bacteria are not known, and the ‘good’ bacteria will soon recolonise, but removing the ‘good’ bacteria will have some effect on your immune system in the meantime. For example, yeast infections can occur after a course of antibiotics, this is because the ‘good’ bacteria that keeps its environment acidic, which is not what yeast thrive on, will have been removed; leaving that environment open for yeast colonisation.

Understanding the microbiome in more depth could prevent this depletion of ‘good’ bacteria and thus maintain the balance required for a healthy body. You may be wondering where the probiotics that you see on many television adverts come into all of this. Taking probiotics and prebiotics presents another potential manipulation method of the microbiome, however, now we are aware that everyone’s microbiome is different, the probiotic or prebiotic that is right for your personal microbiome may not be obvious. This is another controversial area, the benefits of taking probiotics or prebiotics to improve the microbiome is confusing and uncertain. It seems that eating a varied, fibre-rich diet will be beneficial for your health, but the direct impact on the microbiome is still uncertain, but it likely it is impacting in some form. The mysterious microbiome presents another factor in our continuous search for health promotion and understanding our bodies.

Does Our Microbiome Change?

The microbiome composition is constantly changing, especially in infancy and early childhood. Unlike before where we made the link between the uniqueness of everyone’s genome and microbiome, the microbiome and genome differ here. The genome remains relatively constant whilst the microbiome constantly changes. The causes of the changes happening throughout our entire life on microbiome composition include environmental factors such as diet and antibiotic use, but the changing microbiome of an infant is especially interesting. It is believed that the first type of bacteria received by a newborn baby is the bacteria from the mother directly during birth, however, this is disputed. It is thought that perhaps the gut microbiome of an infant is affected by many other factors such as gestational age (full term or premature), the mode of delivery (vaginal birth or caesarean section), the type of feed (breast milk or formula) and maternal nutritional status (overweight or undernourished). There are even some studies that suggest that unborn babies will encounter micro-organisms whilst inside the womb. As you can see, the bacteria exchange points go beyond the point of delivery only.

It is believed that these early changes in microbiota can have impacts later in life and in the development of the infant’s immune system.

The microbiome is thought to generally stabilise by the time we are around three years old, however, our environment and decisions continue to alter our microbiome throughout our entire life.

This concept of change presents another insight into how we determine ‘self’. If the microbiome is something that is determined by what we do and our environment, yet it resides inside us and the rest of our body relies on it, does this mean that the bacteria is part of us, despite it not being encoded by our own genes? Is the microbiome classed as a part of us, or a separate organism entirely? Is the microbiome therefore making us more or less ‘human’?

Is It Only Humans Who Have Microbiomes?

Despite the complexity and uncertainty regarding the human microbiome, the microbiome of other species is even more of a mystery.

We cannot simply state that what is going on in the human microbiome is the same for many other species.

It is likely that in these other animals the microbes are sparser, more transient and unpredictable. Humans rely heavily on their microbiomes to survive; however, it is likely that the microbiome in other species does not contribute to the host survival and functioning anywhere near as greatly. However, it really is species dependent, some animals could rely even more on their microbiome than we do, it is unclear. The type of relationship that other species have with the bacteria of the microbiome has not been concluded.

The difference between the microbiomes of species could be due to diet, such as herbivorous or carnivorous diets. The differences could be down to the physical species itself; bears and ants could not be anymore different physically, so what about internally? Lifestyle and behaviours are likely to play an important role too. The difference between insects and mammals is likely to be the greatest. However, all these ideas are just that, ideas. The true reason for the differences observed between microbiomes remains unknown.

Some animals have been found to have no microbiome, could this be because they have evolved to no longer need the symbiosis?

This uncertainty adds another layer of complexity, confirming yet again that the microbiome is unique.

