by Daniel P. Haeusser
In place of a weekly sermon this month, my church is having members give TED-style talks in their fields of expertise. Like the actual TED series, the idea is for speakers to share "ideas worth spreading", relating novel developments in their field that are shaping humanity’s view of the world, while also describing the ways this view connects with their faith. I had the chance to speak a couple weeks back, and after flirting with the idea of presenting the existence, development, and potential of the CRISPR-Cas system, I instead settled on the other currently reigning en vogue topic of our field: Microbiomes.
With topic fresh in mind, and it being the 'lazy days' of summer, I'm taking the opportunity to review two recent books I've enjoyed and used as a resource both in class and for my 'TED talk' on microbiomes. An explosion of titles has been published on the subject, but as my title for this post alludes to, out of the many, two really stand out. I Contain Multitudes by Ed Yong and The Hidden Half of Nature by Montgomery and Biklé may already be familiar to you, but perchance you have not yet read them, I highly recommend you grab copies, sit back on the beach (or in the AC), and enjoy. But before getting to those reviews, it's worthwhile to take a short Small Things Considered look into the microbiome field.
Treading lightly amid an exciting, but uncertain, field
As readers here know, a lot has been published on the microbiome recently, both in research journals and the popular press. So much that it is often hard to make sense of it all. Over the years we've featured some specific microbiome-related stories here, such as this one from 2015 on honeybees. We've even learned that people's definitions of the term (or the related 'microbiota') differ, complicating clear discussion of the issue.
Yet, though we've brought it up in our features, the microbiome hasn't been a topic that easily fits the culture of the blog, where our editorial focus tends to favor notable updates on rigorously established paradigms – or on forgotten and neglected curiosities – over trendy topics that are largely preliminary in even their broad conclusions. As Elio wrote in 2013 on the past/present microbiome subject:
"Knowledge was mainly descriptive, not much based on ‘experiments’ in the sense that one exposes a subject to experimental variables and observes their effect… The information that is already available is not just colossal but truly exciting, yet it’s distinctly work in progress."
And significant progress has continued to come through the efforts of numerous labs on dissecting the roles of microbial communities on host biology. (The teams led by Ruth Ley, Jeff Gordon, and our own Roberto Kolter spring to mind.) Yet, as becomes apparent each year when 90% of my students come pitching me a microbiome paper for their Small Things Considered assignment, the majority of research under this umbrella remains descriptive: taxonomical surveys with little to no meaningful conclusions.
Nonetheless, research into various microbiomes is obviously an important and exciting focus of current microbiology, and it is capturing broad public interest (particularly the human microbiome) that has led to shifts in society's understanding of, and relationship with, microbes. Whether this is a new or a familiar topic that holds your fascination, or if you simply want to share an overview of the field with family, friends, or students, each of these two books represent an optimal and unique resource.
I Contain Multitudes: The Microbes Within Us and a Grander View of Life
by Ed Yong, August 2016, Ecco Press (HarperCollins Publishers), 368 pages (Hardcover), ISBN: 9780062368591
Readers of this blog are probably not unfamiliar with science journalist Ed Yong. His writing and interests have sparked inspiration for numerous posts of our own, and we recommended an impressively balanced piece he wrote for the New York Times in 2014. My first major sorrow of not being able to attend the general ASM Microbe meeting is that I missed getting to meet him there when he interviewed microbiologist and NASA astronaut Kate Rubins for the 2017 keynote address.
Similar to the articles he has written that form the basis of I Contain Multitudes, Yong explains scientific concepts vividly, with comparisons and prose that mixes moments urgent and poetic with interludes light and humorous.
The stage for Yong's book is set with a review of the scientific discovery of microbes and society's shifting views of their role and importance. After quoting microbiologist René Dubos on the historically dominant association of microbes with the germ theory of disease: "It led to a kind of aggressive warfare against the microbes, aimed at their elimination from the sick individual and community", Yong writes:
"This attitude persists. If I went to the library and lobbed a microbiology textbook out the window, I could easily concuss a passer-by. If I tore out all the pages that dealt with beneficial microbes, I could just about give someone a nasty paper cut."
