Review: Martin Blaser’s Missing Microbes

Blaser, Missing Microbes

“What happens when the ecology changes, not in a forest, but inside a person? What happens when humans lose biodiversity?” —Martin J. Blaser

In 1945 biologist Alexander Fleming described to the world how he fortuitously discovered penicillin on an old petri dish. He remarked that, “penicillin is to all intents and purposes non-poisonous so there is no need to worry about giving an overdose and poisoning the patient.”

Since their introduction, antibiotics have been the foremost treatment for previously incurable bacterial illnesses, such as typhoid fever, scarlet fever, and tuberculosis. Understandably, physicians viewed antibiotics as “magic bullets” for treatment of previously untreatable illnesses. But with the rise of antibiotics came a specific conception of the body and health. The body is seen as a stage upon which physicians detect a specific bacterial pathogen and then attack it with antibiotics, a model that was described by Robert Koch as the ‘‘one-microbe, one-disease’’ model.

Blaser, Missing MicrobesIn Missing Microbes, Dr. Martin J. Blaser challenges this model by arguing that it ignores the collective context of infectious disease, which not only includes an ailing host, but also a symbiotic community of countless microbial organisms on and in the human body—a community better known as the microbiome. Blaser argues that the overuse of antibiotics and the “one microbe, one disease” model, despite having treated a range of diseases, have diminished the diversity of our gut microbiota.

Blaser, building on the work of others, such as microbial ecologist Theodor Rosebury and Joshua Lederberg who coined the term microbiome, posits that the loss of microbial diversity on and within our bodies is exacting a terrible price on our health. This should not come as a surprise; the stories of the unforseen consequences that come with human technological advancements are familiar ones, especially in the Anthropocene. In fact, Blaser compares the overuse of antibiotics to other mainstays of modernity that, although highly innovative, have wrought unexpected havoc, such as the internal combustion engine, the splitting of the atom, and pesticides.

Blaser begins the book describing the large-scale use of antibiotics for humans against bacterial infections and as agricultural inputs for industrial farming operations. Revealing our reliance on antibiotics, Blaser notes that by age 40, the average person in the U.S will have taken nearly 30 courses of antibiotics. Each course of antibiotics has been proven to further reduce the diversity of the microbiome. In addition, 70-80% of all antibiotics consumed in the U.S. are used as feed additives for more efficiently raising livestock and staving off infections. The over-prescription of antibiotics in health care and large-scale use in our food supply are significant contributors to the degradation of the microbiome.

While many have claimed that Blaser argues against antibiotics, he makes clear throughout the text that he is specifically against the overuse of broad-spectrum antibiotics, those that tend to be over prescribed due to the wide range of diseases they treat. Excessive use of broad-spectrum antibiotics is detrimental because it increases the rate at which antibiotic resistant microbes evolve . Blaser is quite critical about antibiotic use throughout the book and favors developing new narrow-spectrum antibiotics to prevent unintended microbial resistance.

“Other self portraits” by Joana Ricou uses the actual microbiome of the subject as an artistic medium. The series invites viewers to consider their other selves, the parts of their body that are not human, and reflect upon the connection they form between all of us. Left: César, Brooklyn. Right: Darren, North Carolina. Click to enlarge.

Troubled by the overuse of broad-spectrum antibiotics, Blaser writes that we are now suffering from what he calls “modern plagues,” which include diseases like juvenile diabetes, celiac disease, obesity, ulcerative colitis, and allergies. Some critics have been rightly suspicious of the broad connections Blaser draws between antibiotics and disease. Because we still don’t understand the causal mechanism by which microbiota are implicated in disease, associating microbiome degradation with “modern plagues” is only supported by a series of correlations. That is to say, these associations may not be incorrect; they just identify preliminary areas in which more work needs to be done.

Blaser argues that we must curb our appetites for powerful broad-spectrum antibiotics. If we do not take action, we will end up in what he calls an “antibiotic winter,” a worldwide plague that antibiotics will not be able to stop. However, Blaser does not end the book apocalyptically. He concludes by describing possible measures to lessen the effects antibiotics are having on our microbiome, cautiously pointing to therapies such as probiotics and fecal transplants.

The title of the book suggests we must restore the microbes we’ve lost to antibiotics if we are to eradicate our “modern plagues.” But Blaser fails to define modern health in positive terms. Throughout the book, health is only defined negatively as the absence of disease. This problem isn’t limited to Blaser; it’s an impasse facing other researchers studying the microbiome. What exactly is a “healthy” microbiome? Answering this question is difficult and widely debated in the field: Is there an ideal microbial composition? Can health only be understood in terms of their efficacy against specific pathogens? Is microbial diversity a good measure of human health? We still don’t know enough to confidently answer any of these questions.

“Other self portraits” by Joana Ricou uses the actual microbiome of the subject as an artistic medium. The series invites viewers to consider their other selves, the parts of their body that are not human, and reflect upon the connection they form between all of us. Left: Roy, North Carolina. Right: Barbara, North Carolina. Click to enlarge.

