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Related Concept Videos

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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Processing and storage methods affect oral and gut microbiome composition.

Dorothy K Superdock1, Wei Zhang2, Angela C Poole1

  • 1Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States.

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|October 19, 2023
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Summary
This summary is machine-generated.

Microbiome sample storage and processing significantly impact results. Lyophilized fecal and fresh saliva samples showed higher diversity, influencing microbial composition and study comparisons.

Keywords:
dentalfreeze driedfrozengutliquid nitrogenlyophilizedmicrobiomesaliva

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Microbiome studies rely on accurate microbial community profiling.
  • Inconsistent sample handling can introduce bias in microbiome data.
  • Standardized protocols are crucial for reliable and comparable results.

Purpose of the Study:

  • To evaluate the impact of different storage and processing methods on microbiome composition.
  • To assess how sample handling affects microbial diversity and community structure.
  • To provide guidance for optimizing microbiome sample analysis.

Main Methods:

  • Collected fecal, saliva, and dental swab samples from 10 individuals.
  • Assessed four fecal storage/processing methods and compared saliva/dental samples to fresh controls.
  • Utilized 16S rRNA gene sequencing to analyze microbial community diversity and composition.

Main Results:

  • Lyophilized fecal, fresh whole saliva, and thawed dental supernatant showed highest alpha diversity.
  • Lyophilized fecal samples exhibited increased Archaea prevalence and a higher Firmicutes/Bacteroidetes ratio.
  • Differences in ASV abundance were observed across various storage and processing conditions.

Conclusions:

  • Storage and processing methods significantly influence microbiome analysis outcomes.
  • Lyophilization for fecal samples and fresh/supernatant fractions for oral samples are recommended.
  • Standardizing sample handling is critical to avoid confounding factors in microbiome research.