Discover how the holobiont concept is transforming our understanding of biological individuality
For centuries, biologists viewed individual plants and animals as autonomous entities—self-contained units whose biology could be understood by studying their own cells and genes. This reductionist perspective dominated life sciences, focusing on taking organisms apart to understand how they work. But a profound paradigm shift is underway, revolutionizing our understanding of life itself. Through the lens of systems biology, we're discovering that complex eukaryotes—from humans and corals to ants and oak trees—are not solitary beings but dynamic ecosystems, living in intimate partnership with trillions of microorganisms that are essential to their development, health, and evolution 1 5 .
This new perspective reveals that what we perceive as an individual organism is actually a collaborative network of species functioning as a cohesive biological unit. These partnerships, known as holobionts, represent one of the most exciting frontiers in modern biology, blurring the boundaries between organism and ecosystem and forcing us to reconsider fundamental concepts of genetics, evolution, and what it means to be an individual 7 8 .
The human body contains approximately 39 trillion microbial cells compared to only 30 trillion human cells.
Microbial cells outnumber human cells in your body
A holobiont refers to a host organism together with all of its associated symbiotic microorganisms—the bacteria, archaea, fungi, viruses, and other microbes that live in or on it throughout a significant portion of its lifetime 2 7 . The term, derived from the Greek words holos (whole) and bios (life), was first introduced by Lynn Margulis in 1991 to describe these multi-species assemblages that function as discrete ecological units 2 7 .
Each holobiont possesses what's known as a hologenome—the collective genomes of the host plus all its microbial partners 2 8 . To appreciate the scale of this genetic partnership, consider that while the human genome contains approximately 20,000 genes, our hologenome contains more than 33 million microbial genes 2 . This vastly expanded genetic repertoire allows holobionts to access capabilities far beyond what their own genes provide.
While holobionts describe partnerships between a host and its microbes, the term superorganism typically refers to social insect colonies—such as ant colonies, beehives, or termite mounds—where many individuals of the same species function as a collective entity with division of labor 7 . These superorganisms themselves can also be viewed as holobionts, as each individual insect hosts its own microbial community 4 .
The distinction is important: an individual ant and its microbes form a holobiont, while the entire ant colony functions as a superorganism 7 . Both concepts represent multi-level biological organizations that challenge our traditional definitions of individuality.
Plant, animal, or human
Diverse microbial communities
Mycorrhizal and other fungi
Phages and other viruses
= Holobiont - A collaborative biological unit
The conceptual roots of the holobiont concept trace back to early biological thinkers who viewed life holistically. Aristotle's philosophy of holism argued that systems should be studied in their entirety, focusing on interconnections rather than individual parts 7 .
The groundwork for today's holobiont theory began with pioneering work on symbiosis. In 1879, Anton De Bary coined the term "symbiosis" to describe the living together of dissimilar organisms 2 .
Konstantin Mereschkowski's 1905 endosymbiosis theory proposed that eukaryotic cells originated through symbiotic mergers of prokaryotes—a theory now universally accepted 7 .
The formal foundations of systems biology were laid fifty years ago with Ludwig von Bertalanffy and Mihajlo D. Mesarović's monographs outlining a "systems theory of biology" 1 5 .
Lynn Margulis formally introduced the term "holobiont" to describe multi-species assemblages that function as discrete ecological units 2 7 .
The relatively recent advent of high-throughput sequencing technologies that truly enabled scientists to appreciate the ubiquity and importance of host-associated microbes, driving the paradigm shift we're experiencing today 2 .
A landmark 2025 study on pea plants and root rot disease provides a compelling example of how holobionts function and evolve. Researchers investigated the pea root rot complex, a serious agricultural problem caused by multiple soil-borne pathogens that collaborate to destroy pea roots, causing massive yield losses 3 .
The research team designed an elegant experiment to answer a fundamental question: Do plants have genetic control over their microbial partnerships, and could this influence disease resistance? They assembled a diverse collection of 252 distinct pea lines, grew them in soil naturally infested with root rot pathogens, and used DNA sequencing to identify the microbial communities associated with each plant genotype 3 .
Through genome-wide association studies (GWAS), the scientists searched for specific genetic variants in the peas that correlated with the presence or abundance of particular microbes. This approach allowed them to determine whether a pea plant's genes influence which bacteria and fungi it hosts 3 .
