Box 1 Glossary

Biogeography—the discipline studying the distribution of species and ecosystems in space and across evolutionarily meaningful timescales.

Community ecology—the discipline studying the organization and function of ecological communities (those organisms actually or potentially interacting, bounded by either geographic or conceptual limits).

Contamination—incidental presence of microbes; not long-term residents of the microbial ecosystem in question.

Cultivation-dependent detection—microbiological techniques that rely on the cultivation of microbes for enumeration and identification; less than 1% of microbes are estimated to have been cultivated in the lab [41, 42], leaving a vast majority of microbial diversity underexplored (Fig. 1d).

Cultivation-independent detection—techniques for the elucidation of microbial communities that do not rely on cultivation of microorganisms; these generally rely on high-throughput, next-generation sequencing technologies (e.g., Illumina, 454 pyrosequencing) that allow for the direct sequencing of DNA from the environment; common techniques include metabarcoding, in which a conserved “barcode” region of the genome is amplified and sequenced from environmental samples, giving information about which taxa are present and their relative abundances, and metagenomics, in which all available microbial DNA is sequenced, giving information about presence and relative abundances of metabolic pathways as well as identities of microbes (Fig. 1e).

Dispersal—the distribution of propagules across space.

Dysbiosis—an alteration of the microbiota from the norm, generally associated with disease states; this may be through shifts in dominance or the addition/removal of key taxa.

Environmental filtering—the process by which potential colonists are selected based on purely ecological factors.

Ecological niche—a broad term encompassing multiple definitions used to describe to an organism’s activity or behavior in response to a given set of biotic and abiotic environmental conditions or resources. Organisms occupy niches by carrying out specific functions, often through competitive or mutualistic interactions. Niche space refers to the set of all possible niches, occupied or unoccupied, in a given habitat.

Hygiene—those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease.

Hygiene hypothesis—the idea that a lack of early childhood exposure to microorganisms increases susceptibility to allergic diseases by suppressing the natural development of the immune system.

Invasion ecology—the discipline studying the alterations to ecosystems resulting from introduction and establishment of taxa originating outside of said ecosystem, and the factors allowing some taxa to invade successfully.

Microbial ecology—the discipline studying the interrelations between microorganisms, including but not limited to community interactions and interactions with the environment.

Microbial load—the absolute abundance of microbes; commonly estimated using cultivation-dependent techniques through quantitative counts of colony-forming units (CFUs).

Microbiota—or microbiome, the ecological community of microorganisms (bacteria, archaea, viruses, fungi, mites, etc.) that share our body space; may be subdivided into cohesive groups, such as the skin microbiota, or the gut microbiota.

Nosocomial—of or relating to hospitals.

Priority effects—the particular influence that early arriving members of a community have on later arriving members.

Protective mutualism—a mutualism in which protection from pathogenic organisms is the result of occupation of niche space within the host habitat, excluding colonization by harmful microbes; often conflated with commensalism (see Fig. 2c).

Sterilization—the removal of all microbes from a surface or object.

Transmission—dispersal and establishment of microbes between hosts.