Microbiome, Diet and Health Glossary

Diversity: number and abundance distribution of distinct taxa of microorganisms.

Ecotype: a genetically distinct population within a species that has adapted to a specific habitat.

Holobiont: an organism and all of its associated symbiotic microbes, including parasites.

Metagenomics: culture-independent sequencing of total microbial community DNA to describe the genomic potential of the microbiota in totality.

Metatranscriptomics: sequencing of cDNA generated from RNA transcripts extracted from a given microbial community. This only detects actively transcribed genes to characterize community function.

Microbiome: the aggregate genomes present in a particular microbial community.

Microbiota: a microbial community that has been established in a given habitat. Often used to refer to the microbial population associated with a healthy individual or tissue.

Pangenome: the full complement of genes in a species or higher-level taxonomy. This typically refers to the union of bacterial or archaeal gene sets, which often vary in genetic content among closely related strains.

Phylotype: a phylogenetic cluster of microbes that share a common ancestor and transcend a threshold of molecular divergence from closely related lineages.

Syntrophy: a relationship by which a microbial phylotype is dependent on another to supplement a nutritional requirement.

16S rRNA amplicon sequencing: PCR amplification and sequencing of hypervariable sequences of the 16s rRNA gene phylogenetic marker to infer bacterial community structure.