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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Lewis Acids and Bases02:33

Lewis Acids and Bases

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In 1923, G. N. Lewis proposed a generalized definition of acid-base behavior in which acids and bases are identified by their ability to accept or to donate a pair of electrons and form a coordinate covalent bond.
A coordinate covalent bond (or dative bond) occurs when one of the atoms in the bond provides both bonding electrons. For example, a coordinate covalent bond occurs when a water molecule combines with a hydrogen ion to form a hydronium ion. A coordinate covalent bond also results when...
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Weak Base Solutions03:21

Weak Base Solutions

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Some compounds produce hydroxide ions when dissolved by chemically reacting with water molecules. In all cases, these compounds react only partially and so are classified as weak bases. These types of compounds are also abundant in nature and important commodities in various technologies. For example, global production of the weak base ammonia is typically well over 100 metric tons annually, being widely used as an agricultural fertilizer, a raw material for chemical synthesis of other...
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Ions as Acids and Bases02:54

Ions as Acids and Bases

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Salts with Acidic Ions
Salts are ionic compounds composed of cations and anions, either of which may be capable of undergoing an acid or base ionization reaction with water. Aqueous salt solutions, therefore, may be acidic, basic, or neutral, depending on the relative acid-base strengths of the salt’s constituent ions. For example, dissolving the ammonium chloride in water results in its dissociation, as described by the equation:
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Base Excision Repair01:54

Base Excision Repair

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
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DNA Base Pairing02:27

DNA Base Pairing

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Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
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Related Experiment Video

Updated: Feb 1, 2026

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

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Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree.

Guanghong Zuo1, Ji Qi2, Bailin Hao1

  • 1T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.

Genomics, Proteomics & Bioinformatics
|December 15, 2018
PubMed
Summary
This summary is machine-generated.

Whole-genome analysis reveals limitations of 16S rRNA sequencing for prokaryotic taxonomy. Genome-based phylogeny offers a more accurate and objective approach to classifying species and resolving genus ambiguity in bacterial classification.

Keywords:
16S rRNA sequenceArchaea and bacteria taxonomyCVTreePhylogenyWhole-genome sequence

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Taxonomy

Background:

  • 16S rRNA gene sequencing is a common method for prokaryotic classification.
  • However, its low resolution can lead to inaccurate phylogenetic placements at the species level.
  • This ambiguity impacts the clear demarcation of genera within bacterial families.

Purpose of the Study:

  • To investigate the limitations of 16S rRNA sequencing in prokaryotic taxonomy.
  • To compare 16S rRNA-based phylogenies with genome-based phylogenies.
  • To establish the utility of whole-genome data for constructing a natural and objective prokaryotic taxonomy.

Main Methods:

  • Phylogenetic trees were reconstructed for over ten thousand prokaryotic genomes.
  • The CVTree method, utilizing whole-genome information, was employed for phylogenetic analysis.
  • Comparisons were made between 16S rRNA-based trees and genome-based trees.

Main Results:

  • 16S rRNA-based phylogenetic trees frequently show polyphyletic placements of closely related species.
  • Genome-based phylogeny using CVTree resolves many genera that appear polyphyletic in 16S rRNA trees into monophyletic clusters.
  • This highlights the superior resolution of whole-genome data.

Conclusions:

  • 16S rRNA sequencing has significant limitations for species-level resolution in prokaryotes.
  • Genome-based phylogeny provides a more robust and accurate framework for prokaryotic taxonomy.
  • As whole-genome sequencing becomes widespread, it is poised to become the definitive method for prokaryotic classification.