The traditional biological view often focuses on the individual organism as a distinct, self-contained entity. The concept of the holobiont challenges this perspective by proposing that all life forms are composite entities made up of multiple species living together. This suggests that a single animal, plant, or fungus should be studied as an integrated system with its associated microbial community. The holobiont recognizes microbes not as mere passengers, but as active, functional partners in a cohesive biological unit. This shift in thinking provides a framework for understanding health, disease, and the mechanisms of evolution.
Defining the Holobiont
A holobiont is formally defined as an assemblage composed of a macroscopic host organism and all the other species living in or on it. The host is typically a multicellular eukaryote, such as a human, a coral polyp, or a tree. These hosts are invariably associated with a diverse community of microorganisms, collectively known as the microbiota or microbiome. This microbial community includes bacteria, archaea, fungi, protists, and viruses.
The relationship between the host and its associated microbes is one of symbiosis, ranging from mutually beneficial to parasitic. Regardless of the interaction’s nature, the holobiont functions as a discrete ecological unit. These partners are often so intimately linked that the host cannot perform necessary biological functions without its microbial associates.
The Hologenome Concept
The genetic dimension of this composite entity is captured by the hologenome concept, which represents the collective genetic information of the holobiont. This comprehensive gene system includes the host’s nuclear genome and the genomes of all its associated symbionts. For example, the human hologenome includes the host’s approximately 20,000 protein-coding genes plus an estimated nine million unique microbial genes found in the gut microbiome alone. This vast microbial gene pool significantly expands the functional potential of the entire biological system.
The genetic material from the microbial community can be transmitted between generations through various mechanisms, such as through the egg, direct contact during birth, or the environment. This intergenerational transmission means that specific microbial genes, alongside host genes, are passed down. The hologenome thus provides a mechanism for the entire holobiont to respond to environmental challenges with a broader set of available genes than the host genome alone.
How Holobionts Function in Nature
Holobionts demonstrate functional integration across all biological kingdoms, with microbial partners performing services the host cannot manage alone. The human gut holobiont provides a clear example, as the host lacks the enzymes to break down many complex plant polysaccharides. Specialized gut bacteria fill this gap by producing necessary enzymes, enabling the extraction of otherwise unavailable energy and nutrients. The microbiota also contributes to the maturation of the host immune system and assists in the synthesis of certain vitamins.
In marine environments, reef-building corals exist as a complex holobiont, relying on single-celled algae called Zooxanthellae for their primary energy source. These algae live inside the coral tissues and perform photosynthesis, providing the host with products necessary for survival and growth. The coral holobiont also includes a diverse array of bacteria, fungi, and viruses that contribute to nutrient cycling and stress tolerance. When environmental conditions change, such as during ocean warming, the host-microbe relationship can shift, allowing the holobiont to acquire new, more heat-tolerant microbes to survive the stress.
Plants also function as holobionts, forming partnerships with microbes in the soil surrounding their roots. Certain bacteria, such as nitrogen-fixers, convert atmospheric nitrogen into forms the plant can absorb, a process the plant cannot perform independently. This exchange allows the plant to thrive in nutrient-poor conditions, while the host provides the microbes with sugars produced through photosynthesis. These microbial communities are instrumental in defending the plant against pathogens and enhancing nutrient uptake from the soil.
Implications for Evolution and Biology
The holobiont concept has triggered a significant theoretical shift in biology, particularly in the study of evolution. The Hologenome Theory of Evolution posits that the holobiont, rather than the host organism alone, serves as the fundamental unit of natural selection. This means that selective pressures act simultaneously on the combined traits of the host and its microbial residents. Variation in the hologenome, caused by changes in either the host’s genes or the composition of the microbiome, can be subject to evolutionary forces.
The theory suggests a mechanism for rapid adaptation that bypasses the slow process of host genetic mutation. The microbial community can evolve and change much faster than the host genome, primarily through acquiring novel microbes or changing the abundance of existing ones. This rapid change in the microbiome can confer immediate new traits to the holobiont, allowing it to adapt swiftly to fluctuating environmental conditions. This concept introduces a form of inheritance where acquired microbial traits can be passed down to offspring, accelerating evolutionary change in the host lineage.