Introducing the microbiome: Interdisciplinary perspectives.

Ecological imaginations of the microbiome: Past and present

As societies all over the world are still struggling with the Covid-19 crisis, the World Health Organization warns about “one of the biggest threats to global health, food security, and development today” (Antibiotic Resistance 2020): the so-called ‘silent pandemic’ of antibiotic resistance. Driven by the fear of a supposed end of the anti-bacteriological era, a paradigm shift in the conceptualization of human-microbe relationships has emerged in scientific and popular discourses in the past years (Bapteste et al. 2021, p. 1). At the same time, microbiome research raises hopes that a better understanding of microbes can offer answers to many pressing questions of our time—such as the problem of diseases of modern society or the challenges of global agriculture or climate change. The holistic perspective offered by the concept of the microbiome questions the predominant antagonism between humans and microbes fundamentally. Microbes are no longer seen merely as a pathogenic threat, but as essential for nearly all life forms on earth. In the last two decades, research on the (human) microbiome has become one of the major research interests, expressed in an enormous number of inter- and transdisciplinary research projects in the natural sciences and biomedicine.

The international and rapidly growing body of microbiome research is continually revealing the manifold intricacies of human-microbe relationships. It has been shown that in a great variety of bacteria, fungi, and archaea as well as viruses, trillions of microorganisms exist on and in our bodies (Turnbaugh et al. 2007). Together they constitute the human microbiome which significantly affects the physical and psychological well-being of humans or their ill-being, respectively (Bassler, 2012). However, just like humans, all other life forms—e.g. animal or plant—together with all habitats of these life forms—such as soils, air, or waters—contain microbiomes.

Since microbes constitute deeply interconnected systems on and in other living beings and belong to the world of living organisms, it comes as no surprise that the most prominent metaphor of this approach towards the intricacies of human-microbe entanglements is the one of ecology (Bapteste et al., 2021, Formosinho et al., 2022, Morar and Bohannan, 2019, Gillings and Paulsen, 2014). All the more so, as modern microbial ecology already had its beginnings in the 1950s (Konopka 2009, p. 92) while the pre-conceptualizations of the microbial realms as a kind of miniature version of macro ecosystems even date back to the nineteenth century (Grote 2022). At that time, the mystery of the microscopic life—was it animal, plant, a hybrid of both, or something entirely different?—had effects even on the linguistic level. The term microbe was coined by the French surgeon Charles-Emmanuel Sédillot in 1878. He suggested the word to provide an inclusive alternative to a variety of different terms in use, such as microphyte, meaning small plant, or microzoarie, meaning little animal, mirroring the complex classificatory problems of microbial life of those days (Microbe, 2020). In 1884, Robert Koch (1843–1910), soon to be icon of bacteriology, spoke of a “very specific flora and fauna of microorganisms“ (Koch 1912, Vol. II, p. 45). This mirrors again a distinct ecological concept of the microbial world and its inhabitants. Today, following the broad definition by philosopher of biology Maureen O’Malley, the term microbe “encompasses all unicellular life forms (prokaryotes, protists, unicellular fungi, and algae) and often includes viruses, even though these entities are not cellular and are rarely considered to be alive in the way that cellular life is” (O’Malley 2014, pp. 1–2).

As intricate as the history of ‘coming to terms’ with microbes has been, the efforts to define the microbiome were just as complicated.1 The current entry of the term “microbiome” in the Oxford English Dictionary speaks of it as a combination of the two words micro, indicating something very small, and biome, defined as “the plant and animal community of a major climatic region or habitat.” However, the dictionary also defines the term “microbiome” in two—fundamentally different—ways: Firstly as a “population of microorganisms inhabiting a specific environment; a microbial community or ecosystem, now esp. that of the body” and secondly as “the collective genomes of all the microorganisms inhabiting a specific environment, esp. that of the body” (Microbiome, 2020). Remarkably, despite the crucial difference of speaking about a population or of collective genomes, the semantic framing of ecology is dominant in both definitions.

Recently, Morar and Bohannan have shown that today, besides imagining the microbiome as an “organ,” an “immune system,” a “superorganism,” or a “holobiont,” the “ecosystem view” seems the most frequent and most inclusive imaginative approach to grasp the alleged paradigm shift to human-microbe interaction (Morar and Bohannan 2019). Nobel Laureate Joshua Lederberg (2000) already demanded to actively replace “the war metaphor with an ecological one” in the year 2000. This notion of a ‘war on microbes’ ultimately aimed towards the eradication of supposedly pathogenic micro-life and was—despite alternative concepts—predominant, especially in biomedical discourse. Gradually following Lederberg's call, current scientific research focuses distinctly on more holistic notions of coexistence (Choffnes et al., 2014, Institute of Medicine, , 2006). This way of thinking is also clearly reflected in the use of metaphors that are strongly related to the semantic field of the environment as well as in visualizations depicting the microbiome as an idyllic and aesthetically pleasing habitat of flourishing microbial diversity.

