Model organisms are central to contemporary biology and studies of embryogenesis in particular. Biologists utilize only a small number of species to experimentally elucidate the phenomena and mechanisms of development. Critics have questioned whether these experimental models are good representatives of their targets because of the inherent biases involved in their selection (e.g., rapid development and short generation time). A standard response is that the manipulative molecular techniques available for experimental analysis mitigate, if not counterbalance, this concern. But the most (...) powerful investigative techniques and molecular methods are applicable to single-celled organisms (‘microbes’). Why not use unicellular rather than multicellular model organisms, which are the standard for developmental biology? To claim that microbes are not good representatives takes us back to the original criticism leveled against model organisms. Using empirical case studies of microbes modeling ontogeny, we break out of this circle of reasoning by showing: (a) that the criterion of representation is more complex than earlier discussions have emphasized; and, (b) that different aspects of manipulability are comparable in importance to representation when deciding if a model organism is a good model. These aspects of manipulability harbor the prospect of enhancing representation. The result is a better understanding of how developmental biologists conceptualize research using experimental models and suggestions for underappreciated avenues of inquiry using microbes. More generally, it demonstrates how the practical aspects of experimental biology must be scrutinized in order to understand the associated scientific reasoning. (shrink)

This is an introduction to the topical collection Microbes, Networks, Knowledge: Disease Ecology in the twentieth Century, based on a workshop held at Queen Mary, University London on July 6–7 2016. More than twenty years ago, historian of science and medicine Andrew Mendelsohn asked, “Where did the modern, ecological understanding of epidemic disease come from?” Moving beyond Mendelsohn’s answer, this collection of new essays considers the global history of disease ecology in the past century and shows how epidemics and (...) pandemics have made “microbes complex”. (shrink)

We know that microbes contribute to the production of odors that some animals use to communicate, but how common is this phenomenon? Recent studies capitalizing on new molecular technologies are uncovering fascinating associations between microbes and odors of wild animals, but causality is difficult to ascertain. Fundamental questions about the nature of these unique host‐microbe interactions also remain unanswered. For instance, do microbes benefit from signaling associations with hosts? How does microbial community structure influence signal production? How (...) do hosts regulate microbes in order to generate appropriate signals? Here, we review the current state of knowledge on microbially produced signals in animals and discuss key research foci that can advance our understanding of microbial‐based signaling in the animal world. (shrink)

A microbial colony needs several essential nutrients in order to grow. Moreover, the colony requires these nutrients in fixed combinations, which are dictated by the chemical composition of its biomass. Unfortunately, ambient availabilities of the various nutrients vary all the time. This poses the question of how microbes can achieve balanced growth.The present solution to this problem is novel in that the allocation of molecular building blocks among assimilatory machineries within the cell is regarded as dynamic. This paper shows (...) that allocation can be adapted so as to achieve balanced growth, nearly regardless of environmental conditions. Moreover, it is shown that a feedback mechanism, which monitors internal stores, is able to achieve this allocation. (shrink)

A microbial colony needs several essential nutrients in order to grow. Moreover, the colony requires these nutrients in fixed combinations, which are dictated by the chemical composition of its biomass. Unfortunately, ambient availabilities of the various nutrients vary all the time. This poses the question of how microbes can achieve balanced growth.The present solution to this problem is novel in that the allocation of molecular building blocks among assimilatory machineries within the cell is regarded as dynamic. This paper shows (...) that allocation can be adapted so as to achieve balanced growth, nearly regardless of environmental conditions. Moreover, it is shown that a feedback mechanism, which monitors internal stores, is able to achieve this allocation. (shrink)

From ancient theorization about invisible forces to the advent of modern microbiology, the pursuit of a detailed understanding of organisms invisible to the human eye has been a recurrent focus in philosophical and scientific communities and beyond. This article interrogates some of the dominant themes of historical scholarship in this area, highlighting in particular the increasing recognition of the social dimension of microbes and microbial science. It also reflects on the porosity between pre- and post-bacteriological concepts of disease and (...) disease causation, noting the continuity of practice observed by many historians of the modern period. Since we are at present grappling with a crisis of antimicrobial resistance, long in the making, the article draws together scholarship which helps us to make sense of how science has framed microbial organisms and our interactions with them. This provides a platform for researchers to explore new responses to contemporary microbiology, as well as find new ways to interrogate past trends. (shrink)

