March 16, 2015, by Brigitte Nerlich

Genes, microbes, us

Jon Turney has just published a fascinating new book about the microbiome and microbiomics entitled I, Superorganism: Learning to love your inner ecosystem. This blog post is a collection of thoughts provoked by this book; it’s not a book review. Coincidentally, Jon’s 1998 book Frankenstein’s Footsteps was my gateway into the social and cultural study of biology.

The Human Microbiome Project

On 19 December 2007 the National Institutes of Health (NIH) in the United States launched the Human Microbiome Project (HMP). This was a five-year multinational study of “the collection of all the genomes of all micro-organisms present in or on the human body” (NIH, press release 19 December, 2007).

The human microbiome is the collection of trillions of microbes living in and on the human body. “A healthy adult human harbours some 100 trillion bacteria in his gut alone.” The HMP focused on sequencing the genomes of these microbes (and in this context ‘microbiome’ means the collective genomes of all the microorganisms inhabiting the human body). As part of this research the NIH also launched an extensive Ethical, Legal, Social Issues (ELSI) programme which asked among other things: “What will be the likely impact of human microbiome research on existing concepts of ‘self’ and personal identity, and on popular understandings of notions such as ‘purity,’ ‘contamination,’ and ‘contagion’?” (see also here) This is, to some extent, the topic of Turney’s book.

The HMP caused far fewer waves in the public sphere than the Human Genome Project and the sequencing of the human genome in 2003, but it poses equally, if indeed not more, intriguing questions about what makes us human. While genetics and genomics focus (mostly) on genes and genomes and how they make us who we are, microbiomics (like other meta-, post- and epi-genetic and genomic enterprises) shifts attention to the microbial communities that, together with genes and genomes, make us who we are… as Turney calls it: a superorganism. Some have qualms about the label ‘superorganism’, as it should be reserved for bees and ants, but let’s stick with it here.

The HMP also participates in another gradual shift in focus – away from seeing microbes as foes (framed in terms of contamination, contagion and combat) towards seeing, at least some of them, as friends and exploring collaborations between microbial communities and genomes and humans; a shift in focus from superbugs to superorganisms.

Communities and communication

For a long time microbes have been seen as enemies to human health, as invaders of the human body against which one has to protect oneself and which have to be eradicated. Antibiotics and antimicrobials were initially hailed as weapons against such bad or unfriendly invaders but then turned against those wielding these weapons. Antibiotic resistance began to emerge and people started to worry about the overuse of antimicrobial agents in the home, in hospitals, on farms etc. and about the way they contaminate our inner and outer ecosystems. In this context some microbes are being enlisted as friends and collaborators in maintaining the health of such ecosystems. We want to have conversations with them, understand how they communicate between each other, protect their communities and through this ourselves. (Sometimes we also want to intercept and interrupt their interactions and communications, but that’s a different story).

All these changes in science and perceptions of genes, genomes and bacteria are based on constant communications and interactions between genomics and microbiology and more (in this microbiomics is similar to synthetic biology). Under the influence of systems biology, both genomics and microbiology are beginning to research human-microbe-genome interactions and to study the communication between microbes in order to find new treatments for illnesses of modernity such as obesity or diabetes.

Alongside metaphors of war and battle, which have been pervasive in microbiology, popular discourses about genomics have been dominated by deterministic metaphors, from ‘reading the book of life’ in the context of genomics to ‘writing the book of life’ in the context of synthetic biology. These types of languages and the sciences that use them are now in a state of reconfiguration and rapprochement and new metaphors are emerging that frame these new ways of seeing and new ways of exploring (see Avise, 2001; Hellsten & Nerlich, 2004; Juengst, 2009).

Microbes are us

Despite a huge increase in scholarly publications about the microbiome and microbiomics over the last five years (charted, read and digested in Turney’s book), the science of the microbiome has only attracted moderate attention in the news media (about 1750 news items over the last five years in all English Language News, using microbiome as search term on the Nexis® database). However, readers of the rare newspaper articles that cover microbiomics may come away thinking nowadays that ‘microbes are us’ rather than ‘genes are us’ (see Nerlich and Hellsten, 2009). Just glancing at one page of results on the Nexis® database, we now find great headlines such as “Show us your Selfie”, “Our basic gut instinct”, “The benefits of eating bacteria” – all December 2013. These headlines are not just journalese, they reflect quite similar headlines in scientific journals, such as this one from 2015 “Being human is a gut feeling” published in the journal Microbiome (an article to which Jon Turney alerted his followers on twitter).

As a microbiome researcher said in an article entitled ‘Extending our View of the Self’: “it seems appropriate to consider ourselves as a composite of many species, human, bacterial, and archaeal — and our genome as an amalgam of human genes and the genes of our microbial ‘selves’. Without understanding the interactions between our human and microbial genomes, it is impossible to obtain a complete picture of our biology.”

I, Superorganism

Although microbiomics has not yet attracted a lot of attention as a new science, some aspects of it have begun to infiltrate popular thinking about health and illness, bacteria, microbes and so on. This has developed mainly through advertising of and debates about probiotics which have been enlisted to fight illnesses and anxieties of modern life.

Turney’s book is both a popular account of the science and it also discusses this popular thinking; indeed it can be seen as something of self-help book in more senses than one – through reading it we learn how to love our microbes and at the same time we learn to love our ‘selves’ as a superorganism.

In the course of my work I have read quite a few popular science books. Some are interesting, some enlightening, some enjoyable. This book has all of these qualities and it does something that good popular science books should do: it makes us think about the world, and in this case ourselves, in new ways; it makes us see ourselves as something else. Read it and you’ll see!

I also enjoyed the ‘further readings’ list which included blogs, such as Jonathan Eisen’s ‘The Tree of Life’ and a twitter account by Elisabeth Bik (@MicrobiomeDigest)!

Image: Lactobacilli and viginal microbiota

Added 22 March 2015: Interesting interview with Hannah Landecker on antibiotic resistance. Landecker is writing a book on “American Metabolism, which looks at transformations to the metabolic sciences wrought by the rise of epigenetics, microbiomics, cell signaling and hormone biology”. Her interviewer, Andrea Núñez Casal, is writing her thesis on ‘Excursus on the Immune System: Differential Bodies and Entangled Environments in the ‘New Biology’ of the Microbiome’.

Added 19 April 2015: A good guide through the various meanings of ‘microbiome’ and what the word tends to mean now: (HT @jonturney)


Posted in antibioticsepigeneticsgenomicsmicrobiome