Our Little Hidden Helpers

What do the human gut and plant roots have in common? Interactions with helpful microorganisms. How do both influence human health? Interactions with helpful microorganisms. In The Hidden Half of Nature: The Microbial Roots of Life and Health by David R. Montgomery and Anne Biklé weave a fascinating story of their journey understanding the importance of microbes in agricultural and human health. Hidden Half weaves together stories of science and society, data and personalities to explore how manufactured diets – whether chemical fertilizers for agriculture or high-fat, high-sugar, low fiber diets for people – have damaged our health.The authors use excellent examples and analogies to deliver the science to a general audience. 

Book cover of The Hidden Half of Nature: The Microbial Roots of Life and Health"

I greatly enjoyed the larger historical and societal perspectives in this book. The stories about Lynn Margulis, Louis Pasteur, Sir Albert Howard, and Justus von Liebig took me back to some of my favorite microbiology and plant pathology classes in college and grad school, such as Dr. Pierson’s Plant Pathology class and research on Pseudomonas sp. Understanding the different personalities and ways individual scientists thinks is an often overlooked, yet important aspect of science. These mini-biographies set the stage for much of the discussion of how our scientific and societal past shaped our present medical and agricultural practices. It is this intertwining of society and microbiology that make Hidden Half a unique book about the microbiome. It is a perfect intersection between history, science, and society. The only issue I had was that sometimes I wondered where the book was headed, but looking back it all made perfect sense and was a lovely journey.

Now that Spring has finally (I hope) reached Maryland, I’m looking forward to digging in the dirt, as usual. Plants and dirt are my therapist and gym all in one. Last year I focused my energies on removing grass from a swath of the front yard to put in a native wildflower garden to increase beauty and wildlife. Ironically, my vegetable garden became a horrid, grass-filled mess. I’ve always been a fan of organic gardening, with one of my peaks of practice after taking Dr. James Brown’s Organic Gardening class at Auburn. Now as I reclaim the vegetable garden, and plant my clover cover crop Dr. Brown’s tips will now be punctuated with stories of the science, people, and microbes that make the practice of organic gardening great. And I’ll be feeding my microbial friends coffee grounds, wood chips, grass clippings, and vegetable bits so that they can feed my garden and it in turn feed me.

I greatly appreciated that Dave and Anne graciously answered some of my questions about The Hidden Half of Nature, which are shared below. I’ll certainly be looking at their microbiome-healthy recipes at the Make the Plate part of their website for some new ideas for our microbial pals!

Interview of Authors David Montgomery and Anne Biklé

Mostly Microbes: What was your purpose in writing the book?

Anne and Dave: Even in the proposal-writing stage, before we’d started the manuscript for The Hidden Half of Nature it was obvious that new findings emerging from microbiome science starkly contrasted with the traditional idea that most bacteria and other microbes are bad for us. And once we were deep into researching the book, especially the historical material, we saw how this idea had become a powerful legacy within the scientific community, governments, companies, and society.

And so our aim in writing the book was to help broaden people’s view of the microbial world to reflect the reality that most microbes, most of the time benefit or enrich our lives in some way. This is what we learned from restoring our soil to make a garden. But at the same time, Anne’s experience with a virus-caused cancer showed us the flipside of the microbial world. And because of this inherent duality, our other aim was to highlight that we all need more nuanced thinking when it comes to microbes. Most of all we hope that our book will help spur people to think differently about our place in nature and her place in us especially the part of nature that we call “the hidden half”.

Mostly Microbes: Your book covers a great deal of ground (no pun intended) about microbes ranging from soil microbiomes to human gut microbiomes. What common themes do you find in these different habitats?

Dave and Anne: As we moved from researching the root / soil microbiome and plant science to the human microbiome, we began to see the root of a plant and the gut of a person in new light. We even came across some of the same terms, like “exudates” and “nutrient exchanges”. Given that the root and the gut have the same job—to acquire nutrients from the outside world—we also began to see that this property made each organ a hotbed of microbiome activity.

For example, healthy plants constantly pump a steady stream of sugars, phytochemicals, and other organic compounds out of their roots to attract and retain a robust microbiome to the surface of all their roots. And in humans, cells lining the small intestine and colon release a prodigious amount of mucus and other compounds, which are akin to the carbohydrate-rich exudates that flow out of a root. Of course, the little-digested complex carbohydrates in our diet that reach our colon add more to our gut microbiota’s dinner plate. And likewise in the soil, this is where organic matter, stuff like bits of wood and dead leaves (even dead microbes!) are the complex carbohydrates of the root microbiome diet. And so long as the root and the gut microbiome get fed, they’ll provide an array of beneficial compounds and nutrients for the host. We think of the root and the colon as grand biological bazaars where the constant exchange of wares and goods between host and microbiome creates the backbone of a built-in health plan for plants and people.

Mostly Microbes: You talk a great deal about the importance of increasing the organic matter level in soil to increase plant growth and the levels of micronutrients and minerals in fruits and vegetables. Can such practices be implemented on large agricultural scales?

