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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