Change Your Gut, Change Yourself?: How Can Changing Your Gut Health Change Who You Are?

Written by: Nick Calvey

Edited by: Sherry Guo, Bailey Van, Emily Choi, Jesslyn Chen, Kayla Joseph

Illustrated by: Gefen Mor

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Introduction

In the past decade, research on the gut microbiome has exploded, not only revealing its flexibility, but the significant influence it can have on our internal biology. In 2014, a landmark study in the Nature journal demonstrated that switching to an all-animal or all-plant diet could reshape an individual’s gut microbiome in as little as five days [1]. The gut microbiome refers to the trillions of bacteria, fungi, and viruses (microbes) inhabiting the intestines that regulate digestion, immunity, and even the neural chemistry that still remains partially understood. While the speed of microbial change is striking in itself, the fact that dietary shifts override each participant’s unique microbial signature sowed the seed for later research seeking to link the influence of these changes to even more significant transformations. Soon after, microbiome research began to connect changes in gut bacteria with changes in chemicals that regulate mood and motivation. In 2018, Dr. Philip Strandwitz’s literature review found that several gut bacteria produce or consume the molecular prerequisites for neurotransmitters such as serotonin and dopamine (the chemicals central to happiness and emotional stability) [2]. 

The ground breaking implication beneath these two fascinating findings is a simple but brooding question. Specifically, if our feelings, energy, and even moods shift with changes to our gut microbiome, what becomes of “me”?

In order to make sense of why these findings matter, let us define some shared vocabulary for the biological concepts that follow. First and foremost, the trillions of microbes in our gut affect most of our physiologic function by influencing digestion, metabolic functions, and even how the immune system learns to distinguish friend from foe. After this article’s analysis of the evidence and questions on identity, it will draw on the Pattern Theory of Selfhood, an idea that presents the notion that your unique personality and ownership of experience are not fixed phenomena, but a pattern and a shifting hierarchy of interactions between biological, psychological, and social processes [3]. This overall connection between our gut and experience is aptly called the gut-brain axis, referring to the bidirectional communication network between our digestive system and our neural, hormonal, and immune pathways in the brain. 

The Science of Modifiability

Since the human genome project, modern tools have allowed scientists to be able to track and monitor genetic changes with astonishing precision. As such, metagenomics was born a few decades later, which is the process of sequencing all microbial genes in a stool sample to effectively track and identify which species thrive and which vanish after some or any intervention. This is often paired with metabolomics, which measures microbial byproducts, such as short-chain fatty acids. Immune panels can then capture how the host’s chemical defenses respond. Together, these methods turn what is a microscopic ecosystem into quantifiable data. These methods help scientists test whether everyday behaviors can reshape this ecosystem fast enough to influence immunity and even mood.

One of the clearest demonstrations of the microbiome’s flexibility comes from dietary interventions. Specifically, Lawrence David and his scientific team found that participants who switched between all-animal and all-plant diets experienced dramatically different microbial profiles in less than a week [1]. The number of bacteria adapted toward meat digestion increased (or disappeared) almost overnight, producing new metabolic byproducts that paralleled the diet’s macronutrient structure almost perfectly. 

Not even a decade later, a 10-week randomized control trial led by Wastyk and colleagues confirmed that dietary interventions can do more than alter the composition of the gut microbiome — they can physically reprogram someone’s immunity [4]. Participants who ate fermented foods (e.g., kimchi or kefir) saw increased microbial diversity, and a subsequent decrease in inflammatory markers across 19 different cytokines (a sign that their immune system was calmer, more balanced, and better able to regulate inflammation). Cytokines are the immune system’s chemical messengers that coordinate inflammation and direct overall immune response. Importantly, research by Miller and Raison found that inflammation’s interaction with the brain drives the development of depression, directly linking gut health with mood and identity [5].

However, what we put into our body is not the only factor. Changing how we use our body can also reshape the microbiome, sometimes just as powerfully as the nutrition we ingest. The physiological changes that come from exercise, such as producing hormones and signaling molecules that communicate with the brain and immune system, can also reshape the microbiome.