Anne and Dave: Yes, they can. A new breed of farmer is practicing what’s called “regenerative agriculture” at both large and small scales. Of course, the way farmers go about this is different than what we did in our garden. They rely on a combination of minimal soil disturbance, a practice termed “no-till”, and alternating cover crops with commercial crops on the same field so that something is always growing. This keeps the soil covered year-round and provides a source of exudates and organic matter for the soil microbiota. Many of the cover crops are legumes, which also keeps the microbes alive that fix nitrogen. After letting the cover crop grow a farmer will kill the vegetative part before it goes to seed. Depending on the region and the farmer, this might occur through a winter freeze, an herbicide, a crop roller (a steamroller-like machine that crushes and crimps the cover crop), or letting livestock graze off the vegetative part of the cover crop.
Any of these methods pretty much does the plant in and so soil microbes begin decomposing the remaining biomass, a good deal of which is below ground in the plant roots. This greatly increases organic matter levels in the soil, as do animal manures for those farmers who let livestock eat up the vegetative part of the cover crop.
Some farmers have seen their soil organic matter increase from less than 2% to more than 6% over the course of a decade. To a soil scientist or farmer this rate of change and the increase in soil organic matter are considered phenomenal.

Modified FAO "Soil the foundation of nutrition" poster to include the hidden half of nature making it all work - microbes!
As demonstrated by this excellent FAO poster, healthy soils are important for micronutrients in plants and human health. However, even the FAO has the microbial contribution hidden!

Mostly Microbes: What were the most interesting findings you made during your research for your book, The Hidden Half of Nature?

Dave and Anne: So much was it’s hard to pick! Some of the molecular and cellular biology was really cool. Even though we are “big picture”, macro-ecology thinkers, it’s satisfying to get down to the mechanistic level and know what molecule, what receptor, which pathways and so forth underlie something like an immune response in a person, or a defensive response in a plant. It gives you a profound appreciation for how few biological screw-ups most of us experience.

We found the research on microbiome-made metabolites and molecules that influence both our well-being, as well as that of our crops particularly interesting. It also speaks to a larger pattern if we’ve got organisms from amoebae to trees to whales that have out-sourced some key aspects of their survival—like immunity, defense, and extracting nutrients and energy from foods—to the tiniest creatures on Earth. The extent of such symbiotic relationships made us realize what an influential (and overlooked) role the microbiome has been throughout the history of life.

The historical research we did gave us an appreciation for the long and tangled relationship we’ve had with the microbial world, from the toll that smallpox took on humanity to the 20th century polio epidemics. The friction between Louis Pasteur and Robert Koch was interesting as was learning about the once common practice of non-hand washing among surgeons. And lastly, the sheer doggedness of Sir Albert Howard in championing life-filled soils impressed us.

In terms of the human microbiome, as wonderful and life-saving as new biomedical products and procedures may be, they are unlikely to ever replace a properly functioning microbiome.

Mostly Microbes: How do you think our increasing understanding about the importance of microbes in soil, plant, and animal health will change our agricultural and medical practices in the future?

Anne and Dave: It seems clear to us that microbiome findings need to be translated and implemented beneath an umbrella of microbiome conservation. In other words, stemming microbiome losses, and restoring species or functional groups to microbiomes where possible should be part of whatever may emerge as a long-term protection strategy for microbiomes.

In terms of the human microbiome, as wonderful and life-saving as new biomedical products and procedures may be, they are unlikely to ever replace a properly functioning microbiome. An analogy from the Pacific Northwest where we live helps to illustrate this point. Salmon have iconic status from an economic, cultural, and natural history perspective in the region. Over the decades we’ve taken various actions to help ensure future runs of salmon, one of which is building fish hatcheries to compensate for lost and degraded habitat . But we’ve learned that trying to substitute a hatchery for the habitat of rivers is near folly for a salmon run. And from where we sit after writing this book, and from what we’ve learned over the course of our careers, too many ecosystems are faltering and unable to function normally. And we certainly don’t want to get to that point with the soils we need to grow food, or our own bodies.

Mostly Microbes: Based on your research for The Hidden Half of Nature, what one lifestyle change do you think is most beneficial to a healthy microbiome?

Dave and Anne: By far, we’ve changed how and what we eat, shifting to eating a lot more plant foods than we did previously. It hasn’t been that hard, and overall it’s not been a complicated change to make. We also had an extra incentive. Had it not been for Anne’s cancer diagnosis, we might not have stuck with this dietary change, or so thoroughly incorporated it into our daily lives. For others who may want make this kind of a change we put something on our website called “Make the Plate”, which has recipes and ideas for meals to cultivate a microbiome that churns out beneficial metabolites.

The research on the byproducts that result from complex carbohydrate fermentation in the colon was really compelling for us. Some of these compounds, like butyrate, have the power of a drug or medicines. We haven’t restricted our diet to plant foods; humans are omnivores after all. But now we make sure we eat a diet rich in plant foods. This keeps our colonic microbiota well-fed, which means we reap their beneficial metabolites. It’s kind of like cultivating your own internal druggist who, instead of waiting to fill a prescription, creates compounds with the power to prevent disease and ailments.

Mostly Microbes: Do you have any other comments for potential readers?

Anne and Dave: In the April, 2016 issue of Natural History magazine there is an excerpt of the chapter, “Thinking Small”, in case any of your blog readers want to check it out. Our website has more about the book. People can follow us on Twitter @dig2grow if they are interested.

Have you read The Hidden Half of Nature? What did you think?

I’d love to hear your thoughts here, on our Facebook or Twitter communities!

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