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Related Concept Videos

Genomics02:02

Genomics

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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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From Sample to Multi-Omics Conclusions in under 48 Hours.

Robert A Quinn1, Jose A Navas-Molina2, Embriette R Hyde3

  • 1Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, California, USA; Department of Pharmacology, University of California, San Diego, San Diego, California, USA.

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|November 9, 2016
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Summary
This summary is machine-generated.

This study developed a rapid, integrated multi-omics pipeline for analyzing human and environmental samples in under 48 hours. Home food fermentation impacts microbial and chemical ecology, increasing gut diversity and transferring food metabolites to skin and stool.

Keywords:
16S rRNAfermented foodmetabolomemicrobiomemolecular networkingrapid response

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Area of Science:

  • Microbiology
  • Metabolomics
  • Bioinformatics

Background:

  • Multi-omics methods offer comprehensive insights into microbial communities but are too slow for routine clinical or industrial use.
  • The time-consuming nature of omics data generation and analysis hinders their application in time-sensitive fields like clinical microbiology.

Purpose of the Study:

  • To develop and apply a novel, integrated multi-omics pipeline capable of analyzing human and environmental samples within 48 hours.
  • To investigate the impact of home food fermentation on the microbial and chemical ecology of human subjects and their household environments.

Main Methods:

  • Integrated analysis of 16S rRNA gene sequencing, inferred gene function (PICRUSt), and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics.
  • Utilized Qiita and GNPS pipelines for data processing.
  • Collected human (skin, feces, oral) and fermented food samples from individuals practicing home food fermentation.

Main Results:

  • The developed pipeline analyzed samples in under 48 hours, matching classic culturing timeframes.
  • Home food fermentation altered microbial and chemical ecologies, with fermented foods influencing household surface microbes.
  • Consumption of fermented foods increased gut microbial diversity and led to the detection of food-derived metabolites in skin and stool samples.

Conclusions:

  • This study demonstrates the feasibility of rapid multi-omics analysis in clinically relevant time frames.
  • The findings highlight the interconnectedness of food, human, and environmental microbiomes and metabolomes.
  • The developed pipeline sets a precedent for implementing advanced omics techniques in clinical medicine and industrial microbiology.