Outlining the field: Directions of microbiome thinking in the humanities and arts

Very important work on microbes and the microbiome has already been initiated in a variety of research fields of the humanities (Greenhough et al., 2020), but first and foremost in the area of medical ethics and medical history (D’Abramo and Neumeyer, 2020, Berg et al., 2020, Cañada et al., 2022, Formosinho et al., 2022, Hoffmann, 2019, Ishaq et al., 2021, Kling, 2019, Ma et al., 2018, Marchesi and Ravel, 2015, Mathias, 2018, McGuire et al., 2012, O’Doherty et al., 2016, Pitlik and Koren, 2017, Prescott, 2017, Rhodes, 2016, Rhodes et al., 2013, Robinson et al., 2022, Smith, 2020, Wilkinson et al., 2021, Woodworth et al., 2017).2 Because microorganisms constitute an essential foundation for the functioning and flourishing of all other forms of life on the planet (Cockell, 2004, Cockell, 2005, Lorimer, 2016, Lorimer, 2017a, Lorimer, 2017b), they are predestined for the research scope of a wide range of disciplines of the environmental humanities. Crucial to the environmental understanding of the microbiome is the deep interconnection of humans and the microbes living in and on them, the intricate entanglements of microbes and all living beings, and microbes’ fundamental importance for the existence of all ecosystems. As nonhuman living beings, they are particularly interesting for non-anthropocentric approaches, which argue for a moral and legal status of individuals (or entities or entireties) other than humans. Hence, microbes are seen as a paradigmatic example for critiquing the—especially in Western cultures—long assumed human superiority, as they show the strong human dependence on other living beings even at the very basic level of physical and psychological health and ‘functioning’ (Cockell, 2004, Rook and Brunet, 2005). In doing so, delving deep into human-microbe-interdependences microbiome thinking may ultimately challenge our concept of self (Ironstone, 2018, Rees et al., 2018, Parke, 2021) and also, as we especially want to highlight, the way we ought to value our bodies’ microbes. In this line of thought it is crucial that we also start giving credit to the multiple conceptions of living together with the nonhuman in Indigeouns scholarship that hithero have to often been appropriated or elided (Benezra 2020, p. 512), to “rethink our relationship with microbes, and our relationships to one another through microbes”(Benezra 2020, p. 524).

How to evaluate microbes’ influence on other living beings is a complex endeavor. Latest scientific research clearly shows that categorization of microbes into ‘good’ and ‘bad’ can no longer be maintained, because, for example, pathogenicity is not an ontological status of microbes but depends, among others, on the bodies they encounter and their condition (Casadevall and Pirofski, 2014, Greenhough et al., 2018). Hence, it becomes increasingly clear that dichotomous thought patterns are outdated and need to be overcome to facilitate innovative and future-orientated research that goes beyond combating microbes as harborers of diseases and death, a way of thinking that is reflected even on a linguistic level (Beck, 2021, Höll and Bossert, 2022, Ironstone, 2018).3 Nevertheless, researchers calling for a more positive perspective on microbes are still often confronted with the need to defend their approaches against the background of the still prominent conception of pathogenicity and the associated possibility of the lethality of microbes. Context-sensitive approaches, which account for the diverse relationships of humans and animals to microbes, would extend valuing the great benefits all living beings gain from the microbial world. At the same time, it is important to acknowledge the challenging aspect of how to deal with potentially harmful encounters between humans and microbes in a context-sensitive way without belittling their sometimes even lethal effects. In other words, as Donna Haraway states, “there is no innocence in these kin stories” (2016, p. 114).4

Within these lines of thought, inspiring theories and visions of multispecies futures have been developed (e.g. Braidotti, 2013, Haraway, 2008, Haraway, 2016, Helmreich, 2014, Kirksey, 2014) that shed light on the interwovenness of all life on earth. Boundary-crossing thinkers like Donna Haraway highlight the ‘multispecies’ constituency of humans:

I love the fact that human genomes can be found in only about 10 percent of all the cells that occupy the mundane space I call my body; the other 90 percent of the cells are filled with the genomes of bacteria, fungi, protists, and such, some of which play in a symphony necessary to my being alive at all, and some of which are hitching a ride and doing the rest of me, of us, no harm. I am vastly outnumbered by my tiny companions; better put, I become an adult human being in company with these tiny messmates. To be one is always to become with many (Haraway 2008, pp. 3–4).