Later, using Wolbachia as an example, Yong further sets out society's changing views of microbes, while stressing the conflict between anthropomorphic 'friend/foe' narratives with the realities of biology:
"We like our black-and-white narratives, with clear heroes and villains. In the last few years I've seen the viewpoint that "all bacteria must be killed" slowly give ground to "bacteria are our friends and want to help us", even though the latter is just as wrong as the former… The very term symbiosis has been twisted so that its original neutral meaning – 'living together' – has been infused with positive spin, and almost flaky connotations of cooperation and harmony. But evolution doesn't work that way. It doesn't necessarily favour cooperation, even if that's in everyone’s interests. And it saddles even the most harmonious relationships with conflict."
I Contain Multitudes is organized through a series of chapter vignettes that largely mirror the individual stories where Yong's journalistic research has taken him. Most of this ultimately focuses on the human microbiome and its impacts, but most of the detailed examples deal with the other animal species that form the backbone of research as model organisms. Yong relates stories to illustrate the beneficial role of microbes in organismal development and function, such as the tale of the biofilm loving tubeworm Hydroides elegans. (The H. elegans larvae are attracted to signals produced by the bacteria; their full development into mature adults requires burrowing into the biofilm.) He then relates how in addition to pathogenesis, sickness may develop from disruptions in microbial ecologies, including an expansion of his article in The Atlantic on the Gordon Lab's research into malnutrition. He next highlights stories that demonstrate a broad, evolutionary perspective to the subject: how microbial-host interactions (such as Buchnera symbiont exchange in aphids) can help drive evolution through processes like gene transfer and niche expansion. Finally, Yong considers what the future may hold for humans and microbes, both via nature and human ingenuity.
With this overall anecdotal nature, some readers may find the structure of I Contain Multitudes to be problematic. There is a clear theme to each of the individual chapters, but even these tend to overlap with reintroductions of concepts. Nevertheless, I had no problem with that. I also found Yong to have a pitch perfect compromise in scientific content, including essential details, but not overburdening a lay audience.
I Contain Multitudes contains clear excitement for microbiology and Yong's fascination with microbes. He relates the details of microbiome studies in ways that acknowledges accomplishments and celebrates possibilities, yet very clearly also points out caveats and the limitations of complexity.
I'll close with some text that summarizes one of Yong's major take-home messages and provides a perfect segue into the next book in this review.
"Would-be microbiome manipulators are trying to introduce microbes to hosts in a bid to restore disrupted ecosystems or even forge new symbioses… This is what medicine looks like when you understand that microbes are not the enemies of animals, but the foundations upon which our kingdom is built. Say goodbye to dated and dangerous war metaphors, in which we are soldiers hell-bent on eradicating germs at whatever cost. Say hello to a gentler and more nuanced gardening metaphor…"
The Hidden Half of Nature: The Microbial Roots of Life and Health
by David R. Montgomery and Anne Biklé, November 2015, W.W. Norton & Company, 320 pages (Hardcover), ISBN: 9780393244403
Though its prose is neither as fluid nor as clever-analogy rich as Yong's book, The Hidden Half of Nature is still superbly written and includes a broader environmental focus, specifically on the microbiomes of plants and soil. One part science and one part memoir, husband and wife Montgomery and Biklé put a deeply personal perspective on the topic, born from Biklé's diagnosis of cervical cancer. Starting treatment, the couple soon begins to learn of research highlighting the important role of the human gut microbiota for our immune system and our overall health. Drawing from Montgomery's expertise in geology and Biklé's in biology (including ecology and public health) the couple tells a connected story built around literal gardening and the gardening metaphor spoken of by Yong.
The structure of The Hidden Half of Nature is more obvious than that of I Contain Multitudes, with a clean division between the literal gardens in the first half of the book and the metaphorical ones that follow. The final chapters draw the environmental and medical focuses together to drive the similarities home, arguing that considerations about the human microbiome are at heart no different than with other microbial ecologies, that medicine could learn something from environmental science.
“The root is the gut and the gut is the root… The biology and processes that bind soil, roots, and rhizosphere together mirror those in the mucosal lining of the gut and the associated immune tissue… The human world and the botanical world share a common theme – lots of communication and exchanges with microbes.”
The Hidden Half of Nature begins with Montgomery and Biklé’s attempts to start a garden on their property and finding poor soil quality that prevented much growth. Their research into the issue soon led to discovery that microbes could transform that desolate soil to conditions where plants could thrive without the use of pesticides.
