Table 1.

Omics Strategies for Discovering Novel LBP Design Elements.

Omics Science	Characterizes/Quantifies	Organisms investigated	Application to LBPs	Refs
Genomics	DNA	Bifidobacterium bifidum, 36 Bifidobacterium spp, Bacillus coagulans, Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides uniformis, Bacteroides vulgatus, Blautia hydrogenotrophica, Collinsella aerofaciens, Clostridium hiranonis, Desulfovibrio piger, Eggerthella lenta, Eubacterium rectale, Faecalibacterium prausnitzii, Prevotella copri	Colonization factors and in vivo adaptation mechanisms via comparative genomics	[15, 18]
			Inter-microbe interactions via profiling compositional changes in native and synthetic communities	[21, 22]
Transcriptomics	RNA	Saccharomyces cerevisiae, Lactobacillus plantarum, Lactococcus lactis, Lactobacillus rhamnosus GG, Lactobacillus crispatus, Bacteroides fragilis, Akkermansia mucinipila, Ruminococcus gnavus, Bacteroides thetaiotaomicron	Inter-microbe interactions via differential expression analysis in synthetic communities	[34, 35]
			In vivo adaptation mechanisms by differential expression analysis in gut-like conditions	[30, 33, 105, 106]
			Genetic parts for engineered LBP design via differential expression analysis in response to defined gut cues	[31, 37, 38]
			Colonization factors via spatially-resolved differential expression analysis	[107]
Proteomics	Proteins	Lactobacillus acidophilus, Lactobacillus salivarius	In vivo adaptation mechanisms via differential proteome analysis in gut-like conditions	[40–43, 108]
			Genetic parts for engineered LBP design via proteomics of engineered strains	[109, 110]
Metabolomics	Metabolites (Excluding DNA, RNA, or protein)	Lactobacillus acidophilus, Bacteroides thetaiotaomicron, Bacteroides ovatus, Bacteroides uniformis, Bacteroides vulgatus, Blautia hydrogenotrophica, Collinsella aerofaciens, Clostridium hiranonis, Desulfovibrio piger, Eggerthella lenta, Eubacterium rectale, Faecalibacterium prausnitzii, Prevotella copri, Ruminococcus gnavus, Ruminococcus bromii	In vivo adaptation mechanisms via metabolomics of gut-adapted strains	[48, 49, 51]
			Inter-microbe interactions via metabolic profiling of synthetic communities	[22, 29]
Functional genomics	Engineered gene function	Escherichia coli Nissle, Bacteroides thetaiotaomicron, Saccharomyces cerevisiae, Saccharomyces boulardii, Bacteroides fragilis	Promoter design	[34, 55, 59]
			Pathway optimization	[56, 57]
			In situ genetic tractability	[53, 54]
			In vivo adaptation mechanisms	[62, 63]