. Author manuscript; available in PMC: 2019 Jul 1.

Published in final edited form as: Biol Blood Marrow Transplant. 2018 Feb 19;24(7):1322–1340. doi: 10.1016/j.bbmt.2018.02.009

Table 5.

Definition of terms

Term	Definition	References
Diversity	Measurement of the number of different types (taxa) of organisms and their abundance. Alpha-diversity and beta-diversity refer to diversity within and between samples, respectively	Lozupone, 2012³⁶
Dysbiosis	Perturbation of the taxonomic structure and function of the microbiota from the healthy state. This can be associated with the development of disease	Petersen, 2014³⁷
Germ-free mice	Mice raised in sterile conditions and free from colonization by all microorganisms. Also referred to as “axenic” mice	Giraud, 2008³⁸
Fecal microbiota transplantation	The transfer of stool from a donor to a recipient via either endoscopy, nasogastric/duodenal tube, capsules, or enema for the purpose of altering the intestinal microbiota of the recipient and restoring health. Stool is obtained from healthy related or unrelated donors, and less commonly from the intended recipient	Borody, 2013³⁹
Microbiota	The entirety of microorganisms (bacteria, archaea, viruses, fungi, and other eukaryotes) within a specific habitat	Marchesi, 2015³²
Microbiome	Includes the biotic (microorganisms and their genomes) and abiotic (environmental) factors present within a particular habitat. This definition is modeled after the meaning of the term “biome”. Many in the field use the term microbiome to refer to the collection of genes and genomes within a particular habitat, although this definition is redundant with “metagenome”	Marchesi, 2015³²