Some researchers in the field aim to answer this question by searching for a baseline of health in a historical context, before modern medical technologies and practices existed. This line of research appears throughout Blaser’s book and leads to some troubling conclusions. For example, he suggests that those living in the Western world may one day fill their modern microbial void by harvesting transplants from the excrement of people who live deep in the Amazon, in the highlands of New Guinea, or villagers in Venezuela, people he understands as having “fully intact microbiomes… who [are] essentially from the Stone Age.” Jeff Leach, a collaborator of Blaser’s, has gone so far as to transplant the excrement of a Hadza hunter-gatherer to his own gut. Leach chose the Hadza people because he sees them as practicing, “the same central-based foraging that has brought people together in microbial-sharing camps/communities for the better part of the Pleistocene.”

Rather than romanticizing the “pre-modern” excrement of other cultures, important work still needs to be done in exploring how the microbiome keeps us healthy. Research should be focused not on defining microbial health according to nostalgic, anti-modern baselines, but on exploring the actual mechanics of microbial ecologies. This requires scientists, physicians, and the general public, to reimagine health not simply as the absence of pathogens, but as a complex ecology, a conception of health that Blaser articulately describes throughout Missing Microbes.

All petri-dish images are from the series Other Self Portraits, by artist Joana Ricou. She explores the intersection between art and science and how each field can support and contribute to the other. Joana has shown and collaborated with galleries, universities and museums internationally including the Andy Warhol Museum, the Carnegie Science Center and Harvard University.  She lives and works in Brooklyn, NYC. TwitterEmailWebsite.

Travis J. De Wolfe is a PhD student in the Department of Food Science. His research focuses on how probiotics, specifically strains of Lactobacillus casei, affect the microbial composition of the gastrointestinal tract in the face of nosocomial diseases like Clostridium difficile infection. More specifically, his dissertation work seeks to understand the mechanism by which probiotics confer various health benefits in the face of a growing dependence on widespread use of antibiotics in humans and animals. TwitterEmail.

7 Responses

  1. Jeff Leach says:

    Travis – Nice piece and great overview of Marty’s book. However, your comment:

    “Rather than romanticizing the “pre-modern” excrement of other cultures, important work still needs to be done in exploring how the microbiome keeps us healthy.”

    kinda misses an important area of research. Trying to characterize the gut microbiota of a free-living population like the Hadza is important to understand what microbes we may have lost and importantly, how much diversity we may have lost. This goes to the core of microbial ecology. For example, we now know that various non western populations around the word harbor a much greater alpha diversity – that this changes seasonally – and that what we may consider normal or typical in the west (say, for example, a gut dominated by bacteroides) is not really seen in remote, non Ag societies. More importantly, vertical and early horizontal transmission in these rural kiddos is an important baseline when we start thinking about autoimmune diseases. And to your comment “exploring the actual mechanics of microbial ecologies” is important and spot on – but doing so without some basic understanding of pre modern human (and non human primate data) is flying without a net – and doing so with “potentially” one had tied behind your back. That said, let the rural and hunter gatherer data amass over the coming years – don’ hender – it will pay dividends my friend. J

    • Travis De Wolfe says:


      Thanks for taking the time to read my review!

      In response to your comment – I believe the goal of displacing the western-microbiome to acquire the diverse microbes we may have lost operates on the problematic assumption that the Hadza possess the equivalent of our ancestral microbiome. Anthropogenic change has had extensive impacts on all of earth’s inhabitants and, importantly, their guts. Inevitably, this has affected the Hadza. Therefore, isolating them as “pre-modern”, unaffected by the far-reaching effects of human induced change throughout the world, attempts to find a constant or baseline where none exists.

      Others in the social sciences have turned to hunter-gather populations to shed light onto the ‘secrets’ of our pre-modern social, economic, political—and now microbial—lives. But it has since been deemed methodologically unsound to identify current practices of some human populations as identical or analogous to pre-modern practices. As Sassaman notes, “[i]t is no longer reasonable to conceptually isolate a hunter–gatherer population for study under the premise that it genuinely represents humanity in a primitive state…” (Sassaman, 2004) Commenting on the 1960s Kalahari Project Sassaman argues that for an array of reasons, one of which include the baseless romanticizing of certain populations as outside institutionalized structures and practices (modernity being one example), ““primitive” societies of the ethnographic present are best understood as components, not antecedents, of complex societies” (ibid).

      Human practices across the globe shift over time so, by definition, no population can represent those of the Pleistocene as you have claimed. I don’t want to leave this as a semantic point, and I agree that the association between diversity and health is important – your data illustrates this. I instead argue that our efforts to restore our microbial diversity should be focused in the present (possibly without having to identify or standardize a baseline) and at an individual scale.

      We know that our microbiome is a rather resilient ecosystem, such as in the case of the fecal transplants, where colonization by a donor community after a fecal transplant is short-lived. This brief example allows us to recognize that standardization of the microbiome to a baseline that, in the case of the Hadza, you believe is ‘healthy’ may not only be a difficult, if not an impossible, objective. It is also an objective that may not lead us closer to understanding the associations between health and the microbiome; for these answers, we need to strive for a fuller understanding of how our gut microbiota keep us healthy—a pursuit in which mechanistic understandings will figure centrally.

      Travis J. De Wolfe

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