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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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Fermentation is a crucial anaerobic metabolic process that enables microbes to derive energy from sugar without relying on oxygen or an electron transport chain. This process is fundamental to various biological and industrial applications and is classified based on the metabolic products generated.Role of Pyruvate in FermentationPyruvate and its derivatives serve as key electron acceptors in fermentative pathways. The oxidation of NADH to regenerate NAD+ is essential for the continuation of...
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Organisms exhibit remarkable metabolic diversity, categorized based on how they acquire energy and carbon. These strategies enable survival in various ecological niches and are essential for maintaining energy flow and nutrient cycling within ecosystems.Energy and Carbon SourcesOrganisms are classified as phototrophs or chemotrophs based on energy acquisition. Phototrophs use light as their energy source, while chemotrophs rely on oxidizing chemical compounds. Further differentiation arises...
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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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Microbial growth media are essential tools in microbiology, providing the nutrients and conditions necessary to cultivate and study microorganisms. These media are categorized by their composition, consistency, and functional roles, enabling researchers to investigate microbial physiology, behavior, and interactions.Types and Consistencies of Growth MediaGrowth media can be solid, liquid, or semisolid. Solid media, often agar-based, allow visible colony growth for isolation and enumeration.
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Microbial growth control refers to various methods employed to inhibit, reduce, or eliminate microorganisms to ensure safety and hygiene across different settings. These methods are categorized based on the target environment and the level of microbial control required.Biocides are versatile agents designed to control microorganisms by either inhibiting their growth or outright killing them. These agents work through various physical, chemical, mechanical, or biological mechanisms. The...
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Pyrosequencing for Microbial Identification and Characterization
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A primer on microbial bioinformatics for nonbioinformaticians.

J A Carriço1, M Rossi2, J Moran-Gilad3

  • 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.

Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases
|January 9, 2018
PubMed
Summary

Microbial bioinformatics helps analyze high-throughput sequencing data for disease surveillance. This review explains processes like read mapping and de novo assembly for non-bioinformaticians.

Keywords:
Bioinformatics softwareGenomic epidemiologyHigh-throughput sequencingMicrobial bioinformaticsMicrobial typing

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Area of Science:

  • Microbial bioinformatics
  • Genomic data analysis
  • High-throughput sequencing

Background:

  • High-throughput sequencing generates vast amounts of data, posing analysis challenges.
  • The complexity of microbial bioinformatics hinders non-expert understanding.
  • Rapid technological advancements require continuous adaptation.

Purpose of the Study:

  • To provide non-bioinformaticians with an understanding of microbial bioinformatic processes.
  • To clarify the journey from raw sequencing data to actionable insights.
  • To demystify complex bioinformatic workflows.

Main Methods:

  • Review of personal experiences with software and analytical strategies.
  • Explanation of bioinformatic processes for clinical and epidemiologic contexts.
  • Comparison of read mapping and de novo assembly strategies.

Main Results:

  • Detailed explanation of transforming raw sequencing reads into meaningful data.
  • Discussion of the advantages and limitations of read mapping versus de novo assembly.
  • Overview of key analytical methodologies and frequently used free software.

Conclusions:

  • High-throughput sequencing revolutionizes outbreak investigation and surveillance.
  • Managing and analyzing large genomic datasets presents new challenges.
  • Expertise in microbial bioinformatics is crucial for leveraging sequencing technologies effectively.