Many scholars who investigate human-nonhuman entanglements, such as Rosi Braidotti (2013, p. 60), call for a “post-anthropocentric turn” in the humanities. With the intriguing concepts regarding a possible coexistence with other life forms, they also establish approaches for thinking about the microbial world.

Important theories for enabling respectful multispecies cohabitations are also found in environmental ethics, which is, as applied ethics, part of practical philosophy. However, and surprisingly, little academic discussion of microbes is found within this discipline. This is astonishing since environmental ethics is centrally concerned with the question of which values can (and should) be assigned to which living beings. Biocentric positions in environmental ethics argue that all living beings—including microbes—are to be morally considered in a direct way (e.g., Taylor, 1989, Schweitzer, 2002, Wienhues, 2020). Nevertheless, biocentrists rarely address microbes explicitly in their theory development (also pointed out in Wienhues 2022). A notable exception is the work of Charles Cockell, who develops an ethical rationale for the rights of microbes using a utilitarian argument (Cockell, 2004, Cockell, 2011) and he elaborates on a biocentric perspective on microbial values (Cockell, 2005). In doing so, he points out the important aspect that for microbes, ethical approaches aimed at the protection or respectful treatment of individuals are not useful, but—unlike with animals and humans—the “protection of microbes must apply on a communal scale” (Cockell 2004, p. 146).

Maureen O'Malley also argues for a more respectful approach to microbes. In her important biological-philosophical work Philosophy of Microbiology (2014, chapters 3 and 4), she highlights how microbes question established concepts and theories, because ‘classical’ species concepts and theories of individuality cannot or only insufficiently be applied to the microbial world.

Microbes also challenge spiritual and religious thinking. For many people particular natural areas, entities, landscapes or processes have a spiritual or religious meaning. Since mircobes are responsible for producing or helping to shape many—if not all—natural areas and ecosystems, they also have an enormous impact on the natural entities that have religious or spiritual meaning for particular groups of people or are part of processes that are valued religiously.

The entanglements between humans and ‘their’ microbes highlight the interconnectedness of humans (seen as interconnected with divinities as well as other living beings) important for some theological theories (cf. Kunnen and Carlson 2017) and lead e.g. Christian theologists to ask the question “what does it mean to be a human created in the image of God in light of the microbiome?” (Hill 2020, 39).

A lot of research that touches upon the topic of microbes, and includes them—at least indirectly—into research questions, from within the humanities can be found in posthumanist approaches. However, posthumanist approaches mostly focus on the deep entanglements and the interwovenness of all (living as well as non-living) entities and thereby do not explicitly address the characteristics of microbes that differentiate them from other living beings and non-living entities.5 Due to the global dominance of an anthropocentric paradigm—among other reasons—the posthumanist research community does not represent a huge part of the scientific community. Academic debates often take place in rather exclusive circles and reach society in abstract ways, and sometimes not at all.

However, literature and arts often function as sensitive seismographs of processes of social and scientific upheaval. Especially the field of BioArt has been intensively engaged with the microbiome. BioArt operates at the interface of art and science, their protagonists becoming “the new symptomologists of the age” (jagodzinski, 2020, p. 66). Artists and scientists work together in laboratories and workshops and use biotechnological techniques and tools on living material. In doing so, they create art that lives, relies on existing life forms, or becomes a new life form itself (Anker, 2014). In consequence, there is an ever-growing corpus of literary and artistic discussion of the challenges, anxieties as well as hopes that microbiome research entails (Hauser 2020). These literary and artistic productions not only delve deep into the “shadows of our understanding” (Bello 2020, p. 9), but they also further the dissemination of scientific discourses in the public sphere.

The goal of the Endeavour special issue: The microbiome and its challenges to the environmental humanities

Despite the aforementioned important work, there is still a precious intellectual treasure to uncover for the (environmental) humanities. Cutting-edge scientific research around the globe has intensely turned to the complex study of the microbiome and the challenges for (human) life worlds that go along with it. However, the humanities, and particularly the environmental humanities, have not been engaged intensively in the groundbreaking topic of the microbiome. This comes as a surprise, since ecological metaphors are used promintently within natural science and medical research on microbes and it is acknowledged that the minute beings constitute an exceptional amount of the world’s biodiversity. Therefore, the goals of this special issue of Endeavour is as follows.