The study of micro-organisms in Britain in the early twentieth century was dominated by medical concerns, with little support for non-medical research. This paper examines the way in which microbes came to have a place in industrial contexts in the 1920s and early 1930s. Their industrial capacity was only properly recognized during World War I, with the development of fermentation processes to make required organic chemicals. Post-war research sponsored by chemical and food industries and the D.S.I.R. established the industrial (...) significance of microbes. The primary focus here is the D.S.I.R. work which aimed to pull microbes away from medical concerns and promote the role of microbes in British industry. (shrink)

This editorial introduces a series of review articles concerning the ways in which recent work on microbial evolution has both deepened and challenged the modern synthesis. The authors develop a framework for thinking about theory change in biology.

In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.

Much microbiota-gut-brain research focuses on the causal role of microbiomes as a whole, rather than their component parts: microbes. Hooks et al. find these whole-community explanations inadequate; however, they do not provide suggestions for better explanations. By appealing to proportionality – a criterion that can be used to develop more appropriate causal explanations – more accurate causal claims can be made.

Arbuscular mycorrhiza (AM), a type of plant‐fungal endosymbiosis, and nodulation, a bacterial‐plant endosymbiosis, are the most ubiquitous symbioses on earth. Recent findings have established part of a shared genetic basis underlying these interactions. Here, we approach root endosymbioses through the lens of the homology and modularity concepts aiming at further clarifying the proximate and ultimate causes for the establishment of these biological systems. We review the genetics that underlie interspecific signaling and its concomitant shift in genetic programs for either partner. (...) Also, through the comparative analysis of genetic modules shared by AM and nodulation symbioses, we identify fundamental nodes in these networks, suggesting the elemental steps that may have permitted symbiotic adaptation. Here, we show that this approach, allied to recent technical advances in the study of genetic systems architecture, can provide clear testable hypotheses for the advancement of our understanding on the evolution and development of symbiotic systems. (shrink)

Aristotelian theory, as found in Michael Thompson and Philippa Foot, claims that to be good is to be good as a member of that kind. Moreover, Foot argues in effect that goodness admits of only the kind-based sort, obtaining solely in virtue of something’s satisfying kind-based standards. However, I contend that something can satisfy kind-relative standards but nonetheless be bad—I propose a hypothetical Ebola-like microbe that meets its kind-standards of being destructive for its own sake, but it would plausibly be (...) bad for doing so. In defending my counterexample, I respond to the Aristotelian contention that evaluations should only be made from “within” the standpoint of a particular lifeform conception, rather than an “external” one from which that kind itself can be judged to be bad. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

Large‐scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of “Western diseases” may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial microbes associated with pathogen resistance, highlighting the emerging role of complex microbial communities in protecting against disease. We discuss ways in which modern lifestyles and practices (...) may deplete physiologically important microbiota, and explore prospects for reintroducing or encouraging the growth of beneficial microbes to promote the restoration of healthy microbial ecosystems. (shrink)

Microbes can influence host physiology and behavior in many ways. Here we review evidence suggesting that some microbes can contribute to host stress (and other microbes can contribute to increased resilience to stress). We explain how certain microbes, which we call “stress microbes,” can potentially benefit evolutionarily from inducing stress in a host, gaining access to host resources that can help fuel rapid microbial replication by increasing glucose levels in the blood, increasing intestinal permeability, and (...) suppressing the immune system. Other microbes, which we term “resilience microbes,” can potentially benefit from making hosts more resilient to stress. We hypothesize that “stress microbes” use a fast life history strategy involving greater host exploitation while “resilience microbes” use a slow life history strategy characterized by more aligned evolutionary interests with the host. In this paper, we review the evidence that microbes affect host stress and explain the evolutionary pressures that could lead microbes to manipulate host stress, discuss the physiological mechanisms that are known to be involved in both stress and microbial activity, and provide some testable predictions that follow from this hypothesis. (shrink)

The future of art is dirt and decomposing shit. A deconstructed intestinal sea of microorganisms, spread out into the soil they were released back into following the extinction of their complex vessel. The genetic information they exchanged with each other as well as with their container, now existing in a vague memory, perhaps a feeling of sadness and longing, as they digest the once cherished artifacts of their human predecessors.

