Rebeca Mendez

Contemporary microbiome science fundamentally challenges the traditional view of the human organism as a self-enclosed biological entity. By framing the human as a holobiont—a symbiotic assemblage of host and microbial partners—biology introduces a profound ontological tension: how can a multispecies collective maintain the functional unity required for individuality? This paper argues that Gilbert Simondon’s process philosophy provides a framework to resolve this tension, moving beyond substance-based ontologies toward an ontology of ontogenesis. Applying Simondon’s concepts of transduction and metastability, I argue that the human individual is not a static entity but a continuous process of individuation. Within this framework, the biological border is reframed from an exclusionary barrier into a regulatory interface—a Simondonian associated milieu—where heterogeneous microbial elements are integrated into the host’s vital operations. Standard objections regarding the instability and internal conflicts of the holobiont are addressed by arguing that these tensions are not failures of individuality but preindividual conditions that drive the system’s ongoing resolution. Ultimately, this Simondonian approach allows for a minimal self that is inherently plural, demonstrating that the human individuates precisely because it contains multitudes. This perspective offers a philosophical foundation for understanding life’s borders as sites of relational integration rather than absolute separation.

Contemporary microbiome research has transformed understanding of the human organism as a multi-species assemblage, yet biomedical frameworks still treat subjective bodily experience as epiphenomenal — leaving untheorized how microbially modulated signals become experientially meaningful and clinically actionable. This paper proposes the Sense of Microbial Harmony (SoMH) as a cognitive-biosemiotic framework in which the human host actively interprets interoceptive signals shaped by microbial ecology. Drawing on Jakob von Uexküll’s Umwelt theory and functional circle, Peircean triadic semiosis, enactive cognition, and Thure von Uexküll’s Situationskreis, microbial metabolites, neuroimmune mediators, and visceral cues are reconceived as sign-vehicles requiring interpretation before they can guide adaptive regulation. SoMH is specified at three analytically distinct levels — as a subjective construct (felt interoceptive attunement), a semiotic process (the recursive functional circle linking microbial activity, signaling, and regulatory response), and an observable outcome (the patterned regulatory state that stabilizes over iterated cycles) — enabling a measurement architecture in which divergences between these levels carry diagnostic significance invisible to single-index approaches. The framework explicitly resists individualist self-monitoring imperatives by situating attunement as a relational, ecologically constrained property of the holobiont system, bounded by structural, social, and Planetary Health conditions. Clinically, SoMH is operationalized through biosemiotic phenotyping — characterizing patients by the coherence or incoherence of their interoceptive-regulatory loop — and through Narrative Medicine as the medium for accessing and therapeutically recalibrating stabilized interpretive habits. The SoMH proposes a holobiont-oriented unit of care in which meaning, not biochemistry alone, occupies the explanatory center of host-microbiota relations in health and illness.

The human holobiont, a host and its symbiotic microbiota, constitutes a multispecies entity where microbial interactions critically govern host physiology, immunity, and metabolism. Integrating holobiont theory with biosemiotics, this paper reframes host-microbe dynamics as co-evolved semiotic networks. Molecular signaling between gut microbiota and host cells adheres to Peircean triadic semiosis: microbial metabolites (representamen) encode environmental states (objects), eliciting physiological interpretants. Hoffmeyer’s semiotic scaffolding helps to explain stabilized interactions, exemplified by quorum sensing-regulated butyrate synthesis and secretory IgA-mediated symbiosis. Uexküll’s Umwelt theory resolves interspecies perceptual divides, positioning shared signs as multidirectional mediators. Within this biosemiotic paradigm, health emerges as semiotic coherence, a state of synchronized, context-appropriate signaling across holobiont agents. Dysbiosis manifests as a semiotic disorder, characterized by dysregulation of interspecies semiotic processes which propagates systemic pathophysiology. Therapeutic strategies, including probiotic supplementation and microbiota transplantation, function by reestablishing semiotic fidelity within these networks. By framing holobiont dynamics as semiotic phenomena, this work challenges reductionist models of host-microbe interactions and advances an interdisciplinary paradigm for understanding health and disease. Coherent cross‑species semiosis is necessary for health, which arises as an emergent property reflecting numerous negotiated meaning‑making processes between the host and its symbionts. Pathology results when these processes collapse. This synthesis advances interdisciplinary models for translational medicine and ecological theory, where health thrives not in isolation, but in the fluency of a co-authored language of life.

La influencia de la microbiota en el comportamiento, la percepción y diversas facultades cognitivas se ha estudiado en diferentes especies, incluidos el humano. Mas directamente se observa por alteraciones en la microbiota intestinal de pacientes con enfermedades neuropsiquiátricas. Los aportes que el estudio de signos y significado enriquecen la información producida por la metagenómica. Este trabajo presenta una introducción al tema de la microbiota/microbioma desde la biosemiótica, usando la teoría del Umwelt y el circulo funcional Uexkülliano como plataforma, no porque sean las únicas, sino por ser parte de los pilares de esta disciplina.