Reimagining our relationship with the microbial world:Infection, antibiotic resistance and peaceful coexistence

Brief and in-Depth Analytical Psychology in the 21st Century
December 14, 2016

Reimagining our relationship with the microbial world:Infection, antibiotic resistance and peaceful coexistence

By Mary Murray

Let me fascinate you with the resilience, sheer scale and beauty of the microbial world! Why? Because it is fundamental to the existence, survival and health of our species and the planet as a whole. I argue that we need a more conscious relationship with the invisible health-giving and illness-producing nature of this world and that we need to challenge the predominant war metaphor which describes and structures much of our collective relationship to microbes.  The phenomenon of growing antibiotic resistance sharpens the urgency of transforming this relationship. Psychotherapy can contribute much to uncovering the personal and collective fear and anxiety about microbes, infection and associated symptoms and perhaps to inducing a process of transformation of these states particularly by using embodied imagination.

Microorganisms make up over 80% of the earth’s biomass – by weight. They are the major component of the biosphere and the oldest of all living species. Microbes are at the heart of ecological systems critical to the functioning of the Earth’s life-support system. In 1997, these free eco-services were estimated to be worth US$ 33 trillion, three times that year’s global gross domestic product.[1]

We know very little about them! Only 5,000 bacterial species have been named. One teaspoon of soil alone contains 4,000 – 10,000 species, 99% of which remain undescribed.[2] It is now thought that anywhere from 5 to 100 million species may exist.

Over 99% of microbes are not only harmless but positively needed for health. The human body is home to many indigenous microorganisms, with distinct communities at different anatomical sites.[3] By the time we are a few years old mature complex microbial communities have established themselves in our bowels and we carry these more or less our entire lives.  Working as communities, evidence is emerging that they promote proper development of host organs, new capillary blood vessels, stimulate the development of the immune system, provide nutrients, regulate fat storage and exclude potential pathogens.[4] Jeremy Nicholson has shown how bodily fluids are filled with metabolites of intestinal bacteria and proposes the influence of these gut microbes to range from the way we metabolise drugs and food to the subtle workings of brain chemistry.

They are not simply random squatters, but organized communities that evolve with us and are passed down from generation to generation. [5]

Bacteria in and on the body outnumber human cells by ten to one. So, who are we?  We know that genomes capture only a part of who we are, but that part may have to take account of the genes of the collective communities of bacteria in the body, known as the microbiome.  These are estimated to contribute 360 times more than the 22,000 genes ‘we each own’ from egg and sperm.[6]  The microbiome is now regarded as an organ of the body, weighing at least as much as other organs – about a kilogram.

Bacteria have fascinating means of communicating with each other, within and across species, and across biological kingdoms – including with us! Bacteria can sense their population density using a stimulus-response system, called quorum sensing, allowing a coordinated collective response. The interaction of communities of microbes is probably much more important than the behavior of single bacterial species in health and disease.

Certain body functions could be the result of negotiations between several partners, and diseases the result of small changes in group dynamics or of a breakdown in communication between symbiotic partners. [7]

Many of the organisms that cause illness in humans live quite happily within us in balance with a myriad of other organisms. Stanley Falkow[8] calls these ‘commensal pathogens’. Something in this balance and/or in our immune system changes and disease results. Relatively few ‘foreign’ organisms literally jump across our defences and overwhelm us, plague being an example.

The evolution of the immune system needs the ongoing stimulus of microbes to enable us to respond to those microbial species that cause infection. This delicate system works both by directly activating the means of destroying invading pathogens – those able to penetrate, survive and replicate in parts of the human body where others cannot – and by enhancing and promoting a complementary host-protective effect.

So it is becoming clear that bacterial diversity and interaction is key for human and environmental health …

… it is not the one pathogen that we meet when we get sick that is the microbe we [should] worry about, it is our entire microbiome that determines health and disease, productivity of our crops, and all the different aspects of life that microbes manage … it is a sort of microbial blanket of the earth … there is no aspect of our planet that is separate from or unaffected by microbial life. [9]

The War Metaphor

Compare the insights into microbes above with the predominant negative way in which microbes are perceived and portrayed. What drives the immense commercial success of antibacterial sprays, wipes and even antimicrobial wall paint offered to sanitise our homes? Preventive measures such as public sanitation and hygiene, along with changed economic and social conditions in 1800s, reduced death from infection.  However, now, we seem vulnerable to undoing this achievement through the image of a completely sterile home. A war metaphor shapes our lives – bacteria the enemy, and antibiotics the weapons.

The war metaphor evolved in parallel with the development of the microscope and germ theory. Medicine succeeded in identifying individual pathogens involved in life-threatening infection and produced life-saving treatments. Penicillin increased the chance of survival of those with blood infections or pneumonia from 10% to 90%. A steady stream of new antibiotics kept coming, the US Surgeon General predicting in 1967 that we could soon close the door on infectious disease.

Massive human and animal use of antibiotics over the last 70 years has driven bacteria to create many ways resist antibiotics. New genetic material is shared between and across species, including with the normal flora in the bowel.  Thus, not only do bacteria spread but also resistance genes, accelerated by the global movement of people, food and animals. Some patients now have multi-resistant infections for which there are no effective antibiotics. No new antibiotic classes have been developed since 1987,. making existing antibiotics a non-renewable resource. We need to release our imaginative capacities to invent approaches that do less collateral damage to health-giving bacteria.

