Table 2.

Approaches to measure functional microbial interactions.

Phenotype category	Phenotype	Measurement level	Phenotyping method	Organism tracing method	Throughput1	References
Morphology	Cellular morphology	Single cell	Flow cytometry	Physical separation by a membrane	Low	Heyse et al., 2019
	Colony morphology	Population	Volatile compounds bioassay	Physical distance		Low	Tyc et al., 2015
Molecular phenotype	Cellular fingerprints	Single cell	Raman spectroscopy	Physical separation by a membrane	Low	Heyse et al., 2019
	Cell surface molecular profile	Population	Imaging mass spectrometry	Physical distance	Low	Chen et al., 2020b
	Metabolomic profile	Community	Nuclear magnetic resonance spectroscopy	Binary combination	Low	Medlock et al., 2018
	Gene expression profile	Community	RNA sequencing	Binary combination	Low	Zuñiga et al., 2019; Ikeyama et al., 2020; Strub et al., 2021
Activity or production	Antimicrobial activity	Community	Agar plug diffusion	Physical separation by a permeable membrane	Low	Pishchany et al., 2018
		Population	Spot on lawn	Binary combination	Low	Weiss et al., 2021
	Respiration	Community	CO2 indicator	Random partition combinatorial design, flow cytometry and T-RFLP	Low	Rivett et al., 2016
	Enzymatic activity	Community	Enzymatic assays	Combinatorial assembly	Low	Sanchez-Gorostiaga et al., 2019
	Ethanol yield	Community	HPLC	Flow cytometry and combinatorial assembly	Medium	Senne de Oliveira Lino et al., 2021
	Acidification	Community	Colorimetric assay with pH indicator in the culture media	Binary combination	Medium	Blasche et al., 2021
Social behavior	Coaggregation	Community	Visual coaggregation assays	Binary combination	Medium	Kumar et al., 2019
	Biofilm	Community	Biofilms formation assay in bioreactor	Combinatorial assembly and selective plate counts	Low	Lapointe et al., 2019
	Dispersal	Population	Distance	Binary combination	Low	Zhang et al., 2018
Impact on host	Gene expression levels	Community	Microarrays and RT-qPCR	Binary combination	Low	Shah et al., 2016
	Intracellular metabolite levels	Community	Metabolomic analysis	Binary combination	Low
	Reproductive success, longevity and development	Community	Plate counts	Combinatorial assembly	Low	Gould et al., 2018

¹Assay format: low=<96, medium=96–500.