Table 1.

Examples of Holo-Omic Studies in the Current Litterature

Omic Levels	Organism	Major Findings	Reference	Arrow in Figure 1
Genome, microbial 16S	Mouse	20 host genes are associated with microbiome composition	Suzuki et al. (2019)	1
Genome, microbial 16S	Human	Genetic disposition for inflammatory bowel disease is associated with a reduction in abundance of the genus Roseburia in the gut microbiome	Imhann et al. (2018)	1
Transcriptome, metagenome	Pill-bug (Armadillidium vulgare)	Potential collaboration between microbiota and pill-bug in degrading lignocellulose	Bredon et al. (2018)	–
Proteome, microbial 16S	Mouse	Lack of the TLR5 protein increases Proteobacteria and decreases Bacteroidetes in microbiome and promotes gut inflammation	Carvalho et al. (2012)	2
Metabolome, metagenome	Thale cress (Arabidopsis thaliana)	Beneficial rhizobacteria induce excretion of the metabolite scopoletin that stimulates iron uptake and suppresses soil-borne pathogens	Stringlis et al. (2018)	3
Metametabolome, transcriptome	Human epithelial cells	Metabolism of microbiota-derived butyrate stabilizes the HIF transcription factor in human epithelial cells	Kelly et al. (2015)	4
Metametabolome, transcriptome	Human epithelial cells	The presence of microbiota-derived indole stimulates the expression of host genes connecting to the formation of tight junctions with a resulting higher pathogen resistance	Bansal et al. (2010)	4
Metametabolome, transcriptome	Mouse	Microbiota-derived indole controls expression of host miR-181 expression that regulates adiposity and insulin sensitivity	Virtue et al. (2019)	4

Examples of studies considering different omic levels from hosts and associated microorganisms at different levels of resolution. When evidence of host-microbiota interactions are available numbers link the table to the corresponding interaction in Figure 1.