Table 1 Glossary of key concepts for interpreting microbiome research
From: The gut microbiome’s role in the development, maintenance, and outcomes of sepsis
Concept | Definition | Notes |
|---|---|---|
Techniques for identifying microbiome components | ||
Culture-based | Uses traditional techniques for culturing bacteria to determine which species are present | Some species (e.g., anaerobes) are difficult to culture; once cultured, definitive identification may be difficult |
16S rRNA sequencing | Uses a conserved region of bacterial RNA to identify bacteria, combined with a species-specific sequence to determine which species are present | Unable to identify genes or presence of non-bacterial components (e.g., protozoa or fungi) |
Metagenomic sequencing | Uses “unbiased” sequencing to determine all genes present in a sample and construct community structure; allows for determination of community composition and function | Remains relatively expensive, although cost has decreased; applications are still most suitable for research |
Classification of microbiome composition | ||
Abundance | Relative amount of specific bacterial groups in a sample | Most techniques only allow for determination of relative abundance of bacteria, not absolute (i.e., unable to determine total number of bacteria present in a sample) |
α-diversity | Within-group microbiome diversity | Describes the makeup of a microbial community from one sample (e.g., one patient or one body site) |
β-diversity | Between-group microbiome diversity | Allows for comparisons between groups of samples |
Dysbiosis | Describes a microbial community that has been altered from its normal structure | Can be nonspecific; for example, unclear if this refers to decreased relative abundance of one group, decreased α-diversity, or another measure |