Table 1 Glossary of terms specific to the microbiota research (alphabetical order)
From: The role of the microbiota in the management of intensive care patients
16S rRNA gene sequencing | A method to analyze bacterial communities by sequencing one or more variable regions of the bacterial 16S rRNA gene by NGS |
Abundance | Total number of a given taxa in a sample |
Actinobacteria | This phylum is mainly composed by Gram-positive bacteria, but is less abundant in gut microbiota. Notably represented by the Bifidobacterium genera, it contains also clinically relevant genera such as Corynebacterium, Nocardia, Actinomyces or Mycobacterium |
Alpha-diversity | Refers to the composition within a sample |
Bacteroidetes | One of the most represented phyla in gut microbiota. It includes mainly commensals and is composed especially by Gram-negative bacilli such as Bacteroides, Porphyromonas, or Prevotella |
Beta-diversity | Refers to the similarity of the composition between samples |
Culturomics | Method for analyzing bacterial composition of complex samples such as human gut, based on extensive culture media and atmosphere combinations |
Diversity | Describes the number of various bacterial communities and their distribution |
Firmicutes | One of the most represented phyla in gut microbiota. It includes mainly Gram-positive bacteria such as genera Staphylococcus, Enterococcus, Streptococcus, or Lactobacillus. Clostridium genera represent 95% of the Firmicutes phyla in the gut |
Next-generation sequencing | Refers to sequencing methods which emerged after the mid-2000s, and which typically yield higher output than Sanger sequencing |
Operational taxonomic unit (OTU) | Clusters of sequences sharing a minimal identity (e.g., 97% is commonly used in 16S studies), referring to a taxonomic group. These clusters and the respective number of reads within are an estimation of the abundance of different taxa in samples |
Phylum | Taxonomic rank that ranks above class and below kingdom. Classical phyla in gut microbiota studies are Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. Firmicutes and Bacteroidetes typically represent 90% of gut microbiota in subjects not exposed to antibiotics |
Proteobacteria | Quasi-exclusively composed by Gram-negative bacteria, this phylum includes especially pathogenic genera such as Escherichia, Klebsiella, Legionella, Pseudomonas, Acinetobacter or Stenotrophomonas |
Protist | Kingdom including predominantly eukaryotic unicellular microscopic organisms |
Richness | Number of different bacterial taxa in a sample |
Shotgun sequencing | A method to analyze bacterial communities by sequencing random DNA fragments by NGS |
Taxon | Taxonomic group of any rank, such as species, family, or class |