Table 1 Definitions of key terminologies.
From: Analysis of microbial compositions: a review of normalization and differential abundance analysis
Term | Definition |
|---|---|
Microbiota | Community of microscopic organisms. |
Microbiome | Genes associated with the microbiota. |
Amplicon | Product of PCR amplification. |
High-throughput Sequencing | DNA sequencing approach that produces large amounts of sequence data rapidly at low cost. |
OTU | Operational taxonomic unit: Group of DNA sequences with 97% similarity. |
SV | Sequence variant: Individual DNA sequences recovered from a high-throughput marker gene analysis following the removal of spurious sequences generated during PCR amplification and sequencing. |
Absolute abundance | Unobservable actual abundance of a taxon in a unit volume of an ecosystem. |
Observed abundance | Observed counts of features (OTUs or SVs) in the feature table. |
Relative abundance | The fraction of the taxon observed in the feature table relative to the sum of all taxa in the sample. It is between 0 and 1. |
Feature Table | A matrix summarizing observed microbial abundances in the sample. Usually, columns represent samples and rows stand for OTUs or SVs. |
Library Size | The total number of observed abundances for all taxa in a sample. |
Microbial Load | The total number of (unobserved) absolute abundances for all taxa in a unit volume of an ecosystem. |
