A surreal illustration showing bleached coral gradually regaining color and health, with symbolic representations of diverse microbes interwoven into the image.

Coral's Secret Weapon: How Microbes are Revolutionizing Evolution

Reese Marlowe in Science & Nature November 2025 • 4 min read.

"A groundbreaking concept born from coral bleaching research is changing how we understand evolution and the interconnectedness of life on Earth."

Imagine a world where evolution isn't just about the survival of the fittest individual, but the success of the most cooperative team. This is the idea behind the hologenome concept, a revolutionary theory that's changing the way scientists view life and evolution. And it all started with a coral.

Every summer, rising temperatures in the Mediterranean Sea cause the stony coral Oculina patagonica to bleach, losing its colorful algae. Back in 1996, researcher Ariel Kushmaro discovered that Vibrio shiloi bacteria were the culprits behind this bleaching. For years, scientists studied this process, seeking to understand the mechanics of coral bleaching at a microbial level.

Then, something unexpected happened: the corals became resistant. The usual V. shiloi strains couldn't infect them anymore, throwing the entire model into disarray. Yet, from this apparent failure emerged a far grander idea: the hologenome concept, which suggests the key to survival lies not just within an organism's genes, but in its entire community of microbes.

What is the Hologenome Concept?

A surreal illustration showing bleached coral gradually regaining color and health, with symbolic representations of diverse microbes interwoven into the image.

At its core, the hologenome concept proposes that an organism (the holobiont) should be viewed together with all of its associated microbes. The term "hologenome" represents the sum of all the genetic information of the host and its microbiome, including bacteria, fungi, viruses, and other microorganisms living in or on it.

Think of it like this: you aren't just you; you're you plus trillions of tiny partners. These microbes aren't just hitchhikers; they actively contribute to your health, digestion, immunity, and even behavior. The hologenome concept argues that evolution acts on this entire package—host plus microbiome—rather than just the individual organism.

Key aspects of the hologenome concept include: Ubiquity: All plants and animals have diverse and abundant microbial symbionts. Transmission: The host genome and its microbiome pass with fidelity from generation to generation. Interaction: The anatomy, physiology, development, metabolism and overall fittness are affected in the holobiont by the microbial symbionts. Genetic Variation: To change more rapidly based on enviromental conditions the holobiont experiences genetic variation.

This seemingly simple shift in perspective has profound implications. It suggests that adaptation and survival aren't solely determined by an individual's inherent genetic makeup. Instead, they depend on the dynamic interplay between an organism and its ever-changing microbial community.

The Future of Evolution is Interconnected

The hologenome concept is more than just an academic theory; it's a call to rethink our relationship with the microbial world. It encourages us to recognize the interconnectedness of life and the crucial role that microbes play in shaping our health, our planet, and the future of evolution itself. From personalized medicine to conservation efforts, understanding the hologenome promises to unlock new solutions to some of the most pressing challenges facing humanity.

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Everything You Need To Know

What is the hologenome concept in simple terms?

The hologenome concept proposes that an organism, called a holobiont, is not just the individual itself, but also includes all of its associated microbes. The hologenome is the sum of all the genetic information of the host and its microbiome. These microbes, including bacteria, fungi, and viruses, actively contribute to the holobiont's health and survival. Evolution, according to this concept, acts on the holobiont—the host plus its microbiome—rather than just the individual organism's genes. This understanding is based on research into coral bleaching, showing the importance of microbial communities to the host's resilience.

How did coral bleaching research contribute to the development of the hologenome concept?

The hologenome concept emerged from studies of coral bleaching in the Mediterranean Sea. Researchers observed that the stony coral *Oculina patagonica* bleached due to rising temperatures. Initially, *Vibrio shiloi* bacteria were identified as the cause. However, when the corals became resistant to the usual *V. shiloi* strains, it led scientists to question the existing understanding of evolution. This unexpected event sparked the idea that the key to survival might not just be within an organism's genes but also in its community of microbes. The hologenome concept was born from this realization.

What are the key aspects of the hologenome concept?

The hologenome concept has several key aspects. First, **Ubiquity** means all plants and animals have diverse microbial symbionts. Second, **Transmission** highlights how the host genome and its microbiome are passed from generation to generation. Third, **Interaction** suggests that the host's anatomy, physiology, development, metabolism, and fitness are affected by the microbial symbionts. Finally, **Genetic Variation** focuses on how the holobiont experiences genetic variation that allows it to respond rapidly to environmental changes. These aspects collectively illustrate the profound interconnectedness between organisms and their microbes, fundamentally changing how we understand evolution.

How does the hologenome concept change our understanding of evolution?

The hologenome concept challenges the traditional view of evolution, which focuses primarily on individual genetic traits. Instead, it suggests that evolution acts on the entire holobiont—the organism and its associated microbes. This means that an organism's ability to adapt and survive isn't solely determined by its own genes, but also by the dynamic interplay with its microbial community. Environmental pressures can influence both the host and its microbiome, leading to changes in the hologenome. This broader perspective emphasizes the importance of cooperation and interconnectedness in the evolutionary process, as opposed to just individual competition.

What are the potential implications of the hologenome concept for the future?

The hologenome concept has wide-ranging implications for several areas. In personalized medicine, understanding the microbiome can lead to tailored treatments. In conservation efforts, it can help to manage and protect ecosystems by considering the microbial communities within organisms. It encourages a re-evaluation of our relationship with the microbial world. It highlights the interconnectedness of life and the importance of microbes in shaping our health, the planet's health, and evolution. This concept could unlock new solutions to many pressing challenges, from disease to environmental conservation, by considering the complex relationships between organisms and their microbial partners.