Table 2.

List of references to other (metaomics) methods that can be used in microbiome modeling.

Data type/Method	References
WGS/amplicon	Segata et al., 2013; Bragg and Tyson, 2014; Jünemann et al., 2017; Frioux et al., 2020; Zorrilla et al., 2021
metatranscriptomics	Gifford et al., 2010; Gosalbes et al., 2011; Bashiardes et al., 2016
metabolomics	Mashego et al., 2006; Zhang et al., 2012; Liu and Locasale, 2017; Bauermeister et al., 2021
enzyme activity assays	Bisswanger, 2011; Stitt and Gibon, 2014
C13-metabolic flux analysis	Wiechert, 2001; Zamboni et al., 2009; Winter and Krömer, 2013
single-cell omics	Wang and Bodovitz, 2010; Duncan et al., 2019
protein interaction data	Zhou et al., 2016
growth screenings	Oh et al., 2007; Maier and Pepper, 2015
knock out screenings and gene essentiality data	Oh et al., 2007
biomass composition	Beck et al., 2018; Lachance et al., 2019
total protein content	Noble et al., 2007; Noble and Bailey, 2009
maintenance coefficients	Stouthamer and Bettenhaussen, 1973; Vos et al., 2016
microscopy	Cesar and Huang, 2017
flow cytometry	Props et al., 2016; Hatzenpichler et al., 2020