Table I.
Definitions
| Microbe: Any microscopic life form. Commonly bacteria or archaea, but many eukaryotes are microbes. |
| Microbiome: An assemblage of microbes in a particular time and place. |
| Virome: An assemblage of viruses in a particular time and place. |
| Microbial community: An assemblage of functionally and metabolically interacting microbes. |
| Metagenome: A composite genome from all organisms in a microbiome. |
| Meta-transcriptome: A composite gene expression profile of all organisms in a microbiome. |
| Richness: The number of bacterial species present in a population (alpha diversity, measured by Good’s coverage). |
| Diversity: The “complexity” or relative distribution of different species present in a population, ecosystem, or biome (beta diversity, measured by Morisita-Horn Index). The similarities between distributions can also be determined. |
| Phylotype: A group of individuals characterized by their phylogenetic relationship to each other; a statistically associated shared richness and diversity of specific organisms within an anatomic site, initially based on an evolutionary relationship. |
| Dysbiosis: Disease-associated alteration in the composition of a microbial community. |
| Pathobiont: A member of the microbiota, often antimicrobial-resistant, that can cause disease on perturbation of the otherwise constraining healthy microbiota. |
| Probiotics: Live commensal microbial organisms (eg, Lactobacillus GG, lactobacilli, bifidobacteria, Streptococci, or Saccharomyces boulardii, alone or in combination) administered to enhance or suppress mucosal integrity, inflammation, or immune response. |
| Common Bacterial Phyla: |
| Bacteroides: Obligately anaerobic gram-negative bacteria. Prevalent commensals in human gut (eg, Bacteroides fragilis). |
| Firmicutes: Very diverse phylum of low G-C gram-positive bacteria, including staphylococci, streptococci, bacillii, and clostridia. Prevalent commensals in human gut. |
| Proteobacteria: Very diverse phylum of gram-negative bacteria, including enterobacteriaceae (eg, Escherichia coli). |
| Actinobacteria: High G-C gram-positive bacteria, including mycobacteria and corynebacteria. |