Every year on June 27, World Microbiome Day provides an opportunity to reflect on how profoundly microbial communities are intertwined with human biology. Once regarded mainly as passengers inhabiting the body, microorganisms are now recognized as participants in processes that influence immunity, metabolism, neurobiology, development, and disease.
Our recent review in npj Biofilms and Microbiomes originated from a question that often arises in cancer research [1]. Colorectal cancer is among the most extensively investigated malignancies, yet substantial variability remains in how the disease develops and progresses. Patients with apparently similar tumors, comparable molecular profiles, and similar treatment strategies can experience very different clinical trajectories. Understanding where part of that variability originates became one of the motivations behind the review.
While examining the literature, a pattern gradually became difficult to ignore. Research from cancer genomics, immunology, microbiology, metabolism, and systems biology repeatedly pointed toward the gut microbiome as a relevant component of colorectal cancer biology. Important questions regarding causality remain, but the volume and consistency of observations emerging from different disciplines suggested that microbial communities deserved closer attention.
Several studies were particularly striking because they moved beyond association. Certain bacterial species produce genotoxins capable of damaging host DNA. Others influence epithelial barrier integrity, immune responses, and metabolic pathways. Reports describing microbial-associated mutational signatures in colorectal tumors added another layer of interest, linking microbial exposure with detectable alterations in cancer genomes [1]. Such observations encouraged a broader view of microbial involvement in carcinogenesis than was common only a few years ago.
During the early stages of writing, we expected to organize the review around individual microorganisms. As the manuscript evolved, that structure became increasingly difficult to maintain. Similar biological patterns appeared repeatedly across different taxa, and many mechanisms seemed to depend less on a single bacterium than on interactions occurring within microbial communities. Biofilms became particularly relevant in this context. Rather than functioning as isolated organisms, microorganisms within these structures interact metabolically, influence local immunity, and contribute to persistent inflammatory conditions. Looking at colorectal cancer through an ecological framework helped connect many observations that initially appeared unrelated.
The same process also changed how we approached the broader narrative of the review. Instead of emphasizing lists of microorganisms, attention shifted toward biological networks. Immune, metabolic, neural, and endocrine pathways appeared repeatedly throughout the literature, often interacting with one another rather than operating independently. A systems-oriented framework ultimately provided a more coherent way to interpret the complexity of host–microbiome interactions in colorectal cancer.
Similar themes have emerged in other areas of microbiome research. Work in gastric cancer has reported microbial alterations associated with disease progression, immune regulation, and therapeutic response, suggesting that host–microbiome interactions may extend across multiple cancer types rather than being restricted to a single organ [2].
At the same time, microbiome science has begun to move closer to clinical practice. Research increasingly focuses on how microbial ecosystems relate to disease susceptibility, treatment response, and patient outcomes. Questions that were largely exploratory a decade ago are now being investigated within translational and clinical settings, creating opportunities to evaluate how microbiome-informed approaches might complement existing medical strategies [3].
Another topic repeatedly surfaced while drafting the review: time. Circadian rhythms regulate metabolism, immunity, hormone secretion, and tissue repair throughout the body. Microbial communities also fluctuate across the day in response to feeding behavior, sleep patterns, and host physiology. Work from several groups indicates that these rhythms are closely interconnected, adding a temporal dimension to host–microbiome interactions that remains only partially understood [4].
Questions surrounding microbial influences are not limited to primary tumors. Research exploring metastatic disease has raised the possibility that microbial signals may contribute to processes involved in dissemination and colonization of distant tissues. Although many mechanistic details remain unresolved, such observations broaden the scope of microbiome research beyond tumor initiation alone [5].
Perhaps the most encouraging aspect of the field is the growing number of opportunities for intervention. Dietary modulation, microbiota-directed therapies, engineered microbial platforms, bacteriophage-based approaches, and ecosystem restoration strategies are all being explored in different contexts. Some remain experimental, while others are already entering clinical evaluation. Together, they illustrate how microbiome research is progressing from descriptive observations toward practical applications [3].
World Microbiome Day also serves as a reminder that host–microbiome interactions begin long before disease develops. Microbial colonization during infancy contributes to immune maturation and physiological development, while microbial communities continue to change throughout life in response to environment, diet, medications, and aging [6]. Understanding those dynamics may be as important as identifying individual microorganisms associated with specific diseases.
At Universidad de Las Américas (UDLA) in Quito, Ecuador, and the Universidade da Coruña (UDC) in Coruña, Spain, we continue exploring these questions through studies that integrate microbiome science with immunology, metabolism, neuroscience, and clinical research. Rather than focusing exclusively on microbial composition, our interest lies in understanding how host and microbial systems interact across different biological scales and how those interactions may contribute to health and disease.
World Microbiome Day offers a useful reminder that microbial communities are deeply embedded within human physiology. Exploring those relationships may provide valuable insights not only into disease mechanisms but also into the biological processes that help maintain health throughout life.
References
- Bautista, J. et al. Gut microbiome-driven colorectal cancer via immune, metabolic, neural, and endocrine axes reprogramming. npj Biofilms and Microbiomes (2026).
- Bautista, J., Maldonado-Noboa, I., Maldonado-Guerrero, D., Reinoso-Quinga, L. & López-Cortés, A. Microbiome influence in gastric cancer progression and therapeutic strategies. Front. Med. 12, 1681824 (2025).
- Bautista, J. et al. The human microbiome in clinical translation: from bench to bedside. Front. Microbiol. 16, 1632435 (2025).
- Bautista, J. et al. Bidirectional interactions between circadian rhythms and the gut microbiome. Appl. Microbiol. Biotechnol. 109, 218 (2025).
- Bautista, J., Fuentes-Yépez, M. P., Adatty-Molina, J. & López-Cortés, A. Microbial signatures in metastatic cancer. Front. Med. 12 (2025).
- Bautista, J. & López-Cortés, A. Microbial beginnings: determinants and disruptions of the neonatal microbiome. Front. Microbiol. 16 (2025).