Before going into the details of what bacterial communities are doing in soil, Montgomery and Biklé cover the basics of microbiology for a lay audience, including an obligatory history of the field's development. Notably, in addition to the familiar germ theory driven research of Koch and Pasteur, they include ecological perspectives as well, such as those from botanist Sir Albert Howard, the 'father' of composting. They write with awe-filled wonder at the discoveries they make about microbial power in shaping the garden environment:
“One review found that root exudates can account for 30 to 40 percent of a plant's photosynthetic production of carbohydrates! That's like a farmer setting about a third of each harvest at the edge of the field for passerby to take for themselves. Why would plants give away such bounty? They don't. They trade exudates – for things they cannot make or do for themselves… Seducing microbes with sugars and other substances might sound pointless, but it's the heart of the botanical world's defense strategy.”
Their writing is bright and relatable even for a reader untrained in any microbiology. Elio provided a blurb for the book, describing it as "a friendly and highly readable excursion." (Elio also helped check the scientific details that the authors cover, which earned him a grateful acknowledgment in the book.) I fully agree with his assessment, but their tone at times veers too far into a 'Kumbaya' vibe that neglects the point that Yong stresses regarding co-evolution not really being about a 'friend or foe' dichotomy.
This optimism and sense of wonder continues to permeate the second section of the book, which understandably helps brighten the terror that would accompany a cancer diagnosis. Biklé writes:
“I was vaguely aware of the Human Microbiome Project that the newspaper articles described, but I didn’t know that the scientists running the project had published their findings… I was agog. Bacteria, viruses, and more were at work in my body and David's body in ways I never imagined… I waded into this new world of microbes within us… It took both of us to decipher the near-impenetrable cell and molecular biology jargon masking the paradigm-busting ideas of microbiome researchers… I am not who I thought I was. And neither are you. We are all a collection of ecosystems for other creatures…”
Relating similar stories regarding human microbiome research as Yong does, Montgomery and Biklé one up him in making it seem personally meaningful, and they simplify the science a bit more. But this comes at the cost of having fewer caveats and not always referencing their sources as clearly as a professional science journalist does. Someone with a science background or familiar with the topic will know when to just take something with a grain of salt, and yet will still probably learn something new and valuable from The Hidden Half of Nature, particularly in the ecological “lively historical vignettes” as Elio puts it. For those without much of a science background, they may get some overly optimistic or generalized ideas, but in reality, the books ability to get them excited and curious about the wonders of microbes more than makes up for those negatives.
General Biology IS Microbiology
What I Contain Multitudes and The Hidden Half of Nature make abundantly clear is that the life that most of humanity routinely sees and considers on Earth is the minority exception and is dependent in far more ways than ever imagined on the invisible microbes. General introductory biology courses and nature programs of 'life' are overviews of the oddball eukaryotic exceptions. The abundance, variety, and foundational power of biology lie in the prokaryotic realms. As our colleague and friend 'Doc' Mark Martin preaches: Microbial Supremacy! Or as Montgomery and Biklé state:
"The growing awareness that we and all plants and animals evolved along with our microbiomes is helping to crystallize new views of the natural world and our place in it. Views so radically different that when we cracked open our college biology textbooks they had nothing much to say about our microbial side."
Perhaps this is a paradigm shift that should leave textbooks rewritten, where the evolution of life and microbiology is the introductory biology taught, a pedagogical foundation that corresponds to its biological foundation. Then one can learn about the macro diversity, and its unique exceptions, that only exist upon that foundation. At the very least, it is indeed time for our microbial sides to get a lot more focus in those textbooks, courses, media, and all society.
Am I crazy? If so, it's probably because I am not just me. Multitudo sum.
Daniel is an Assistant Professor in the Biology Department of Canisius College in Buffalo, New York. He teaches courses in the freshman and sophomore introductory sequence, General Microbiology, and an integrated Environmental & Pathogenic Microbiology course. In his lab he focuses on undergraduate research mentoring through projects on bacterial cell division and phage factors that subvert the bacterial cytoskeleton. In addition to science, he enjoys reading, writing, and film. He can be found on Twitter and his book reviews at Reading 1000 Lives or on Goodreads.
Front page: Aeromonas hydrophila on TCBS agar - detail. Image credit: Nathan Reading CC BY-NC-ND 2.0