Table 2.
Summary of studies involving use of one or more omics methodologies and the statistical data reduction commonly applied.
| Ref. | Omics field | Study subject | Subject type | Experiment | Highlighted number of features | Data reduction |
|---|---|---|---|---|---|---|
| Imdahl et al. (2020) | Transcriptomics | Salmonella enterica serovar Typhimurium | Bacteria | Late stationary phase, anaerobic shock, NaCl shock | Pool: 101 (anaer.); 274 (NaCl) Single c.: 63 (anaer.); 131 (NaCl) |
Unbiased clustering by PCA, DEGs (DESeq2) |
| Laguna-Teno et al. (2020) | Transcriptomics | Saccharomyces cerevisiae | Fungi/yeast | Toxicology exposure, two GOs vs. control | 1,181 (GOC); 340 (GO) | PCA, DEGs, FDR, FC, functional annotation |
| Semmouri et al. (2020) | Transcriptomics | Zooplankton community | Environmental community | Seasonal community characterization | Over 3,000 annotated transcripts per sample | Functional interpretation |
| Bengtsson et al. (2016) | Proteomics | Hypocrea jecorina | Fungi | Secretome characterization | 155 identified proteins | Hierarchical clustering |
| Bona et al. (2019) | Proteomics | Vitis vinifera cv. Pinot Noir rhizosphere | Environmental community | Proteome and taxonomy characterization | 579 identified proteins | Functional interpretation |
| Knox et al. (2016) | Proteomics | Aspergillus fumigatus | Fungi | ISS strains vs. clinical isolates | N/S | One-way ANOVA, comparison of fold change (Log2) |
| Ram et al. (2005) | Genomics Proteomics |
Natural acid mine drainage biofilm | Environmental community | Characterization of a naturally occurring biofilm | 2,003 identified proteins | Functional interpretation |
| Zhang et al. (2014) | Proteomics | Shewanella oneidensis | Bacteria | Alginate entrapped cultures vs. biofilms | 1,712 identified proteins | Student’s t-test |
| Khakimov et al. (2017) | Metabolomics | Streptoccoccus thermophilus | Bacteria | Several time points through fermentation process | 64 identified peaks | PARAFAC2, PCA, ASCA |
| Favre et al. (2017) | Metabolomics | Persicivirga (Nonlabens) mediterranea; Pseudoalteromonas lipolytica; Shewanella sp. | Bacteria | Characterization of response to culture medium, growth phase, culture mode | 155 ± 22 m/z features | PCA, PLS-DA |
| Lu et al. (2019) | Metabolomics | Uropathogenic Escherichia coli | Bacteria | Comparison between biofilm and planktonic stages | 38 differential metabolites | Unsupervised PCA, PLS-DA, heatmap |
| Stipetic et al. (2016) | Metabolomics | Staphylococcus aureus | Bacteria | Comparison between biofilm and planktonic stages | 530 significant metabolites | Bayes moderated t-tests, FDR, PCA |
| Afshari et al. (2020) | Genomics Metabolomics |
Cheddar cheese microbial community | Environmental community | Comparison between industrial vs. traditional cheese, outer surface vs. core | 46 metabolites (GC–MS) 8,000 features (LC–MS) |
ANOSIM, PCA, MCIA (integration), Spearman analysis |
| Parrot et al. (2019) | Genomics Metabolomics Imaging |
Fucus vesiculosus surface microbiome | Environmental community | Comparison of surface metabolome with whole tissue extract | 50 metabolites (surface) 27 metabolites (extracts) | One-way PERMANOVA, PCoA, HAC |
PCA, principal component analysis; DEGs, differentially expressed genes; Ref., reference; FC, fold change; ISS, international space station; N/S, not stated; N/A, not applicable; Single c., single cell; anaer., anaerobic; ASCA, ANOVA-simultaneous component analysis; PLS-DA, partial least-squares discriminate analysis; FDR, Benjamini and Hochberg false discovery rate; MCIA, multiple co-inertia analysis; HAC, hierarchical ascendant classification; PCoA, principal coordinates analysis; ASV, amplicon sequence variant; WWTP, wastewater treatment plant.