Discovering the Human Holobiont: How the Microbiome Affects Human Health

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: 15 July 2025 | Viewed by 3137

Special Issue Editors


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Guest Editor
Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
Interests: nutritional genomic (nutrigenetic, nutrigenomic, metagenomics); human body; composition; human holobiont; personalized nutritional assessment; expsome
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Guest Editor

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the human holobiont concept, which introduces a new level of complexity to the idea of individuality and, further, allows us to expand our understanding of the relationships between the environment and health. Currently, the scientific literature is examining a range of components within the holobiont concept, providing new insights that will lead to testable hypotheses regarding the nature of the interactions that occur within host-associated communities and between hosts and these communities. Several studies have used the partitioning of variance among gene expression patterns, the relative abundance of biont component species, or metric-based combinations of physical and molecular interaction patterns to indicate that the structures observed are not likely to show the randomness that would typically be seen in transparent and standardized physical systems. The research into holobionts also raises important questions related to the structure and dynamics of communities living in coral colonies. Research on the microbiome is providing evidence that suggests a role for other microorganisms besides the bacterial and archaeal species that usually come to mind when we think about holobionts. The study of the microbiome is rapidly becoming an exciting new area of research in modern ecology and evolutionary biology. The relationship between the human host and its microbiota (along with dietary changes and other factors) plays a major role in driving evolution. The gut microbial flora, which is largely made up of bacteria, with smaller numbers of archaea, viruses, and single-celled and multi-celled eukaryotes, represents a complex community in itself. To understand the holobiont concept fully and to better understand the relationships among its parts, we need to focus on the effect of the entire microbiome of an organism and identify subsets of the microbiome in the potential roles of the superorganisms that shape and structure the microbiomes of holobionts.

Potential topics include, but are not limited to, the following:

  • the human holobiont;
  • the microbiome;
  • the environment;
  • ecosystems;
  • the role of diet;
  • future directions;
  • exposomes;
  • noncommunicable chronic diseases.

Prof. Dr. Laura Di Renzo
Dr. Paola Gualtieri
Guest Editors

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Keywords

  • holobiont
  • diet
  • microbiota
  • probiotic and prebiotic
  • gene expression
  • body composition

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Published Papers (2 papers)

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Review

31 pages, 5840 KiB  
Review
Holobiome Harmony: Linking Environmental Sustainability, Agriculture, and Human Health for a Thriving Planet and One Health
by Gissel García, Martha Carlin and Raul de Jesus Cano
Microorganisms 2025, 13(3), 514; https://doi.org/10.3390/microorganisms13030514 - 26 Feb 2025
Viewed by 1293
Abstract
The holobiome is an interconnected network of microbial ecosystems spanning soil, plants, animals, humans, and the environment. Microbial interactions drive nutrient cycling, pathogen suppression, and climate regulation. Soil microbiomes facilitate carbon sequestration and enhance soil fertility, while marine microbiomes contribute to carbon capture [...] Read more.
The holobiome is an interconnected network of microbial ecosystems spanning soil, plants, animals, humans, and the environment. Microbial interactions drive nutrient cycling, pathogen suppression, and climate regulation. Soil microbiomes facilitate carbon sequestration and enhance soil fertility, while marine microbiomes contribute to carbon capture and climate stability. However, industrial agriculture, extensive herbicide use, antibiotic overuse, and climate change threaten microbial diversity, leading to ecosystem and health disruptions. Probiotic interventions help to restore microbial balance. In human health, probiotics support gut microbiota diversity, reduce inflammation, and regulate metabolism. In agriculture, soil probiotics enhance microbial diversity, improve nutrient cycling, and degrade contaminants, increasing crop yields and soil health. Case studies show that microbial inoculants effectively remediate degraded soils and enhance nutrient uptake. Artificial intelligence is transforming microbiome research by enabling predictive modeling, precision probiotic design, and microbial consortia optimization. Interdisciplinary collaboration and supportive policies are essential for restoring microbial equilibria, ensuring ecosystem resilience, and promoting long-term sustainability. The integration of artificial intelligence, clinical research, and sustainable practices is crucial for advancing holobiome science. The holobiome framework underscores the need for interdisciplinary collaboration to address global challenges, bridging environmental sustainability, agriculture, and public health for a resilient future. Full article
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19 pages, 1260 KiB  
Review
From Dysbiosis to Hepatic Inflammation: A Narrative Review on the Diet-Microbiota-Liver Axis in Steatotic Liver Disease
by Andrea Pasta, Elena Formisano, Francesco Calabrese, Elisa Marabotto, Manuele Furnari, Giorgia Bodini, Maria Corina Plaz Torres, Livia Pisciotta, Edoardo Giovanni Giannini and Patrizia Zentilin
Microorganisms 2025, 13(2), 241; https://doi.org/10.3390/microorganisms13020241 - 23 Jan 2025
Viewed by 1352
Abstract
The gut microbiota has emerged as a critical player in metabolic and liver health, with its influence extending to the pathogenesis and progression of steatotic liver diseases. This review delves into the gut-liver axis, a dynamic communication network linking the gut microbiome and [...] Read more.
The gut microbiota has emerged as a critical player in metabolic and liver health, with its influence extending to the pathogenesis and progression of steatotic liver diseases. This review delves into the gut-liver axis, a dynamic communication network linking the gut microbiome and liver through metabolic, immunological, and inflammatory pathways. Dysbiosis, characterized by altered microbial composition, contributes significantly to the development of hepatic steatosis, inflammation, and fibrosis via mechanisms such as gut barrier dysfunction, microbial metabolite production, and systemic inflammation. Dietary patterns, including the Mediterranean diet, are highlighted for their role in modulating the gut microbiota, improving gut-liver axis integrity, and attenuating liver injury. Additionally, emerging microbiota-based interventions, such as fecal microbiota transplantation and bacteriophage therapy, show promise as therapeutic strategies for steatotic liver disease. However, challenges such as population heterogeneity, methodological variability, and knowledge gaps hinder the translational application of current findings. Addressing these barriers through standardized approaches and integrative research will pave the way for microbiota-targeted therapies to mitigate the global burden of steatotic liver disease. Full article
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