Table 1.
Definitions of main terms and nomenclature.
| Term | Definition | References |
|---|---|---|
| Dysbiosis | Non-homeostatic imbalance and loss of diversity in the resident microbial community often associated with disease states | (Petersen and Round, 2014) |
| Microbiota | All the microorganisms inhabiting a specific niche | (Lederberg, 2000; Turnbaugh et al., 2007) |
| Microbiome | Collective genetic material of all microorganisms and particles (bacteria, viruses, fungi, protozoa) present in a community | (Lederberg, 2000; Turnbaugh et al., 2007) |
| Bacteriome | Collection of all the bacterial genomes present within a community | |
| Mycobiome | Collection of all the fungal genomes present within a community | |
| Virome | Collection of all the viral genomes present within a community | |
| Resistome | Collection of all the genes and genetic precursors of anti-microbial resistance, found in both pathogenic and non-pathogenic bacteria | (Wright, 2007) |
| Next-generation sequencing (NGS) | High-throughput technologies facilitating rapid, parallel and cost-effective DNA sequencing | |
| Metagenomics | Functional analysis of all the collective genomes obtained from every individual member of the microbial community, including archaea, viruses and fungi | (Tringe and Rubin, 2005) |
| Metabolomics | Analysis of the complete set of metabolites from all processes present in a population | (Siggins et al., 2012; Aguiar-Pulido et al., 2016) |
| Metatranscriptomics | Study of microbial gene expression within habitats, providing insights on what genes are functionally active in a community | (Aguiar-Pulido et al., 2016) |
| Metabologenomics | Study, identification and correlation of microbial gene clusters responsible for the biosynthesis of expressed metabolites | (Goering et al., 2016) |
| Marker Gene Analysis (MGA) | Amplicon based culture-independent method often used for microbial classification by targeting 16S, 23S or 18S rRNA genes | |
| Whole Genome Shotgun Sequencing (WGSS) | Culture-independent genome wide NGS approach used for gene cataloging and functional inference | |
| Whole Genome Sequencing (WGS) | Culture-dependent NGS of whole cells, low throughput but provides practical data to improve metagenomics | |
| Operational Taxonomic Unit (OTU) | Clusters of related sequences within a percent sequence similarity threshold (>97% similarity), proxy for species-level divergence | |
| Multi-omics | Assimilation of data from various “omics” technologies such as microbiomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics | (Vilanova and Porcar, 2016) |
| Genome Mining | Computationally intensive process of exploiting genomic information to isolate, characterize and experimentally verify products of potentially useful genes | (Corre and Challis, 2010) |
| Prebiotics | A substrate that is selectively utilized by host microorganisms conferring a health benefit | (Gibson et al., 2017) |
| Probiotics | Live microorganisms which when consumed in adequate amounts confer a health benefit on the host | (Food and Agriculture Organization and World Health Organization Expert Consultation, 2001) |