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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