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Related Concept Videos

Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
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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Related Experiment Video

Updated: Jun 26, 2026

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
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Identifying optimal bioinformatics protocols for aerosol microbial community data.

Katie Miaow1, Donnabella Lacap-Bugler1, Hannah L Buckley1

  • 1School of Science, Auckland University of Technology, Auckland, Auckland, New Zealand.

Peerj
|October 27, 2021
PubMed
Summary
This summary is machine-generated.

This study optimized bioinformatics pipelines for analyzing aerial microbial DNA, improving data quality and taxonomic assignment for bacteria and fungi. The findings enhance our understanding of microbial dispersal and ecosystem connectivity.

Keywords:
BacteriaBioaerosolBioinformaticsDada2DecontaminationFungiMicrobial aerosolMicrobial ecologyNGSUSEARCH

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Ecology

Background:

  • Understanding microbial dispersal is crucial for predicting ecosystem changes, especially in a warming world.
  • Aerial microbial dispersal via bioaerosols is poorly understood, yet these particles can harbor pathogens.
  • Molecular methods and bioinformatics are essential for characterizing microbial communities due to difficulties in culturing most microbes.

Purpose of the Study:

  • To develop and validate an optimal bioinformatics pipeline for processing microbial bioaerosol sequencing data.
  • To systematically compare different bioinformatics tools and databases for maximizing data quantity and quality.
  • To provide a reproducible framework for analyzing microbial communities in bioaerosols.

Main Methods:

  • Comparison of two amplicon sequence variant (ASV) inference tools: Dada2 and USEARCH.
  • Evaluation of taxonomic assignment using two databases and development of a combined approach.
  • Assessment of decontamination methods, specifically "decontam" and "microDecon".

Main Results:

  • USEARCH demonstrated higher consistency and read counts compared to Dada2 for ASV generation.
  • A combined taxonomic database approach increased assignment rates by 12-15% (77% for bacteria, 47% for fungi).
  • "microDecon" was selected for its effective background contamination removal in bioaerosol samples.

Conclusions:

  • A systematic, scorecard-based approach can determine the optimal bioinformatics pipeline for microbial bioaerosol data.
  • Optimized pipelines are essential for accurate characterization of aerial microbial communities.
  • This research provides a foundation for future studies on microbial dispersal and its ecological implications.