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Related Concept Videos

Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...

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Related Experiment Video

Updated: May 12, 2026

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
08:05

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

Toward reproducible pig gut microbiome profiling through standardized methodologies.

Timur Yergaliyev1,2, Samuel O Enokela1,2, Gabi Eberhardt1,2

  • 1Hohenheim Center for Livestock Microbiome Research (HoLMiR), University of Hohenheim, 70599 Stuttgart, Germany.

ISME Communications
|May 11, 2026
PubMed
Summary

Choosing the right DNA extraction kit is crucial for accurate pig microbiome studies. Different kits significantly impact 16S rRNA gene sequencing results, while shotgun metagenomics offers more robust data, though genome recovery varies by kit.

Keywords:
16S rRNA gene amplicon sequencingmetagenomemicrobiomepigs

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Area of Science:

  • Microbiology
  • Genomics
  • Animal Science

Background:

  • Reproducible microbiome profiling is critical for understanding host health.
  • Standardized DNA extraction protocols are lacking in pig microbiome research.
  • Methodological variations hinder cross-study comparability.

Purpose of the Study:

  • To benchmark the influence of 12 DNA extraction kits on pig fecal microbiome analysis.
  • To compare the impact of extraction kits on 16S rRNA gene amplicon sequencing and shotgun metagenomics.
  • To establish a framework for evaluating DNA extraction methods in animal microbiome research.

Main Methods:

  • Benchmarking 12 DNA extraction kits using pig fecal samples.
  • Analyzing outcomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.
  • Utilizing spike-in controls, taxonomic resolution, and metagenome-assembled genomes for evaluation.

Main Results:

  • Extraction kit choice significantly biases 16S rRNA gene datasets (DNA yield, diversity, composition, spike-in recovery).
  • Shotgun metagenomics shows greater robustness in taxonomic and functional profiling compared to 16S rRNA gene sequencing.
  • Kit selection impacts Gram-positive vs. Gram-negative bacterial recovery, affecting biological interpretation.
  • Metagenome-assembled genome recovery quality and quantity are dependent on the extraction kit.

Conclusions:

  • 16S rRNA gene amplicon sequencing is highly susceptible to extraction-driven artifacts, compromising reproducibility.
  • Shotgun metagenomics is comparatively robust but still influenced by extraction methods regarding genome recovery.
  • Standardized DNA extraction protocols are urgently needed for reproducible and comparable pig microbiome studies.