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Related Concept Videos

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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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The shearing strain represents a cubic element's angular change when subjected to shearing stress. This type of stress can transform a cube into an oblique parallelepiped without influencing normal strains. The cubic element experiences a significant transformation when exposed solely to shearing stress. Its shape alters from a perfect cube into a rhomboid, clearly demonstrating the effect of shearing strain. The degree of this strain is considered positive if it reduces the angle between the...
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Related Experiment Video

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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Profiling microbial strains in urban environments using metagenomic sequencing data.

Moreno Zolfo1, Francesco Asnicar1, Paolo Manghi1

  • 1Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy.

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|May 11, 2018
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Summary

Advanced metagenomic profiling tools successfully characterized urban microbiomes, enabling pathogen surveillance and revealing higher microbial strain diversity than in human samples. This research supports high-resolution analysis of city-associated microbial communities.

Keywords:
MetagenomicsStrain-level microbial genomicsUrban microbiome

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Environmental Science

Background:

  • Shotgun metagenomics extensively characterizes microbial communities in human and natural environments.
  • Urban microbiomes are crucial for human health but less studied than others.
  • Recent computational methods for metagenome profiling have not been applied to urban settings.

Purpose of the Study:

  • To test available metagenomic profiling tools on urban metagenomes.
  • To characterize urban organisms at single-strain resolution.
  • To discuss biological insights from high-resolution urban microbiome analysis.

Main Methods:

  • Applied MetaMLST, StrainPhlAn, and PanPhlAn to 1614 urban metagenomes.
  • Identified known sequence-types and inferred phylogenetic structures of microbial strains.
  • Utilized SNV-based and pangenome-based profiling for evolutionary and genetic analyses.

Main Results:

  • Identified 121 sequence-types from 15 clinically relevant species, including Acinetobacter strains.
  • Observed higher strain-level heterogeneity in urban environments compared to human microbiomes.
  • Demonstrated that SNV and pangenome profiling offer complementary insights into microbial evolution and virulence factors.

Conclusions:

  • Strain-level metagenomic analysis methods are effective for urban microbiomes.
  • Opportunistic pathogens can be tracked and monitored in urban environments.
  • This study provides a foundation for high-resolution microbiome analysis in urban and transportation settings.