Strangers Within Us Help to Shape Who We Are

We are a holobiont: How the microbes inside us shape mind and self

Posted December 3, 2025 | Reviewed by Davia Sills

Our eyes see everything around them, but cannot see themselves. To see themselves, they need a mirror. Scientists often use mirrors to study self-consciousness in animals. They place a mark on the animal’s face, and if the animal recognizes the mark while looking in the mirror, it suggests self-awareness.

We often believe we know ourselves directly and without doubt, unlike how we recognize our external appearance in a mirror. However, psychological science challenges this assumption. Our self-knowledge is prone to biases and gaps. Do we ever know ourselves directly, or is the “I” always built from signals, some from the body, some from the world outside?

The concept of self-consciousness is inherently paradoxical. When I am aware of something outside myself, I am the subject, and those things are the objects of my consciousness. However, when I turn myself into the object of my own consciousness, the subject and the object become one, which seems paradoxical [1].

Therefore, earlier thinkers proposed that the real self, which is aware of its own existence, must be distinct from the physical body. Thinkers like Descartes and his followers concluded that the root of the true self is immaterial and resides in the soul, which they believed was connected to the body through the pineal gland, thus resolving the paradox. Of course, accepting a self separate from the body introduces a new problem: What kind of separate substance is this, and how is it aware of itself? This reasoning suggests the possibility of yet another self beyond that substance, potentially leading to an infinite regress . Modern science, however, offers a different path out of this paradox, not by searching for a separate substance, but by looking deeper into the intimate conversation between the body and the brain.

The brain receives signals from within the body and interprets them as subjective experiences

Interoceptive sense is a new perception that helps the brain to be aware of the body’s status and better control inner conditions. Interoception, the sensing of internal bodily signals from organs such as the heart, lungs, immune system, gut, and microbiome , serves as a crucial foundation for numerous cognitive functions by providing a continuous stream of information about the body’s physiological state. These interoceptive signals, often processed unconsciously in brain regions like the insula and anterior cingulate cortex, directly influence emotional experiences, decision-making processes, and self-awareness. For instance, the feeling of a racing heart can intensify anxiety , while gut cues can subtly guide intuitive choices, ultimately shaping our subjective reality by grounding cognitive and affective processes in the ever-changing landscape of our internal bodily milieu [2].

Are we composed of one thing or two distinct things?

Among the many internal signals the brain receives, the one from our microbiome is unique. Trillions of microorganisms, bacteria, fungi, and viruses live inside our bodies. They have their own genes and metabolisms, live mostly in harmony with us, and are essential for both our physical and mental health. The community in our gut is a key part of this “microbiome.” How it affects the brain has become a major focus of modern science.

Often called the “second brain,” the enteric nervous system (ENS) is a huge network of neurons in the gut wall. It can sense microbial products like short-chain fatty acids and neurotransmitters and send those signals up to the central nervous system. The vagus nerve acts like a direct cable, carrying these gut messages to important brain areas that control mood and appetite , such as the brainstem and hypothalamus.

Furthermore, the gut microbiota helps regulate our immune system, influencing the production of inflammatory signals (like IL-6 and TNF-α). These signals can cross into the brain, activate immune cells there (microglia), and change brain inflammation, which then affects how neurons work and even our behavior. So, through a mix of nerve signals (the ENS-vagus axis) and body-wide immune changes, the gut and brain are in constant, two-way communication.

Changes in the microbiome are linked to several mental health conditions, including stress , anxiety, Alzheimer’s, and schizophrenia. The microbes inside us might even influence our food cravings and our desire for certain activities, like exercise. This deep level of influence on our mind raises a philosophical question: What does it mean to be a “self”?

This science shows we are not alone. We are deeply intertwined with a vast community of other living beings inside us. We are a holobiont, a single biological unit made of a host and all its symbiotic microbes. This view urges us to rethink the mind and consciousness, which we usually think of as belonging only to the brain [3].

A new dualism, but not so radical

Overall, the “I” we see in the mirror is not just a trick of the brain. It is a living agreement, a moment-by-moment conversation between your 86 billion brain cells and the trillions of microbes living in your gut, on your skin, and throughout your body.

These microbes aren’t just visitors or pests. They are partners in making you who you are. Every chemical signal from your gut to your brain, every immune message sent from a microbe, is a quiet reminder: “You exist because I am here, inside you.”

Our sense of self is not created in the lonely silence of the skull. It emerges from this constant, silent dialogue with a biological “other.” So, when we say “I am,” we’re really admitting we’ve never been alone. From the start, we have always been a holobiont, a single living unit made of “us” and our microbial partners. Our boundaries do not end at our skin, but extend to the innermost molecules produced by the bacteria within us.

The classic mirror test shows self-awareness when an animal recognizes its visible reflection. But human self-consciousness may be revealed by something else: the trillions of microbial partners who constantly send back an invisible reflection of our inner state to the brain.

Durt, C. (2020). The Embodied Self and the Paradox of Subjectivity. Husserl Studies, 36 (1), 69-85.
Seth, A. K., Suzuki, K., & Critchley, H. D. (2011). An interoceptive predictive coding model of conscious presence. Front Psychol, 2, 395. doi:10.3389/fpsyg.2011.00395
Nagpal, J., & Cryan, J. F. (2021). Host genetics, the microbiome & behaviour-a 'Holobiont' perspective. Cell Res, 31(8), 832-833.

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Hamid Zand, Ph.D., is a professor of Biochemistry at the Department of Cellular and Molecular Nutrition at Shahid Beheshti University of Medical Sciences in Tehran, Iran.

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This article is part of the Bringwise Psychology Journal — daily insights on human behavior, mental health, and personal growth.