This is a highly welcome book that offers a fresh perspective on the philosophy of biology. It is of interest to both philosophers and biologists and to experienced readers as well as novices. The book is structured into four sections ‘Science’, ‘Biology’, ‘Microbes’ and ‘Humans’ and consists of a collection of articles written by John Dupré over the past few years.

Consideration of the experimental activities carried out in one discipline, through the lens of another, can lead to novel insights. Here, we comment from a biological perspective upon experiments in quantum mechanics proposed by physicists that are likely to feasible in the near future. In these experiments, an entire living organism would be knowingly placed into a coherent quantum state for the first time, i.e. would be coerced into demonstrating quantum phenomena. The implications of the proposed experiment for a biologist (...) depend to an extent upon the outcomes. If successful, then the organism will have been temporarily in a state where it has an unmeasurable metabolism—not because a metabolic rate is undetectable, but because any attempt to measure it would automatically bring the organism out of the state. We argue that this would in essence represent a new category of cryptobiosis. Further, the organism would not necessarily retain all of the characteristics commonly attributed to living systems, unlike the currently known categories of cryptobiosis. If organisms can survive having previously been in a coherent state, then we must accept that living systems do not necessarily need to remain in a decoherent state at all times. This would be something new to biologists, even if it might seem trivial to physicists. It would have implications concerning the physical extremes organisms can tolerate, the search for extraterrestrial life, and our philosophical view of animation. (shrink)

Recent advances in research on iron metabolism have revealed the identity of a number of genes, signal transduction pathways, and proteins involved in iron regulation in mammals. The emerging paradigm is a coordination of homeostasis within a network of classical iron metabolic pathways and other cellular processes such as cell differentiation, growth, inflammation, immunity, and a host of physiologic and pathologic conditions. Iron, immunity, and infection are intricately linked and their regulation is fundamental to the survival of mammals. The mutual (...) dependence on iron by the host and invading pathogenic organisms elicits competition for the element during infection. While the host maintains mechanisms to utilize iron for its own metabolism exclusively, pathogenic organisms are armed with a myriad of strategies to circumvent these measures. This review explores iron metabolism in mammalian host, defense mechanisms against pathogenic microbes and the competitive devices of microbes for access to iron. (shrink)

In this essay, I explore non-human multispecies interactions in soils polluted by electronic waste and subsequently bioremediated by plants and microbes. I argue that regenerative transformation in polluted soil environments is principally through microbial degradation, a significant process for survival amidst disaster. In doing so, I combine two separate research areas – the materiality of electronic waste and of soils – thus contributing to theorization on the persistent problem of anthropogenically polluted soils. I do so by examining the process (...) of bioremediation, which ties anthropogenic pollution with underground soil processes, notably those that occur at the soil interface surrounding plant roots, the rhizosphere. Using empirical examples from scientific literature on the bioremediation of electronic waste-contaminated soils in China, I demonstrate that degradation, symbiosis, and sequestration are instrumental processes in polluted soils. The micro-scaled perspective of these relational processes and their toxic alterlives contributes to materialist, chemosocial understandings of toxic and polluted environments. (shrink)

Period homeostasis is the defining characteristic of a biological clock. Strict period homeostasis is found for the ultradian clocks of eukaryotic microbes. In addition to being temperature-compensated, the period of these rhythms is unaffected by differences in nutrient composition or changes in other environmental variables. The best-studied examples of ultradian clocks are those of the ciliates Paramecium tetraurelia and Tetrahymena sp. and of the fission yeast, Schizosaccharomyces pombe. In these single cell eukaryotes, up to seven different parameters display ultradian (...) rhythmicity with the same, species- and strain-specific period. In fission yeast, the molecular genetic analysis of ultradian clock mechanisms has begun with the systematic analysis of mutants in identified candidate genes. More than 40 “clock mutants” have already been identified, most of them affected in components of major regulatory and signalling pathways. These results indicate a high degree of complexity for a eukaryotic clock mechanism. BioEssays 22:16–22, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