First, we bring the topic of microbes’ impact on the planet, and microbe-human-animal-plant-relationships to the attention of a greater variety of disciplines within the environmental humanities. The microbiome is as a fascinating research field for the humanities as it is for natural sciences. We invite scholars of the environmental humanities, particularly from philosophy, ethics, literary and cultural studies, and the history of science to investigate these research questions with their particular lenses to enrich the discourse. Therefore, we offer articles from different environmental humanities’ perspectives in this special issue, in order to bring forward an important, yet still underrepresented field of research.

Second, we initiate a closer exchange between the medical and environmental humanities. Microbes and microbiomes are currently more intensively researched within the medical humanities than in the environmental humanities; however, a fruitful dialog between these fields promises to be highly beneficial for academic research about the microbial world. Within the concepts of One Health6 or Planetary Health,7 the importance of intersecting medical and environmental factors has already been addressed. However, we make the case for deepening the exchange between the two disciplines beyond the current biomedical focus, since posing research questions about (non)human entanglements with microbes at the intersection of medical and environmental humanities could enrich academic discourse even beyond the complex of the microbial world.

Contributions of this special issue

According to that line of thought, we combine research that focuses on microbes and the microbiome from different perspectives of the humanities in this pioneering special issue of an interdisciplinary science studies journal. In doing so, we exemplify the scientific benefit of approaching the fascinating matter of the microbiome from an interdisciplinary perspective.8

The first two contributions by Mathias Grote and Hub Zwart approach the microbiome from a historical and epistemological perspective, respectively. In his contribution “’Aus dem kleinen bauen sich die Welten’: Christian Gottfried Ehrenberg's ecological microbiology avant la lettre,” historian of science Mathias Grote (2022) explores the ambivalent position of the German “Humboldt en miniature” Christian Gottfried Ehrenberg (1795–1876) on the eve of modern microbiology. Grote shows how Ehrenberg, on the one hand, thoroughly examined the life forms found in water or air microscopically and collected samples from all over the world, thus describing numerous microbes called “infusoria” as well as their effects, yet denied their involvement in infectious diseases. However, Grote points out, that Ehrenberg’s ecological view of the microcosm seems to speak to the present in a surprising way especially because many of the premises of Pasteur and Koch seem outdated in the age of genomics. In doing so, Grote gives an exciting glimpse into a chapter of the pre-history of thinking on the microbiome.

Philosopher Hub Zwart (2022) argues in his paper “’Love is a microbe too’: Microbiome dialectics” that whereas the Human Genome Project was an anthropocentric research endeavor, microbiome research entails a much more interactive and symbiotic view of human existence. Zwart, building on previous authors, adopts a dialectical perspective on microbiome research that strives to supersede the ontological divide between self and other, humans and microbes, and to incorporate the microbiome as a crucial dimension of human existence, not only corporally, but also in terms of mood and cognition. Taking also into account the practical level of human-microbiome interplay, Zwart demonstrates how microbiome-informed insights promise to offer opportunities for self-care and self-management, allowing us to consciously interact with our microbiome to foster wellness and health. Again, he adopts an interactive (dialectical) approach and argues that practices of the self should result from mutual learning between laboratory research and life-world experience.

The contributions of Anna Wienhues (2022) and co-authors Laÿna Droz, Romaric Jannel, and Christoph Rupprecht (2022) shed light on different ethical dimensions of engaging with the microbiome. In her paper “Looking Through the Microscope: Microbes as a Challenge for Theorizing Biocentrism within Environmental Ethics,” Wienhues investigates from an explicitly environmental ethics perspective how microbes challenge what we as humans consider to be ethically relevant. She focuses on the question of how microbes can simultaneously support and challenge biocentric theories, which attribute direct moral consideration to them. Her paper lays out crucial aspects of these challenges and present some initial arguments about why not all of them pose a serious threat to biocentric theorizing—including biocentric theories of interspecies justice. With this, Wienhues charts a pioneering pathway grounded in environmental ethics, analyzing the consequences of including microbes in biocentric theories in detail and thus greatly contributes to the academic discourse on interspecies justice.

In their paper “Living through Multispecies Societies: Approaching the Microbiome with Imanishi Kinji” environmental ethicist Laÿna Droz, philosopher Romaric Jannel, and geographer Christoph Rupprecht discuss current research on the microbiome by exploring the thoughts of Japanese ecologist Imanishi Kinji. They present some of Imanishi’s key concepts regarding the world of living beings and multispecies societies and link them to seven types of relationships concerning the human microbiome, human beings, and the environment. With that approach and inspired by Imanishi’s work, their paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota and human beings. In doing so, the authors offer a valuable contribution for further rethinking human's place in the world and underpinning – in line with, most prominently, Haraway – that humans are some kind of ‘multispecies beings.’ Through investigating the microbiome with Imanishi’s ideas, the paper enriches this special issue with a non-Western perspective, highly important yet still rarely part of the scientific discourse on microbes and the microbiome.

