Abstract
The dual role of microbial communities as either beneficial/functional or harmful/pathogenic involves two issues concerning causality in physiology and medicine, etiology of disease, and the notion of function in biology. Causal explanation formulated by the germ theory of disease and the Koch postulates connects the existence of a specifically identified microbe to disease by the isolation and identification of a pathogen from an organism with the disease and the successful infection of a healthy individual. Similarly, microbiome research in medicine centers on taxonomic composition in correlation with physiological conditions and germ-free mice experimentations to establish causal connections. However, because the microbiome is an ecological community, it lacks the specificity of identification assumed in the germ theory. Furthermore, the ecological aspects within and between microbiomes such as background conditions, microbial interactions, and interdependence, are treated as confounding. Looking at ecological studies, the causal explanations are less specific regarding complex systems with their processes of interactions. This article makes the following two points: One is that microbiome causality in the host should be understood similarly to the microbiome causality in an ecosystem. The second is that if considering a microbiome’s causality in the host as an ecosystem, its etiological explanation needs to be revisited to include a heterogeneous and mutual notion of interactions. Finally, according to the second point, the notion of function in ecology with its relevant notion of causality should be considered accordingly.
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Notes
Addressing microbes by their physiological function in the host such as the labeling of commensal, beneficial, or pathogenic bacteria is also within the etiological view.
The launches of the human microbiome project 2007 (archived): https://www.genome.gov/26524200/2007-release-nih-launches-human-microbiome-project.
I suggested taxonomic composition, not genes, as the focal causal entity because of the attention this level receives in biomedical literature. Also, when looking at the selection of genes within a microbiome, that means the consideration of community as a unit of selection or looking at the processes of co-evolution within the community. In the next section, I discuss such a possibility within new perspectives and analysis of function in ecology and microbiology.
Such distinction between intrinsic properties and context is blurry when dealing with microbes with dynamic interactions such as horizontal gene transfers and mobile genetic elements (Quistad et al. 2020).
Though I agree with this analysis of SE ecological function, I will not discuss it further here due to the article's scope, connecting the microbiome functional understanding with etiological understanding. This new analysis of ecological function also has promising potential in analysis and understanding the holobiont from an eco-evolutionary perspective.
This view is in line with the ideas of extended health which emphasize interactions as part of the factors causing disease. For more details, see Morar and Skorburg (2018).
Some conditions can be defined as pathological such as C. difficile disorder or type 1 diabetes. C. difficile disorder is when this microbial group, which already exists in the gut, triggers the immune system to a strong inflammatory response that can lead to the destruction of gut walls and, ultimately, death. Type 1 diabetes is a condition where the process of insulin production in the pancreas is missing.
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Schneider, T. The Microbiome Function in a Host Organism: A Medical Puzzle or an Essential Ecological Environment?. Biol Theory 19, 44–55 (2024). https://doi.org/10.1007/s13752-023-00434-4
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DOI: https://doi.org/10.1007/s13752-023-00434-4