Notably, a study from the Oxidative Medicine and Cellular Longevity Journal highlights that exercise enriches some hormonally beneficial microbial species, and even boosts overall microbial diversity [6]. This diversity is largely positive, mainly seeing a spike in commensal bacteria, which are the bacteria in our bodies that help us maintain our gut homeostasis. Vincenzo Monda et al., concluded that physical activity fosters microbial resilience at both the intestinal and systemic levels by supporting anti-inflammatory metabolites and improving barrier function (the process in the intestine that allows essential nutrients to enter and prevent toxins from entering the bloodstream) [7].

This research allows us to define a positive feedback loop directed at promoting longevity and well-being. In this perspective, every moment of physical activity can be seen as an act of subtle self engineering.

Taking this a step further, fecal microbiota transplantation (FMT) and other novel medicinal techniques have shown that, beyond dietary and exercise-induced changes, we can fight serious illnesses by focusing on the gut microbiome. After processing the healthy stool into capsules or other infusional vehicles, FMT sees their insertion into a recipient’s colon or small intestine. The goal of FMT is to restore a balanced microbial community that is capable of suppressing pathogens (immunity).

This approach was originally developed for treating recurrent Clostridium difficile infections (rCDI), a condition for which antibiotics are growing alarmingly futile. Van Nood et al., reported cure rates above 85%, vastly outperforming antibiotic therapy. Subsequent studies using FDA-approved, encapsulated microbiotas have replicated this success under strict clinical supervision. (E.g. SER-109, Vowst) [8].

These findings show that we have the direct ability to radically change the microbiome. While diet and exercise tweak the ecosystem, FMT can completely overhaul it, revealing how lifestyle and medicine are entwined.

The biological shifts discussed thus far are of course important for ordinary health reasons, but the deeper reflections lie in how these changes appear in the brain. Research has shown that microbes can influence mood through numerous pathways [2]. In 2018, a literature review by Philip Strandwitz found that microbes produce and/or consume the building blocks of neurotransmitters (like serotonin and dopamine, the hormones that make us feel happy) responsible for stress, motivation, and general emotional balance [9]. Additionally, microbial metabolites stem from the gut and drive communication with the brain, influencing the activity in certain brain regions linked to emotional regulation, like the amygdala and prefrontal cortex [7]. Microbes and cytokines also coordinate inflammation inside the body, and spikes in certain inflammatory molecules are strongly linked to anxiety and depression [10, 11]. Looking at these mechanisms, we see that shifts in the microbiome can influence the brain, linking the microbiome to mood and experience. 

Because mood and general emotional regulation are core components of personality, microbial induced changes in these domains raise deeper questions about identity. This blurring of science and philosophy introduces the possibility that if these traits can be altered by changes in the gut, then some portion of what we treat as stable identity may actually be biologically negotiable. Gallagher’s Pattern Theory of Selfhood offers a potential framework to include the gut microbiome [3]. Within this “pattern” of self identity, microbes represent one of the most flexible components. As we’ve seen, they participate in shaping our moods and immunity, yet are also seemingly transient, responsive, and shared with the world around us. 

Philosophically, this positions the “self” as an embodied and extended phenomenon, one that pushes back on notions of a single point of consciousness. Instead, consciousness, seen in this way, seems more like a dynamic network of relationships, including those inside the gut. This invites us to ask how we should understand ourselves in an age when we can directly edit our biology.

If we can begin to understand how changes in microbes influence mood and energy, should we begin to use such interventions as tools for therapy or even self expression? Unfortunately, such a promise comes with some unignorable risks and complications.

Imagine a future where the booming wellness industry now markets “precision-microbiome” products that promise sharper minds and improved personality traits (e.g., anti-depression microbes). Overstating what probiotics or microbiome tests can do risks reducing personhood to a purchasable product. For example, let’s imagine a subscription service that promises boosted confidence, claiming to have found microbial influencers of extroversion and emotional stability. In such a world, identity itself would begin to look like something to buy, upgrade, and even compare, rather than a unique reality. This will inevitably risk these products requiring access, nutritional literacy, and professional guidance.

