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Insular Microbiogeography: Three Pathogens as Exemplars

IBM Almaden Research Center, San Jose, CA, USA
Division of Molecular Biology, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Laurel, MD, USA
Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, CDC, Atlanta, GA, USA
School of Veterinary Medicine, University of California Davis, 100K Pathogen Genome Project, Davis, CA, USA
Authors to whom correspondence should be addressed.
Curr. Issues Mol. Biol. 2020, 36(1), 89-108;
Received: 2 July 2019 / Revised: 7 August 2019 / Accepted: 9 September 2019 / Published: 9 October 2019


Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.

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MDPI and ACS Style

Kaufman, J.H.; Elkins, C.A.; Davis, M.; Weis, A.M.; Huang, B.C.; Mammel, M.K.; Patel, I.R.; Beck, K.L.; Edlund, S.; Chambliss, D.; Douglas, J.; Bianco, S.; Kunitomi, M.; Weimer, B.C. Insular Microbiogeography: Three Pathogens as Exemplars. Curr. Issues Mol. Biol. 2020, 36, 89-108.

AMA Style

Kaufman JH, Elkins CA, Davis M, Weis AM, Huang BC, Mammel MK, Patel IR, Beck KL, Edlund S, Chambliss D, Douglas J, Bianco S, Kunitomi M, Weimer BC. Insular Microbiogeography: Three Pathogens as Exemplars. Current Issues in Molecular Biology. 2020; 36(1):89-108.

Chicago/Turabian Style

Kaufman, James H., Christopher A. Elkins, Matthew Davis, Allison M. Weis, Bihua C. Huang, Mark K. Mammel, Isha R. Patel, Kristen L. Beck, Stefan Edlund, David Chambliss, Judith Douglas, Simone Bianco, Mark Kunitomi, and Bart C. Weimer. 2020. "Insular Microbiogeography: Three Pathogens as Exemplars" Current Issues in Molecular Biology 36, no. 1: 89-108.

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