I examine the feminist epistemic values in science, presented by Helen Longino, and their role in framing microbiome causality in the study of inflammatory bowel disease (IBD). In particular, I show how values presented as feminist give an alternative view in scientific theories—focusing on ontological heterogeneity and mutuality of interactions rather than simplicity and one causal direction—when looking at relations between organisms and microorganisms, and between organisms (particularly humans) and their environment. I identify two approaches in microbiome study, an immunological (...) approach that looks at the microbiome pathogenicity and an ecological approach that studies the microbial activity and functions. I show the puzzles stemming from the traditional background beliefs of the immune self and germ theory in the study of IBD causality. Furthermore, I argue for the benefits of a shift to the ecological view of body-microbe interrelations. I conclude with the benefits and advantages of feminist values over traditional ones, both in creating new ways of understanding organisms’ physiology and immune systems and for future biomedical studies involving microbiome causality. (shrink)

It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term “holobiont” was introduced as a name for the biological unit made up by a host and all of its associated microorganisms, (...) and much of this new debate about biological individuality has focused on whether holobionts are integrated individuals or communities. In this paper, I show how parts of the holobiont can span both characterizations. I argue that most holobionts share more affinities with communities than they do with organisms, and that, except for maybe in rare cases, holobionts do not meet the criteria for being organisms, evolutionary individuals, or units of selection. (shrink)

Microbiome research is changing how ecosystems, including animal bodies, are understood. In the case of humans, microbiome knowledge is transforming medical approaches and applications. However, the field is still young, and many conceptual and explanatory issues need resolving. These include how microbiome causality is understood, and how to conceptualize the role microbiomes have in the health status of their hosts and other ecosystems. A key concept that crops up in the medical microbiome literature is “balance.” A balanced microbiome is thought (...) to produce health and an imbalanced one disease. Based on a quantitative and qualitative analysis of how balance is used in the microbiome literature, this “think again” essay critically analyses each of the several subconceptions of balance. As well as identifying problems with these uses, the essay suggests some starting points for filling this conceptual gap in microbiome research. (shrink)