The results were striking. The researchers identified 54 quantitative trait loci (QTLs)—specific chromosomal regions in the pea genome—that significantly influenced the abundance of 98 different microbial taxa 3 . The most significant genetic region was located on chromosome 6, which contained 10 distinct QTLs affecting 50 different microbes 3 .
| Genomic Region | Number of QTLs | Microbial OTUs Affected | Potential Function |
|---|---|---|---|
| Chromosome 6 | 10 | 50 | Major regulatory hub for microbiome assembly |
| Various Locations | 54 | 98 | Specific microbial abundance control |
| Additional Loci | 20 | Multiple each | Multi-microbe regulation |
Crucially, the research demonstrated that these microbial partnerships had real-world consequences for plant health. The abundance of certain microbes was strongly correlated with resistance or susceptibility to root rot disease 3 .
| Microbial Group | Correlation with Disease | Effect on Plant |
|---|---|---|
| Fusarium species | Positive | Increased infection |
| Dactylonectria | Negative | Resistance to root rot |
| Chaetomiaceae | Negative | Resistance to root rot |
Perhaps most importantly, when the researchers used this microbial information to predict disease resistance, they found that including microbial data significantly improved prediction accuracy compared to using plant genetic markers alone 3 . This has profound implications for agricultural breeding programs.
| Predictor Model | Predictive Ability | Application Potential |
|---|---|---|
| Plant QTLs alone | Lower | Traditional breeding |
| Microbial abundance | Significantly better | Microbiome-assisted breeding |
| Combined holobiont approach | Best | Next-generation crop improvement |
This study provides compelling evidence that hosts can actively shape their microbial communities through genetic mechanisms, and that these microbial partnerships have tangible effects on health and disease resistance. The findings support the holobiont concept by demonstrating that host genetics, microbiome composition, and phenotypic outcomes are intimately connected 3 .
Sanger Sequencing
Microarrays
Next-Gen Sequencing
Single-Cell & AI Analysis
The holobiont concept is revolutionizing medicine. Human health is now understood through the lens of host-microbe interactions, with implications for treating inflammatory diseases, metabolic disorders, and even mental health conditions 1 2 .
The recognition that our microbial partners play essential roles in immune system development, nutrient extraction, and protection against pathogens has spawned entire new fields of therapeutic intervention 2 9 .
Fecal microbiota transplants, for instance, represent a direct application of holobiont theory—acknowledging that sometimes the best way to restore health to a human host is to restore its microbial community 2 .
In agriculture, holobiont thinking is leading to more sustainable approaches to crop production and protection 3 9 . The pea root rot study exemplifies how plant breeding programs might incorporate microbiome management to develop more resilient crops 3 .
Rather than relying solely on pesticides and fertilizers, we're learning to harness beneficial microbial communities to support plant health and productivity 3 .
Environmental conservation is also benefiting from this perspective. Coral reefs—iconic examples of holobionts where coral animals partner with photosynthetic algae—are under threat worldwide 7 .
Holobiont theory has profound implications for our understanding of evolution. The hologenome concept suggests that natural selection acts on the collective genome of the host and its microbiota, potentially accelerating adaptation 8 .
This perspective helps explain how some organisms rapidly adapt to changing environments—they can leverage the genetic diversity of their microbial partners rather than waiting for mutations in their own genome 8 .
Ecologically, viewing life as networks of holobionts interacting with each other provides a more accurate picture of ecosystem dynamics 6 .
As research continues to reveal the intricate partnerships that define plants, animals, and even ourselves, we're forced to abandon outdated notions of biological individuality in favor of a more nuanced, integrated perspective. The tools of systems biology—from single-cell sequencing to advanced computational modeling—are rapidly improving, promising ever deeper insights into how these biological partnerships form, function, and evolve.
The holobiont concept represents nothing short of a revolution in how we understand life on Earth. As one researcher noted, "Holobiont research is now an imperative across numerous fields of the life and medical sciences" 2 .
The implications extend far beyond basic biology. Medicine, agriculture, conservation, and even our understanding of ourselves are being transformed by the recognition that we are not autonomous individuals but collaborative networks. As we learn to nurture these partnerships rather than simply attacking microbial "invaders," we may discover powerful new approaches to some of our most pressing challenges in health, food production, and environmental sustainability.
"Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes" 8 .
Embracing this reality doesn't diminish the wonder of individual organisms but rather enhances it, revealing the invisible partnerships that make life as we know it possible.