An important example regards mosquitoes; the bacteria in the gut of mosquitoes has been shown to modulate their ability to transmit disease, whether that is through enhancing or suppressing pathogen transmission. The microbes can modulate the pathogen inside the mosquito, which indicates that manipulation of the microbiota can be harnessed as a mosquito control method. If the microbes were responsible for enhancing pathogen development, treating the mosquitoes with antibiotics to remove the bacteria could halt pathogen development and thus transmission. Additionally, there is evidence to suggest that the bacteria in the mosquito gut could be altering mosquito propensity to blood feed; yet another way the microbiome could alter disease transmission, this time via mosquito behaviour manipulation. This is a complex field that considers many interactions; such as the different kinds of mosquito species and pathogen interactions with microbes. What is certain is that mosquito microbiomes are playing a big role in pathogen transmission, and the question is how we can use this information to reduce the spread of mosquito-borne diseases.

What Is an Organism?

Before discovering how the microbiome is challenging the concept of an organism, it is important to understand how an organism is currently defined. The concept of the organism has been a centre of interest in recent years for both biologists and philosophers, and a lot of work has been conducted to answer the question ‘What is an organism?’. Deciding whether a given object is an autonomous organism or just a part of another organism is where the complexity lies, and it is the reason why there is no single universal concept of the organism; rather there are numerous alternative concepts. In a research paper by Clarke(1), the 13 definitions of an organism are listed and explained, but this post will only look further at two of those which were initially explored in greater detail by Stencel and Proszewska(2).

The first is the Developmental Concept of the Organism, which is a popular definition that states that organisms are not fixed units but dynamic entities which undergo a process of development from simple to complex beings. This allows us to identify a point in space and time as the beginning of an organism and thus allows us to distinguish one organism from another. The beginning could be the point of fertilisation.

The second is the Cooperation-Conflict Concept of the Organism, whichstates that an organism is a functional system built of elements that cooperate to sustain its stability. The greater the degree of cooperation and the lesser of conflict between elements of such a system means that the unit is defined as more of an organism. Cooperation refers to the possession of mechanisms that make a group of elements a cohesive, functional whole. Conflict arises when something within a group does not act in a way that promotes the functionality as a whole, but rather it acts in a selfish manner. An example of conflict could be a parasite or a cancer, which will diminish the functionality of a host and will require a conflict-suppressing mechanism to overcome it.

How Is the Microbiome Challenging the Concept of an Organism?

The Developmental Concept of the Organism is grounded upon the foundation that an organism comes entirely from within (for example, developing from a fertilised egg), however the microbiome challenges this. External microbial cells from the environment which proceed to form our microbiome are also responsible for our development. The organism does not solely rely on processes within our body, but also the impact of external influences on our microbiome. The Developmental Concept also assumes that a sharp distinction between an organism and its environment exist, yet often the full development of an organism relies on the acquisition of microbes from its surroundings. If an organism cannot achieve full functionality without the attainment of external microbes, maybe the microbiome should be considered part of the organism, part of us, rather than solely an influence of our environment. 

The Cooperation-Conflict Concept of the Organism presents an even greater level of abstractionism and challenge when regarding the microbiome. Following the foundation of the Cooperation-Conflict, if our microbiome were to go out of balance, would that higher level of conflict warrant ourselves to be defined as ‘less’ of an organism? Questions like this highlight just how versatile the definition of an organism can be, and the added layer of complexity the microbiome contributes.


We all possess a microbiome; it is essential for our proper functioning and survival. Where exactly we obtained its constituents is not absolutely known, but likely our environment and consumption choices play an important role. The microbiome changes alongside us, and this means the potential for its manipulation for health therapies presents an exciting challenge for the future. Discovering how our microbiome differs from the microbiome of other animals could help further understand why we are different in ways beyond just physically. The concept of the organism has been disputed for many years, and it continues to change as scientific discovery and philosophical insight merge. The microbiome is a concept causing the collaboration between scientists and philosophers, and in my opinion, more concepts should be viewed in this inquisitive light.


  1. Clarke E. The Problem of Biological Individuality. Biological Theory 2010;5:312-25.
  2. Stencel A, Proszewska AM. How Research on Microbiomes is Changing Biology: A Discussion on the Concept of the Organism. Foundations of Science. 2018;23:603-20.

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