
A “new” biology of organisms. Research published by the Holobiont Biology Network
15.11.2024
Since Darwin's time, plants, animals, and humans have been studied as autonomous entities, with their physiology and life primarily determined by their genes. The new research published in «Science» titled "The disciplinary matrix of holobiont biology. Uniting life’s seen and unseen realms guides a conceptual advance in research" proposes a radical paradigm shift that is more advantageous in the study of living organisms.
The study is the result of the Holobiont Biology Network, a scientific pool that includes faculty from various universities such as Penn State University, University of Copenhagen, NTNU University Museum, University of Pittsburgh, and National University of Colombia. Maria Elena Martino from the Department of Comparative Biomedicine and Food Science at the University of Padua participated in the international research team.
To understand the scope of this new conceptual perspective, it is useful to refer to two concepts: holobiont and microbiome. A holobiont is a set consisting of a host and many other species that live within or around it. The microbiome is the total genetic heritage and environmental interactions of all microorganisms in a defined environment. The publication explores the biology of holobionts viewed as an aggregation of host cells and a vast community of symbiotic microorganisms, living in close interaction and synergy.
This model emphasizes the importance of studying and analyzing these interactions to fully understand the life of organisms, health, and the onset of diseases. In particular, the research highlights how the symbiosis between animal and plant hosts and their microbiomes affects fundamental biological functions such as immunity, growth, pathogen resistance, and adaptation to environmental stresses. For example, if the organism is a holobiont, its genome will be a hologenome, which is the combination of the host organism's genome and the genomes of the microorganisms inhabiting it. The human hologenome, that is, the combination of the human genome and the gut microbiome, has proven in various scientific studies to be a more effective predictor compared to the analysis of the human genome alone for several traits, including body mass index, HDL cholesterol, colon cancer risk, the onset of various metabolic diseases, fasting glucose levels, physical characteristics like hip circumference, and many others.
Today, the primary approach used to predict the onset of diseases and assess the health status of humans and animals is DNA analysis through genetic testing. This method is based on genome sequencing to identify mutations or genetic variants associated with specific pathologies. However, this method does not consider the multifactorial aspect that contributes to the development of diseases and the physiological conditions of an organism, including non-genetic factors such as microbial identity and the role of the microbiome.
"The biology of holobionts allows us to better understand the interdependence between the host and its microbiome, surpassing the traditional approach that studies organisms as isolated entities. This new paradigm offers an innovative perspective on how the health and resilience of ecosystems depend on complex biological interactions," says Maria Elena Martino, co-author of the study. "This scientific viewpoint opens new avenues for biodiversity conservation, environmental health, and agroecological sustainability. Adopting a holistic approach in human and animal medicine, as well as in environmental health, biodiversity maintenance, and agroecological sustainability, allows us to tackle issues by integrating different methods and solutions, thereby maximizing their effectiveness. For example, in terms of biodiversity, global strategies are being developed for coral reefs," Martino emphasizes, "which involve the dissemination of probiotic bacteria capable of protecting corals and ecosystems from the devastating effects of climate change, helping to reverse bleaching and biodiversity loss. This approach, which leverages the beneficial potential of microbiomes, can therefore be applied to various contexts, from human and animal medicine to agriculture."
A crucial aspect of the publication is the response that could be provided to the "missing heritability problem." This refers to the discrepancy between the estimated heritability of certain complex traits (such as height, disease risk, etc.) and the genetic variation explained by known variants. In such traits, genetic studies explain only a part of the observed variation, leaving a significant portion still unjustified by the identified genetic variants. This portion is largely determined by the role of the microbiota, which, by interacting with the host genome and influencing important physiological functions, significantly contributes to the heritability of these traits.
"The hologenomic model, which jointly considers the host DNA along with the microbiome—both the type of host genome and the type and function of its microbiome—allows for a greater part of phenotypic variability to be explained, offering a deeper understanding of traits such as pathogen resistance, adaptability to climate change, and resilience to environmental disturbances. The study," concludes Maria Elena Martino, "also highlights the importance of global hologenomic databases, like the Earth Hologenome Initiative, which catalogue and standardize information on the combined genomes of hosts and microbes. These platforms represent a unique opportunity for scientific research and for the formulation of environmental policies based on concrete data, promoting a more informed and sustainable ecosystem management. This research marks a milestone in understanding the symbiosis and interconnectedness of life on Earth."