These identity-adjacent interventions (e.g., diet coaching, fermented food intake, or clinical FMT) are and will not be evenly distributed. If self-directed microbial modification becomes a marker of health or even success, it could deepen existing social and economic inequalities. Public health policy can combat this by making guidance affordable, emphasizing culturally appropriate foods, and ensuring therapies remain medically supervised.

Conclusion

As we’ve seen, the gut’s microbiome is highly plastic. Diet and exercise can reshape and reorganize its residents in just a few days, while FMT can rebuild it from scratch. In doing so, such changes can cascade through the immune system, neural chemistry, and change our mood and behavior. Such mechanisms powerfully emphasize the gut as one of the most responsive systems in the incredibly complex human body. 

However, this very tractability makes it difficult to comprehend selfhood in generic or single-perspective ways. If we can be manipulated by microbes to feel and act differently, then “I” becomes a consortium, not some singular phenomenon. Gallagher’s Pattern Theory further frames microbial modification as part of the shifting architecture shaping thought, emotion, and behavior [2].

Overall, this article has shown that such modification holds huge welfare and therapeutic potential, but also raises new ethical challenges of identity, autonomy, and equity. Important questions stem directly from the studies and revelations discussed in this article, and it may be helpful to end with the central ones. Notably, what is really “me” if microbial changes influence our mood and behaviour in the ways suggested by the research? Who will have access to identity-shaping interventions… and who will not? And, as a final warning, how can we prevent the slippery slope of microbiome medicine’s consumerization?

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References

[1] David, Lawrence A et al. “Diet rapidly and reproducibly alters the human gut microbiome.” Nature vol. 505,7484 (2014): 559-63. doi:10.1038/nature12820 

[2] Patel, Ruhina Afroz et al. “Gut microbiome-gut brain axis-depression: interconnection.” The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry vol. 26,1 (2025): 1-36. doi:10.1080/15622975.2024.2436854 

[3] Patel, Ruhina Afroz et al. “Gut microbiome-gut brain axis-depression: interconnection.” The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry vol. 26,1 (2025): 1-36. doi:10.1080/15622975.2024.2436854 

[4] Wastyk, Hannah C et al. “Gut-microbiota-targeted diets modulate human immune status.” Cell vol. 184,16 (2021): 4137-4153.e14. doi:10.1016/j.cell.2021.06.019 

[5] Miller, Andrew H, and Charles L Raison. “The role of inflammation in depression: from evolutionary imperative to modern treatment target.” Nature reviews. Immunology vol. 16,1 (2016): 22-34. doi:10.1038/nri.2015.5 

[6] Monda, Vincenzo et al. “Exercise Modifies the Gut Microbiota with Positive Health Effects.” Oxidative medicine and cellular longevity vol. 2017 (2017): 3831972. doi:10.1155/2017/3831972

[7] Wallace, Caroline J K, and Roumen Milev. “The effects of probiotics on depressive symptoms in humans: a systematic review.” Annals of general psychiatry vol. 16 14. 20 Feb. 2017, doi:10.1186/s12991-017-0138-2

[8] E van Nood, Els et al. “Duodenal infusion of donor feces for recurrent Clostridium difficile.” The New England journal of medicine vol. 368,5 (2013): 407-15. doi:10.1056/NEJMoa1205037 

[9] Strandwitz, Philip. “Neurotransmitter modulation by the gut microbiota.” Brain research vol. 1693,Pt B (2018): 128-133. doi:10.1016/j.brainres.2018.03.015 

[10] Cryan, John F et al. “The Microbiota-Gut-Brain Axis.” Physiological reviews vol. 99,4 (2019): 1877-2013.

doi:10.1152/physrev.00018.2018 

[11] Shreiner, Andrew B et al. “The gut microbiome in health and in disease.” Current opinion in gastroenterology vol. 31,1 (2015): 69-75. doi:10.1097/MOG.0000000000000139