Book Review
Fundamentals of Microbiome Science:
How Microbes Shape Animal Biology
We seem to be in the midst of a revolution in our understanding of the inner workings of the world around us—our planet, our ecosystem, even our own bodies. It turns out that many (most?) of the control mechanisms about our health and function do not come from our own cells but from other smaller cells—microbes—that live on and inside of us. Indeed those cells outnumber our own. So are you saying that what makes us, us, is mostly not human cells? Yes, that’s what I’m saying. (You really need to read this book!) A few decades ago, science looked to the Human Genome to tell us about who we are and how we function. Scientists today are still looking for many of those answers and finding them in our Microbiome. Clearly the general public is curious and eager to learn more as well; several best-selling books have been published recently including I Contain Multitudes and Eugenia Bone’s Microbia (reviewed above). For readers wanting to learn more, and who have a pretty good understanding of microbiology, an excellent primer on the topic is Angela Douglas’s Fundamentals of Microbiome Science.
Angela Douglas is the author of two previous books on microbes and symbioses, Symbiotic Interactions (1994, by Oxford University Press) and The Symbiotic Habit (2010, by Princeton University Press). In her new book, Fundamentals of Microbiome Science, Douglas synthetizes data from the burgeoning field of microbiome science in eight highly informative chapters. Topics include the origins of the animal microbiome, what we know about the microbiome’s interactions with the immune system, hints at how microbes drive animal behavior, and how the gut microbiota are involved in gutbrain communication. Each of the eight chapters has a summary at the end that I found very helpful. The book also clearly delineates the influence of the microbiome in determining human health and disease (e.g., there is a fine line between proper gut function with microbes doing a beneficial service and causing problems like irritable bowel syndrome and even Crohn’s disease). The microbiome revolution is expanding at breakneck speed and moving from “the study of correlation to causation and mechanism.” More examples of how research is revealing the role of microbes in human health and disease are coming from studies with model animals. For example, mice lacking the leptin gene, which regulates satiety, consume more food and become obese. When the microbiota of obese mice are transferred to lean mice, the lean mice then become obese.
When considering animals as hosts to microbes, probably the most fundamental question is: Why support microbial communities at all? The functional explanations are twofold: microorganisms provide metabolic capabilities that are lacking in animals; and microorganisms modulate the signaling networks that regulate animal functions required for sustained animal health and vigor. Without doubt microbes do much good for us and their other hosts (be they plant, animal, or other organisms). Microorganisms can modulate the immune function of animals (dampening the immune system of their host as in many parasitic symbioses) but there is much evidence that the microbiota also contribute directly to the defense against other pathogens and parasites in many animals. For example, Hydra are readily infected by the fungus Fusarium when the bacterial communities associated with their epithelial cells are depleted. The selective advantage to the animal host can be profound. A North American, Drosophila species, D. neotestacea, is parasitized by a nematode parasite Howardula, which causes reproductive sterility of the female flies, but the deleterious effect of the parasite is strongly ameliorated in flies that bear a maternally inherited Spiroplasma symbiont (a bacterium), which confers a very substantial selective advantage in natural populations of the drosophilid flies. This results in the spread of the bacterial-colonized flies from east to west across North America. (This discovery was made by John Jaenike; the sterilizing nematodes were discovered in the flies decades ago and in the 1980s Jaenike made a landmark discovery that if the flies consumed Amanita mushrooms they would rid themselves of the gonad parasites, and be able to reproduce, thus selecting for mycophagy of amatoxin containing mushrooms. This was later found out to be incorrect. It now seems that the bacterium is the puppet master conferring the selective advantage.)
All concepts are explained really well; Douglas uses a great deal of illustrations and examples. Here is one as it pertains to one of the hottest research areas in microbiology: quorum sensing. Quorum sensing (QS) molecules allow bacteria to sense density among other things. For a population of bacteria of a single genotype, the capacity to sense density is important because some bacterial functions are adaptive only at high density. For example, light production by luminescent bacteria is costly (it consumes ATP) and, because high densities of luminescent bacterial cells are required for the production of detectable amounts of light, it is adaptive for expression of luminescence genes to be suppressed in dilute suspensions of bacteria. Another situation where bacteria need to know “how many of us are there,” is in the production of biofilms. This is a very important trait of many bacteria, but is expensive to make and only works if there is a certain density of similar members of the community on hand.
In the final chapter, Douglas delves into some interesting and provocative topics and brings to the forefront the need to reframe our understanding of animals. Here, she includes a discussion of climate change and its potential effects on microbiota. A widely reported consequence of climate change is an increased range for animals into higher elevations and higher latitudes. How, Douglas wonders, will microbiota acquired in these new environments influence animals? This is an area in which “data are almost entirely lacking.”