Based on Hans Blumenberg’s philosophical concept of »reoccupation«, the study analyzes why the microbe has never really been situated in the world, demarcating ontological shifts in modeling microbes. The shifts are related to techniques such as sequencing and digitizing, to microbe banks acting as world models, and to metaphysical vacancies co-created. These can be operated on a historiographic level, as highlighted by the world formula of bacterial photosynthesis. It allowed for imaginations of the Early Earth and an Iron-Sulfur-World. In (...) sum, collecting and cultivating are shown to be crucial pre-operations for operative bio-ontologies, exemplified by a case study on the German Collection of Microorganisms (DSMZ). (shrink)

In 1890, Sergei Nikolaevich Vinogradskii (Winogradsky) proposed a novel life process called chemosynthesis. His discovery that some microbes could live solely on inorganic matter emerged during his physiological research in 1880s in Strassburg and Zurich on sulfur, iron, and nitrogen bacteria. In his nitrification research, Vinogradskii first embraced the idea that microbiology could have great bearing on agricultural problems. His critique of agricultural chemists and Kochian-style bacteriologists brought this message to the broader agricultural community, resulting in an heightened interest (...) in biological, rather than chemical methods to investigate soil processes. From 1891 to 1910, he directed the microbiological laboratory at the Imperial Institute of Experimental Medicine in St. Petersburg, Russia, where he expanded his chemosynthesis research to a broad investigation of the manifold significance of autotrophic organisms in soil processes. This work and that of his students attracted the serious attention of agricultural chemists and soil scientists in Russia and abroad, changing essentially the way they understood and investigated the role of microbes in the soil. His student, Vasilii Omelianskii, effectively integrated Vinogradskii’s approach into Russian and Soviet, and international agricultural microbiology. Vinogradskii’s activities in the late 19th century reflect the changes occurring more broadly in science. At that time, microbiologists such as Louis Pasteur, Eugenius Warming, and Martianus Beijerinck were contributing new laboratory methods and theoretical perspectives to incipient disciplines closely related to agriculture: ecology, soil science, and soil microbiology. (shrink)

Based on Hans Blumenberg’s philosophical concept of »reoccupation«, the study analyzes why the microbe has never really been situated in the world, demarcating ontological shifts in modeling microbes. The shifts are related to techniques such as sequencing and digitizing, to microbe banks acting as world models, and to metaphysical vacancies co-created. These can be operated on a historiographic level, as highlighted by the world formula of bacterial photosynthesis. It allowed for imaginations of the Early Earth and an Iron-Sulfur-World. In (...) sum, collecting and cultivating are shown to be crucial pre-operations for operative bio-ontologies, exemplified by a case study on the German Collection of Microorganisms (DSMZ). (shrink)

All organisms live in close association with microbes. However, not all such associations are meaningful in an evolutionary context. Current debate concerns whether hosts and microbes are best described as communities of individuals or as holobionts (selective units of hosts plus their microbes). Recent reports that assortative mating of hosts by diet can be mediated by commensal gut microbes have attracted interest as a potential route to host reproductive isolation (RI). Here, the authors discuss logical problems (...) with this line of argument. The authors briefly review how microbes can affect host mating preferences and evaluate recent findings from fruitflies. Endosymbionts can potentially influence host RI given stable and recurrent co‐association of hosts and microbes over evolutionary time. However, observations of co‐occurrence of microbes and hosts are ripe for misinterpretation and such associations will rarely represent a meaningful holobiont. A framework in which hosts and their microbes are independent evolutionary units provides the only satisfactory explanation for the observed range of effects and associations. (shrink)

This paper shows that the identity of living things is a composite reality. It also suggests that the immune system constitutes a unifying process for the organism.

Abstractabstract:Long before COVID-19 made social distancing familiar, people with cystic fibrosis (CF) already practiced such behaviors. CF is held up as a classic example of genetic disease, yet people with CF are also susceptible to bacteria from the environment and from other CF patients. Starting in the 1980s, a bacterial epidemic in the CF population highlighted clashing priorities of connection, physical safety, and environmental protection. Policymakers ultimately called for the physical separation of people with CF from one another via recommendations (...) that reconfigured the CF community. Simultaneously, medical researchers recognized that one highly transmissible CF pathogen called cepacia was being developed for environmental applications and got the EPA to limit cepacia's environmental deployment. Environmental regulations speak to the challenge of useful microbes that harm a minority, but CF cross-infection also involves legal implications for microbial and genetic discrimination, social consequences for CF communities, and ethical questions about balancing autonomy, harms, and benefits. As scientists increasingly study connections between host genetics, microbial genetics, and infectious risks, CF is a vital referent. (shrink)

