Analyzing the Human Microbiome: A 'How To' Guide for Physicians
Analyzing the Human Microbiome: A 'How To' Guide for Physicians
To understand the complexity of the human microbiome, it is important to recognize the genetic and evolutionary relationships between species. All living organisms are currently hierarchically classified into eight major levels, with domain being the most general and species the most specific (Figure 1). There are three domains of life (Archaea, Bacteria and Eukarya). At each lower level, organisms are classified with their most similar cousins based on common features. To better illustrate the nature of this hierarchical system, one might consider our own species Homo sapiens and the well known bacteria Escherichia coli (Figure 1). Although the most precise information is gained from species-level analysis, there is also value in higher-level analyses, especially in cases where species identification is not possible. In the case of H. sapiens, the phylogenetic relationship between it and related species is extremely well defined. Bacteria, on the other hand, display more complex evolutionary relationships, and new species and even phyla are still being discovered. Furthermore, microbial genomic plasticity confuses the analysis of mixed microbial communities, as horizontal gene transfer ( Box 1 ) and the subsequent phenotypic differences between ostensibly closely related strains makes the definition of species in the context of microbes much more fluid.
(Enlarge Image)
Figure 1.
Hierarchical organization of taxonomic levels used for classifying organisms. Escherichia coli electron micrograph provided by Rocky Mountain Laboratories NIAID, NIH (Hamilton, MT).
Phylogenetics—The Basics
To understand the complexity of the human microbiome, it is important to recognize the genetic and evolutionary relationships between species. All living organisms are currently hierarchically classified into eight major levels, with domain being the most general and species the most specific (Figure 1). There are three domains of life (Archaea, Bacteria and Eukarya). At each lower level, organisms are classified with their most similar cousins based on common features. To better illustrate the nature of this hierarchical system, one might consider our own species Homo sapiens and the well known bacteria Escherichia coli (Figure 1). Although the most precise information is gained from species-level analysis, there is also value in higher-level analyses, especially in cases where species identification is not possible. In the case of H. sapiens, the phylogenetic relationship between it and related species is extremely well defined. Bacteria, on the other hand, display more complex evolutionary relationships, and new species and even phyla are still being discovered. Furthermore, microbial genomic plasticity confuses the analysis of mixed microbial communities, as horizontal gene transfer ( Box 1 ) and the subsequent phenotypic differences between ostensibly closely related strains makes the definition of species in the context of microbes much more fluid.
(Enlarge Image)
Figure 1.
Hierarchical organization of taxonomic levels used for classifying organisms. Escherichia coli electron micrograph provided by Rocky Mountain Laboratories NIAID, NIH (Hamilton, MT).
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