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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Related Experiment Video

Updated: Dec 7, 2025

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
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Microbial high throughput phenomics: The potential of an irreplaceable omics.

Marta Acin-Albiac1, Pasquale Filannino2, Marco Gobbetti1

  • 1Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy.

Computational and Structural Biotechnology Journal
|September 30, 2020
PubMed
Summary

Phenomics, the study of phenotypes, offers a powerful way to understand microbial functions and their genetic basis. This review explores phenomics applications, particularly with the Omnilog platform for lactic acid bacteria (LAB).

Keywords:
Lactic acid bacteriaMicrobial metabolismOmnilog data analysisPhenomicsPhenotype microarray

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Area of Science:

  • Microbiology
  • Genomics
  • Systems Biology

Background:

  • Phenotype-genotype relationships are crucial for understanding microbial function under environmental pressures.
  • Phenomics, the study of the complete set of phenotypes, has the potential to revolutionize functional genomics by linking observable traits to genetic information.
  • Understanding microbial consortia assembly and functionality is enhanced by phenomic data.

Purpose of the Study:

  • To review the development and applications of phenomics in microbial studies.
  • To explore the use of the Omnilog platform for phenomic analysis, focusing on lactic acid bacteria (LAB) metabolic traits.
  • To introduce novel phenomic approaches and data analysis strategies.

Main Methods:

  • Review of existing literature on phenomics and functional genomics.
  • Application and revision of the Omnilog platform for microbial phenotyping.
  • Introduction of 'phenotype switching' for bacterial physiology insights.
  • Overview of data management and analysis methodologies.

Main Results:

  • Phenomics provides a framework to understand microbial consortia assembly and function.
  • The Omnilog platform is a valuable tool for studying LAB metabolic traits in food processing.
  • 'Phenotype switching' offers new insights into bacterial physiology.
  • A critical analysis of current phenomic data analysis pipelines was performed.

Conclusions:

  • Phenomics is an emerging omics approach with significant potential in microbiology.
  • The proposed R pipeline offers automated analysis of Omnilog data, integrating novel concepts.
  • Further development and application of phenomic strategies are essential for advancing microbial functional genomics.