Paris conference examines how microbes change our understanding of everything

An interdisciplinary conference in Paris in March discussed how expanding knowledge of the way microbes interact with Earth’s environment is revolutionizing not only science and medicine, but the fields of law, philosophy and the arts.

Every human being carries trillions of microbial cells, inside the body and on the skin, including many that are absolutely necessary for existence. These microbes (bacteria, archaea, protists, and viruses) as a totality constitute the human microbiome.

Recently it has become understood how much larger microbial communities (biomes) in the oceans and on land interact to drive chemical, biological, climatic and even geological processes. 

Thinking of the total global microbiome as a single interacting unit changes the prevailing concept that distinct individuals and species are the operative agents in the evolution and survival of life on the planet. And this in turn affects our notions in a broad array of disciplines. 

Many expert views on these new ideas were presented at a March 23 conference in Paris titled “New Challenges Induced by Microbiomes.” A report on the conference, co-authored by 16 of the participants, appears in the journal Biology, July 12.

Beginning with Gaia

Sébastien Dutreuil, a historian and philosopher of the environment at Aix-Marseille University, opened the conference with a discussion of the work of James Lovelock and Lynn Margulis in developing the Gaia hypothesis in the 1960s and 1970s. Gaia is the idea that living organisms may regulate the composition of the oceans and atmosphere as well as the climate, all adding up to act like the work of a single individual entity. Dutreuil stressed that the interdisciplinary collaboration between a chemist (Lovelock) and a microbiologist (Margulis) was essential for recognizing this far-reaching influence of bacteria and other organisms.

An expert in microbial oceanography at Sorbonne University, Fabrice Not, stressed the changes that have taken place in our understanding of the ocean ecosystem over the past 50 years by taking into account the role of the marine microbiome in driving ocean biogeochemical cycles, particularly the carbon cycle. But, he told the conference, “a shockingly large proportion” of marine microbial genes and species remain unknown. 

Catherine Larose, a microbial ecologist at the CNRS Ampère Laboratory in Lyon, stressed the importance of new models of ecological feedback in understanding the role that microbes in the polar regions play in global climate. The ecosystems of cold habitats, she emphasized, are largely inhabited by microbial cells that evolved over long time periods and “may switch between active and dormant life styles” as climate changes. 

Microbes in popular science and art

The second conference session focused on the changing view of the microbial world in popular scientific presentations and art. 

Liliane Campos of the Institut Universitaire de France opened with an analysis of the imagery of the microbiome in popular biology. The metaphors and images involving microbes used in books for general audiences and children, she said, are evolving from primarily military to environmental images, such as the zoo or the garden, and stories told about microbes have moved away from primarily human agency to collective actors. 

Marie-Sarah Adénis, creative director of a biotechnology enterprise (PILI) and a board member of La Chaire Arts and Sciences of the Ecole Polytechnique, made the case for using the visual arts to teach the fundamental ecological roles of microbes. She noted the work of F. Joseph Lapointe, a University of Montreal biologist and bio-artist, who has drawn popular attention to the dynamics of contamination by tracking changes in his own bacterial identity (see "handshake" illustration). 

Soil microbiologist professor Marc-André Selosse of the National Museum of Natural History in Paris, reported that the minute size of microbes has left them mostly invisible to the general public, except when their effect becomes noticeable first on our species and then our environment. He also stressed that a deeply entrenched anthropo-zoo-centrismin in our culture forms a challenge to a broader understanding of the huge role of the microbiome and its diversity. As he sees it “we are living in a microbial world and we need to understand non-animal organisms . . . . If we consider only their direct links to us, or overuse metaphors derived from animals [such as intelligence, sensitivity] we turn these organisms into pale copies of our own essence.”

Rethinking the Koch postulate

The third session addressed novel implications of the microbiome considering and going beyond purely medical interests. 

Philippe Gérard, microbiologist at the Micalis Institute in Paris which researches the microbiology of food, suggested a provocative challenge to the Koch postulate by referencing new studies that suggest entire microbial communities, not merely a single microbe, can be causal in disease. This new view requires an expansion of the Koch postulate that defines the rules for establishing a single microbial species as the cause of a pathology. 

As an example he cited how transplants of human microbiota to healthy mice allowed researchers to demonstrate the role of the microbiome in alcoholic liver disease and high cholesterol. 

Because changing the microbiome alters the individual phenotype, the use of such treatment in medicine presents a novel ethical problem, Gérard noted.

The microbiome in forensics and law

Canadian microbiologist François-Joseph Lapointe described the novel possibility that statistical analyses of microbiomes could soon become “effective proxies of their host’s identities.” This could lead to identification of suspects, more accurate reconstruction of crime scenes, and also provide a microbial clock to determine time of death. 

A legal expert from the University of Paris, Géraldine Aïdan, next proposed how microbiomes might achieve the status of “right-holders,” the sort that some glaciers or rivers now possess, giving them standing in courts. This would involve a change of the traditional anthropocentric attitude in which microbes are considered of inferior status to humans and animals, for example. An understanding that human identity is partly shaped by microbiomes will help to grant such protected status. 

The microbiome and the concept of identity

The last session of the conference took up some of the philosophical questions raised by an expanded understanding of microbiomes.

First, an expert in soil ecology, Dr. Manuel Blouin of the University of Burgundy, showed the importance of regarding ecosystems, not only individuals, as units of natural selection. He proposed that select microbiomes can be studied under laboratory conditions, as Darwin did with the artificial selection of pigeons, to demonstrate how the entire microbiome can be a unit of selection. Small samples of microbial communities might be grown in the wells of microplates and, by changing the nutritive solution over several generations, selected for certain qualities as we now breed seeds or dogs. His work so far has led him to view microbiomes as “novel evolutionary individuals in their own right.”

Gaia and clade selection

Evolutionary biologist Ford Doolittle of Dalhousie University in Nova Scotia, famous for his challenge to an aspect of the Gaia theory and his defense of the notion of “junk” DNA, introduced the concept of “clade selection” to the conference. A clade is a group of organisms believed to have descended from a single ancestor. The concept of clade is thus broader than that of species. 

A clade can only persist or go extinct, and therefore the competition among clades must be competition to persist over time, not competition to reproduce, as is usually thought to be the case with species. “Simply put, a clade X can be said to be fitter than a clade Y, if X has a higher propensity to persist for Z amount of time than Y, write the co-authors of the Biology paper. The properties that allow a clade to persist are not those of a single species but the collective properties of an ecosystem, such as diversity, geographic dispersion, and cooperation (by transfer of metabolites or genes, for example). 

While Darwinian selection of species could never lead to so complex a system as Gaia, the broader concept of clade selection might do so, according to Doolittle, producing a global homeostatic machine. 

Philosopher of biology Frédéric Bouchard of the University of Montreal pointed out how microbiome studies are leading to the concept of “transient biological individuality.” Instead of the standard account of evolution of populations of homogeneous individuals (species) that reproduce together, the concepts of microbiome and ecosystem lead to the idea of evolutionary persistence of a more complex and interacting system. Species are not necessarily preserved but the system as a whole is. 

In summarizing this work, philosopher of science Philippe Huneman of the University of Paris-Sorbonne University, spelled out three key points achieved by microbiome studies.  

“[These] led to novel units of selection being proposed, enhanced systemic perspectives of the concepts of identity and individuality, and encouraged researches to complement traditional tree-based approaches to evolution, such as the use of phylogenies to describe the divergent of monophyletic groups [clades] by more general network-based frameworks, better suited to describe the evolution of microbiomes and of interacting lineages.”