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Related Concept Videos

Modern Molecular Taxonomy01:29

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
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MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data.

D R Finn1,2, J Yu3,4, Z E Ilhan4,5

  • 1School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Australia.

FEMS Microbiology Ecology
|June 27, 2020
PubMed
Summary
This summary is machine-generated.

Microbiologists can now quantitatively assess microbial niches using new ecological indices. These tools help identify specialists and generalists in complex environments like the human gut and soil crusts.

Keywords:
community ecologyniche theoryproportional similarity index

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Area of Science:

  • Ecology
  • Microbiology
  • Bioinformatics

Background:

  • Niche is a core ecological concept defining taxon distribution based on environmental needs.
  • Quantitative methods for microbial niche analysis are currently lacking.
  • Understanding microbial niches is crucial for fields from medicine to environmental science.

Purpose of the Study:

  • To test and validate quantitative approaches for analyzing microbial niche breadth and overlap in amplicon sequencing data.
  • To identify generalists, specialists, and environmentally dependent taxa within microbial communities.
  • To provide accessible tools for microbial ecological research.

Main Methods:

  • Tested four distinct quantitative indices for niche analysis.
  • Validated indices using in silico datasets with known conditions.
  • Applied indices to real-world datasets from human gut and desert soil crust microbiomes.
  • Incorporated a limit of quantification based on species rank to refine specialist identification.

Main Results:

  • All tested approaches successfully identified predefined conditions in in silico data.
  • A rank-based limit of quantification improved the accuracy of specialist classification.
  • Quantitative evidence found specialists (e.g., Bacilli, Gammaproteobacteria) enriched in the human gut post-bariatric surgery.
  • Differential niche distributions of cyanobacteria were characterized concerning precipitation in biocrusts.

Conclusions:

  • The developed quantitative approaches are effective tools for microbial niche assessment.
  • These methods enable quantitative analysis of microbial environment-taxon and taxon-taxon relationships.
  • The R package "MicroNiche" is now available to facilitate these analyses in ecological research.