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Related Concept Videos

Microbial Morphologies01:29

Microbial Morphologies

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Bacterial and archaeal cells exhibit remarkable diversity in shape and structure, critical in their adaptability and functionality. Among bacteria, the most commonly observed shapes include cocci and bacilli. Cocci are spherical and may exist singly or in groupings such as pairs (diplococci), chains (streptococci), clusters (staphylococci), or tetrads. Bacilli, in contrast, are rod-shaped and can also occur as single cells, in pairs, or chains, depending on their environmental and genetic...
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Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
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Related Experiment Video

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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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animalcules: interactive microbiome analytics and visualization in R.

Yue Zhao1,2, Anthony Federico1,2, Tyler Faits1,2

  • 1Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.

Microbiome
|March 29, 2021
PubMed
Summary
This summary is machine-generated.

animalcules is a new R package for microbiome analysis, offering interactive tools for 16S rRNA, shotgun metagenomics, and metatranscriptomics data. This toolkit aids researchers in analyzing complex microbial community data for health and disease insights.

Keywords:
Biomarker identificationInteractive toolkitMicrobiome analysisVisualization

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Area of Science:

  • Microbiome research
  • Bioinformatics
  • Computational biology

Background:

  • Human-associated microbial communities are crucial for health and disease.
  • Advances in sequencing technologies allow high-resolution microbiome studies.
  • Analyzing and visualizing large microbiome datasets pose significant challenges.

Purpose of the Study:

  • To develop an accessible, interactive toolkit for analyzing diverse microbiome data.
  • To integrate novel and existing analytical methods, visualizations, and machine learning models.
  • To address the challenges in microbiome data analysis and visualization.

Main Methods:

  • Development of the 'animalcules' R package.
  • Integration of analyses for 16S rRNA sequencing, shotgun DNA metagenomics, and RNA-based metatranscriptomics.
  • Provision of both a command-line R package and an interactive R Shiny interface.

Main Results:

  • animalcules offers traditional analyses (alpha/beta diversity, differential abundance) and biomarker identification.
  • The toolkit includes interactive, dynamic figures for enhanced data exploration and insight discovery.
  • It supports the analysis of 16S rRNA, shotgun metagenomics, and metatranscriptomics data.

Conclusions:

  • animalcules is the first R package to support comprehensive analysis of 16S rRNA, shotgun metagenomics, and metatranscriptomics data.
  • It provides an interactive platform for microbiome data analysis via R Shiny or command-line functions.
  • The package is available for download from GitHub and Bioconductor.