In his Treatise of Human Nature, David Hume asked how people succeed in constructing edifices of belief from their limited store of sensory impressions and derived ideas. Hume could adduce no evidence to support the existence of an inner self that intelligently manipulates impressions and ideas. At the same time, he recognized in himself the conviction that there is inner self. Today, there is a growing conviction among cognitive neuro-scientists, behavioral scientists, science journalists, and their publics that neuroscience is on (...) the verge of providing us with the ultimate solution to ‘‘Hume’s problem.’’ This article describes two approaches to this solution. (shrink)

Rather than ‘superbugs’ signifying recalcitrant forms of life that withstand biomedical treatment, drug resistant infections emerge within and are intricate with the exercise of social and medical power. The distinction is important, as it provides a means to understand and critique current methods employed to confront the threat of widespread antimicrobial resistance. A global health regime that seeks to extend social and medical power, through technical and market integration, risks reproducing a form of triumphalism and exceptionalism that resistance itself should (...) have us pause to question. An alternative approach, based on a postcolonial as well as a ‘post-colony’ approach to health and microbes, provides impetus to challenge the assumptions and norms of global health. It highlights the potential contribution that vernacular approaches to human and animal health can play in altering the milieu of resistance. (shrink)

This article traces the historical co-evolution of microbiology, bacteriology, and virology, framed within industrial and agricultural contexts, as well as their role in colonial and national history between the end of the 19th century and the first decades of the 20th century. The epistemology of germ theory, coupled with the economic interests of European colonies, has shaped the understanding of human-microbial relationships in a reductionist way. We explore a brief history of the medical and biological sciences, focusing on microbes (...) and the difficulty of implementing germ theory outside of biology laboratories. Furthermore, we highlight the work of Lynn Margulis, who conceptualized microbes within their ecological contexts. Such research shows the active role microbes play in handling life-sustaining biological and biochemical processes. We outline how the industrial and technological advancements of the last two centuries not only impacted almost all human societies, but also changed the world on microbial, biological, and geological levels. The narration of these histories is a complex task, and depends on how national, international, and intergovernmental institutions (such as the World Health Organization) conceive of the selective environmental pressures exerted by industry and biotechnological companies. (shrink)

Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host–microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms (...) that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host–microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease. (shrink)

Animals exist as biodiverse composite organisms that include microbial residents, eukaryotic cells, and organs that collectively form a human being. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body or the holobiont secures growth, health, and reproduction. As such, the survival of a holobiont is dependent on the maintenance of biological order including metabolic homeostasis by tight regulation of the communication between its eukaryotic and prokaryotic residents. In this review (...) an overview and perspective are provided on the bidirectional communication between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships between the components of the holobiont. An emphasis is placed on exemplifying microbiome‐mediated effects on host functions—aiming to integrate microbiome functionality to host physiology, be it health or disease. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex transkingdom interactions are provided. (shrink)

Microbes often live in association with dense multicellular aggregates, especially biofilms, and the construction of these aggregates typically requires microbial cells to produce public goods, such as enzymes and signaling molecules. Public-goods producers are, in turn, vulnerable to exploitation by free-rider cells that consume the public goods without paying for their production costs. The cell population of a biofilm or other microbial aggregates are expected to pass through bottlenecks due to a wide range of factors, such as antibiotic treatments (...) and dispersal. The goal of this article is to make the case for the relevance of population bottlenecks at shaping the social interactions within microbial aggregates. The effect of bottlenecks on microbial aggregates is complex in that bottlenecks can favor producers under certain circumstances, but not in others. The concept of the Volunteer’s Dilemma from game theory will be used to motivate the hypothesis that this partly occurs because of how bottlenecks alter the risk of being a producer in a microbial aggregate. Finally, the role of bottlenecks in the microbial world impacts key issues in evolutionary biology, including the importance of ecology at shaping social evolution, and the evolution of multicellularity from unicellular ancestors. (shrink)