What has this to do with psychotherapy?

It is as if our socialization into living the war metaphor over the past 70 years and an associated sense of human power over microbes through antibiotics has masked a pre-existing deep fear of contagion resulting in a collective contagious anxiety to get rid of bacteria altogether. We are over-concerned at home, paradoxically inattentive where we should be alert, such as in hospitals, with no deep knowledge about how to act regarding the bacteria we should fear nor appreciation of our essential dependence on microbes. We need more radical imagination to be able to encompass both personal and collective fear of a real and specific bacterial threat together with joy of connection with the invisible, holistic and health-giving eco-world. Embodied imagination provides such a therapeutic tool that may help uncover images of new paradigms of relationship with microbes.


Fear of Germs      G, a 12 year old boy, had had a two-year history of stomachache following possible threadworm infection. Following sudden weight loss, nausea and anxiety, he stopped sucking his fingers for fear of germs, started washing his hands frequently and used a tissue to pick up food to avoid germs. Homeopathy treatment stopped the excessive hand-washing and use of the tissue. However, the anxiety returned a year later, with abdominal pain when he focused on germs and use of a tissue to handle food.


G, keen to work on his ‘ sensitive stomach’, began seeing a therapist who uses a combination of mindfulness, sandplay and embodied imagination. In the first session,  she asked him to draw the germs. When I am happy, they are happy, when I am sad, they are sad. If I could speak to them I would tell them to go away. She asked him to think of a safe place. Using embodied imagination she established that he feels safe and happy in his bed at night and senses that in his stomach. Asked what else he could see around the room, G notices on the wall his drawing of a shark eating fish. The therapist guided him to ‘transit’ in to the shark. Transit is a term for allowing ones full concentration to focus on the shark – its detail, its posture – until through mimesis, the presence of the shark grows and the person is able to participate in the phenomenon of the shark, sense its intelligence and nature while staying in dual consciousness.  Shark is the king of the sea – ‘I am the best’ – powerful. I am eating fish.  The following week he had tried being brave and twice ate with his hands.

Then G did a number of sandtrays. In week 6, during a war between two armies, G identified one soldier holding a grenade. The soldier was feeling both courage and pride that he might win a medal – but also afraid that he might die. He felt pride in his chest and fear brought butterflies to the stomach.

After 10sessions G was eating with his fingers frequently and had a tiny bit of fear. The therapist suggested he be like a scientist exploring the germs, observing them closely.  They are green and yellow dots of medium brightness. When I am frightened they are jumping around and they are shaky. At other times when I am calm they are still. When the therapist suggested bringing an attitude of friendliness to them, he said they are jumping up and down like they are happy. Subsequently, G could lick his fingers, his own sense of power and strength developed, more confidently interactive with his friends, being more comfortable with angry feelings and able to say what he thinks even if not positive.  Anxiety about germs was re-rooted to a real fear – of dying – while G’s ability to tolerate dual feelings of  courage and fear of dying (just) developed with perhaps a hint of joy in germs.


Other experiences with embodied imagination illustrate possibilities. One person developed the capacity to ‘companion’ his immune system, changing his embodied emotional relationship to his bowel and the path of severe colitis.  He became able to allow emotions to generate and find expression realizing their power when ‘pushed down’ to his gut and on its resident microorganisms.  A cutting-edge microbiologist explored image and feeling of ‘being transported’ into the unknown world of a microorganism under study. Images in a subsequent dream awakened realization that he had never viewed microorganisms without a strong sense that life and death mattered. Now able to sense the dance of microbes, what descriptions might emerge from research if he moves out of the perspective of the physician and enters the embodied world of microbes?


Atrophy of the capacity to imagine is the breeding ground for self-inflicted misery. When old mythologies are corrupt and dysfunctional, one solution is to replace the ideas they symbolized by demonstrating their falseness, using the rationality of science. But for the psyche, the weakening of imagination is a trauma because what is lost in the imaginal realm can only be replaced by images, not by abstract concepts. Joy is a better teacher than pain – always. [10]

So might we say about infection, microbes and our immune system.  We are living without images, trying to turn the concepts of science into something to live by.  Without a new paradigm, a new mythology– without the capacity to imagine,– a generalized anxiety about the threat of invisible microbes, symptoms and death robs us of our capacity to act, to adapt, to be an integral part of an ever changing inventive ecosystem.  Embodied imagination can help uncover images symbolizing our intimate relationship, personal and collective, to the microbial world.


[1] Constanza et al

[2]  Michael Gillings, interview, Microbes and Metaphors report, 2011

[3] Dethlefsen  L, McFall-Ngai M, Relman DA . An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007 Oct 18;449(7164):811-8.

[4] Flint et al., Interactions and competition within the microbial community of the human colon: links between diet and health. Environ Microbiol. 2007 May, 9(5):1101-11; Tappenden and Deutsch, The physiological relevance of the intestinal microbiota–contributions to human health. J Am Coll Nutr. 2007 Dec;26(6):679S-83S; Cogen et al., Skin microbiota: a source of disease or defence?  Br J Dermatol. 2008 Mar;158(3):442-55.

[5]  Courtney Humphries The Body Politic feature , April 14, 2009.

[6]‘NIH Human Microbiome Project defines normal bacterial makeup of the body’, June 2012

[7] Courtney Humphries, ibid


[9] Interview with Jo Handelsman, Yale University, by Satya Sivaraman and Mary Murray. To be published at