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Related Concept Videos

Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Bacterial Phylum Proteobacteria01:26

Bacterial Phylum Proteobacteria

Proteobacteria, one of the largest and most diverse bacterial phyla, encompasses a wide range of Gram-negative bacteria distinguished by their outer membrane composed of lipopolysaccharides. These microorganisms exhibit various metabolic capabilities, including phototrophy, chemolithotrophy, and heterotrophy, and thrive in diverse environments from soil to aquatic systems and host-associated niches. The phylum is divided into six classes: Alphaproteobacteria, Betaproteobacteria,...
Phylogenetic Species Concept in Microbiology01:22

Phylogenetic Species Concept in Microbiology

The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...
Bacterial Phylum Tenericutes01:24

Bacterial Phylum Tenericutes

The phylum Tenericutes, which includes the single class Mollicutes, comprises bacteria that lack cell walls. The term "Mollicutes" derives from the Latin word mollis, meaning "soft." These organisms are among the smallest known and are commonly referred to as mycoplasmas due to the prominence of the genus Mycoplasma, which includes well-known human pathogens. Despite their inability to stain gram-positively (a result of their lack of cell walls), mycoplasmas are phylogenetically related to the...
Microbial Classification System01:24

Microbial Classification System

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...
Bacterial Phylum Planctomycetes01:26

Bacterial Phylum Planctomycetes

Planctomycetes are a group of morphologically distinct bacteria predominantly classified into two orders: Planctomycetales and Brocadiales. These gram-negative bacteria exhibit unique features, including division by budding and the presence of stalks or appendages. Their cells are often found in rosette arrangements, and they are notable for possessing an S-layer in their cell envelope, which is relatively uncommon among bacteria. Additionally, Planctomycetes frequently exhibit intracellular...

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

A phylum-level bacterial phylogenetic marker database.

Zhang Wang1, Martin Wu

  • 1Department of Biology, University of Virginia, USA.

Molecular Biology and Evolution
|March 23, 2013
PubMed
Summary
This summary is machine-generated.

Researchers developed a new bacterial phylogenetic marker database for evolutionary and ecological studies. This database enhances the accuracy of bacterial phylogenetics and metagenomic analyses, offering a valuable resource for scientific research.

Keywords:
bacterial systematicsbacterial tree of lifebioinformaticsmetagenomicsphylogenomicsphylotyping

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A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Genome-level molecular phylogenetic analyses are crucial for understanding bacterial evolution and ecology.
  • Existing methods face challenges in resolution and robustness for large-scale bacterial studies.

Purpose of the Study:

  • To construct a robust, phylum-level bacterial phylogenetic marker database.
  • To improve the accuracy and power of bacterial phylogenetics and metagenomic analyses.

Main Methods:

  • Surveyed complete bacterial genomes to identify widely distributed single-copy genes within each of the 20 bacterial phyla.
  • Constructed phylum trees using the novel marker set and compared them to trees based on universal markers.
  • Integrated the database into an automated phylogenomic inference application (Phyla-AMPHORA).

Main Results:

  • The novel marker database yielded highly resolved and robust bacterial phylum trees.
  • Phylum trees generated were more reliable than those based on 31 universal bacterial marker genes.
  • The database significantly enhanced the power of metagenomic phylotyping, as demonstrated with the Global Ocean Sampling data.

Conclusions:

  • The developed phylum-level bacterial phylogenetic marker database offers a significant advancement for bacterial systematics and phylogenetics.
  • The publicly available Phyla-AMPHORA application provides a centralized, powerful resource for researchers.
  • This resource is expected to have broad applicability in diverse bacterial evolutionary and metagenomic studies.