Thursday, November 13, 2014

My Book Review of The Hologenome Concept by the Rosenbergs

"Holos" means whole in Greek and genome is of course all of the DNA in an organism. Thus, hologenome is the term that captures the intergenomic networkism present in every animal and plant and parallels the term holobiont - the sum of all organisms present in an animal or plant.

Microbe magazine published my book review of the Hologenome Concept: Human, Animal and Plant Microbiota. As good friend Dr. Laura Williams pointed out to me, the review is unfortunately under a paywall. I believe this book will strike a chord with everyone interested in the life sciences. It is a form of heightened pattern recognition in biology. Hence, I'm posting the original text of the review here. 

Eugene Rosenberg and Ilana Zilber-Rosenberg (ed.). Springer, New York, 2014, 178 p., $149 (eBook) or $189 (hardcover).

So, like it or not, microbiology is going to be in the center of evolutionary study in the future—and vice versa.” -Carl Woese, The Hologenome Concept, pg. 109

In The Hologenome Concept: Human, Animal and Plant Microbiota, Eugene Rosenberg and Ilana Zilber-Rosenberg methodically advance the postmodern synthesis in which the holobiont — the host plus its associated microorganisms— forge a unique biological entity subject to the fundamental tenets of biological evolution. This book is based on the popular idea that no “individual” plant or animal, including Homo sapiens, exists independently of microbes. The authors were in fact among the fırst serious advocates of this view and have published a number of conceptual papers on the hologenome. Now backed by a symphonic-like arrangement of hard evidence, The Hologenome Concept is poised to be an influential piece of literature that encompasses biology’s most signifıcant developments in the last decade. What has led Rosenberg and Zilber-Rosenberg to this inflection point?

Looking back in history, the germ theory of disease is a perfect starting point to put The Hologenome Concept in context. The germ theory left two lasting legacies on biology. First, it massively widened the focus of biology on diagnosing, treating, and eradicating infectious diseases. Second, it narrowed biology’s focus on microbes to such an extent that all host-associated microbes were essentially viewed as harmful and thus extrinsic entities to animals and plants. Today, there are of course a myriad of reasons to doubt that all microbes are bad (indeed quite the opposite), and this shift in thinking gained notable momentum in the mid- 20th century. Ivan Wallin’s and Lynn Margulis’s plights in convincing biologists that mitochondria were bacterially derived were among the seminal turning points in adjusting perceptions toward the broader nature of evolution.

In the last few decades, microbiology has made revolutionary contributions to all disciplines of biology. From Carl Woese’s evolutionary tree of life to the universality of microbiomes in plants and animals, there is a tangible sense that something substantial is affecting how we study, understand, apply, and teach the life sciences. More than just advances in technology and more than realizing the central importance of microbiology in shaping life, the postmodern synthesis that we are now witnessing is tackling additions and upgrades to theories that seem untouchable, including the Darwin and Wallace theory of evolution by natural selection.

Rosenberg and Zilber-Rosenberg demonstrate with precision that this inflection point in the history of biology is not just a common sense issue, but one that is scientifıcally grounded in a treasure of data. Chapters are devoted to illustrating how the canonical mechanisms of evolutionary change seamlessly fıt into a hologenomic unit of selection, namely genetic variation in the hologenome, maternal transmission between holobiont generations, and multi-level selection theory and fıtness. They bring together a vivid recipe for how variation in plants and animals exists beyond the nuclear genome, spanning microbial amplifıcation, acquisition of novel microbes, and horizontal gene transfer. In particular, genetic variation of complex organisms is not restricted to the nuclear genome and cytoplasm, but to the general microbiome as well. This variation encodes phenotypes subject to natural selection. Thus, the central tenet of the book is that the hologenome is a newly appreciated unit of variation and evolution in which the amalgam of genomes in the host and symbionts collectively are a target of natural selection.

For those that have seen the central role of symbiosis in biology, this book will be an essential reference of key papers, defınitions, teaching, inspiration, and future discourse. It was for me. For others that doubt the emerging horizon of the microbiome’s role in evolution, this book will fuse their familiarities with frontier research to form a new appreciation on how variation and selection on the host-associated microbiota is equal to these same forces acting on the nuclear genome. Indeed in my own analysis of the book, I have found it most helpful to ask, when are the evolutionary properties of a nuclear gene any different than those of a microbe in the microbiome? I have not yet been able to discriminate the two, and this simple exercise is the essence of The Hologenome Concept.

The book is written exceptionally clearly and provides bullet points at the end of each chapter to emphasize key themes in the text. The fırst chapter is one of the most important of the book because it frames the concepts and definitions in such a clear manner that confusion over nomenclature, which can be widespread in the early phases of introducing new concepts, is erased in favor of a vibrant appreciation for a hologenomic level of selection. What is and is not the hologenome makes the rest of the arguments seamlessly fall into place. The hologenome is not a metagenome, superorganism, organ, or the singular unit of selection in evolution. It is a body of scholarship that fıts squarely into genetics and multilevel selection theory in which the genome, DNA-containing organelles, and microbiome cooperate and clash to forge a source of variation for evolution by natural selection and the origin of species. The Hologenome Concept: Human, Animal and Plant Microbiota brings forth an upgraded “grandeur in this view of life.”

Seth Bordenstein
Vanderbilt University
Nashville, Tenn.