The final papers of this special issue focus on artistic access to the intricacies of the microbiome and microbiome research. In the essayistic paper “Hypersymbiotics: An Artistic Reflection on the Ethical and Environmental Implications of Microbiome Research and New Technologies,” BioArtist Anna Dumitriu (2022) describes her ongoing series “Hypersymbiotics,” which explores the potential ways in which our microbiome, genetics, epigenetics, and even our environment could potentially be enhanced to turn us into human ‘super-organisms.’ Her essay discusses artworks using synthetic biology techniques including CRISPR genetic modification in bacteria and yeasts, and gene editing in plants, as well as using artificial intelligence and stem cell research. The series is deeply concerned with promoting public understanding of the ethical implications of new scientific developments. At its core, the artwork is about knowledge, power, and control, and with this, it intriguingly demonstrates the important role of art in reflecting on social developments, practices, and technologies.

Poet and professor of poetry Adam Dickinson (2022) creatively addresses the fascinating topic of Horizontal Gene Transfer (HGT) in his contribution “Neck of the woods: Microbes, memory, and resistance”, especially against the backdrop of the ongoing antibiotic crisis. HGT is a key mechanism allowing bacteria to enact genetic changes in response to shifting environmental conditions. The swift lateral movement of genes makes possible antibiotic resistance, which is an increasing medical and ultimately cultural problem. There is evidence that HGT also takes place between species. Bacterial DNA appears in the human mitochondrial genome of acute myeloid leukemia (AML) samples. Responding to a recent diagnosis of AML, Dickinsion ingeniously imagines a literary form of HGT, exploring the lateral movement of memory and family history through concerns with antibiotic resistance, illness, writing, science, and adjacency.

Looking ahead: A call for microbial ethics

One of the great challenges of the future is to investigate the means of how to live a respectful life with our microbial cohabitants. Therefore, this special issue also calls for microbial ethics that might facilitate engaging considerately with the realm of microbes that constitute our lifeworlds. The development of microbial ethics is still in its infancy; however, posthumanist and environmental, and especially animal-ethical theories offer many valuable starting points and demonstrate the importance of such an endeavor. Existing explorations of ethical issues concerning microbes find many analogies with animal ethics and its highly significant approaches to achieving an ethically sound treatment of and living together with other living beings. (cf. Beck 2021, working with Haraway’s companion species concept and other animal-ethical ideas; Hird, 2010, Lorimer, 2017b) It seems, the closer other living beings are to humans, the easier it is for academics to develop theories of an ethically sound treatment of them. And, certainly, microbial ethics can make many ideas and perspectives of animal ethics useful for themselves. However, it is also important to accept other living beings (this holds for animals as well) in their fundamental otherness and to establish a respectful way of treating them, no matter how distant they are from us. Therefore, we need “a more respectful and responsible ‘living-together’ with the nonhuman both ‘big like us’ as well as small and not like us” (Beck 2021, p. 373).

As a whole, this collection is an important contribution to including microbes as a pressing topic in environmental humanities research. The articles exemplify the manifold perspectives applicable to the microbiome which bring forward new ways of thinking, ultimately helpful to produce novel knowledge. This includes a comprehensive, coherent, and consistent theory of microbial ethics, which asks how—in the light of the findings of microbiome research from the natural and biomedical sciences as well as from the humanities—human interaction with microbes can and should be shaped. Although the importance of the (human) microbiome(s) is significant regarding human well-being and health, there is a strong need for non-anthropocentric microbial ethics, as microbes are not only significant for humans, but for all life on the planet and, depending on the perspective, may also be morally relevant for their own sake. Novel approaches towards a more sensitive ‘being-with’ microbial beings have already been initiated, such as altered antibiotic stewardship and the questioning of long-standing hygiene regimes (Finlay et al., 2021, Greenhough et al., 2018, Living with Resistance project, 2018, Landecker, 2016, McLeod et al., 2020, Podolsky, 2018). Both approaches are essential for human as well as nonhuman and microbial well-being and thus once again demonstrate the close entanglement of the human with the nonhuman—always and especially in times of pandemic crises.

Funding

Davina Höll's research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanýs Excellence Strategy – EXC 2124 – 390838134.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.