Table 1.
Examples of the applications of human-based (meta)omics and multi-omics approaches to investigate host–microbiota–pathogen–nutrition relationships.
| Type of Omic Approach | Type of Model | Description/Major Findings | References |
|---|---|---|---|
| Multi-omics | hGoC | Identification of specific human microbiome metabolites modulating EHEC pathogenesis | [116] |
| Metagenomics/Metabolomics | HITChip/M-SHIME | In-depth microbial characterization of luminal and mucosal gut microbes | [122] |
| Metagenomics/Metabolomics | Human subjects/stool samples | Characterization of the gut microbiome of individuals living in the Amazon showed striking differences in the microbial communities from these two types of populations | [123] |
| Metabolomics | In vitro SIHUMIx | Analysis of the impact of functional food on the microbic metabolic pathways | [124] |
| Multi-omics | Human subjects/stool and plasma samples | Investigation of the interplay between the human gut microbiome and the host metabolism | [125] |
| Meta-proteomics | Human subjects/stool samples | Extensive microbiome comparison between infants and the identification of previously undetected microbial functional categories | [126] |
| Transcriptomics/Metatranscriptomics | hiOs | Exploration of the interaction of Salmonella enterica serovar Typhimurium with hiOs; clear changes in transcriptional signatures were detected | [127] |
Abbreviations: hGoC, human gut-on-a-chip; EHEC, enterohemorrhagic Escherichia coli; HITChip, human intestinal tract chip; M-SHIME, mucosal-simulator of a human intestinal microbial ecosystem; SIHUMIx, simplified intestinal human microbiota; HiOs, human intestinal organoids.