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Related Concept Videos

Bacterial Phylum Spirochaetes01:30

Bacterial Phylum Spirochaetes

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Spirochetes, unique bacteria in the phylum Spirochaetes, are gram-negative, motile, tightly coiled, slender, and flexible. They inhabit aquatic sediments and animals, with some causing diseases like syphilis. Spirochetes are classified into eight genera based on habitat, pathogenicity, phylogeny, and characteristics.Their distinctive motility arises from endoflagella, located within the cell’s periplasm. These endoflagella anchor at the cell poles and extend along the cell length, encased...
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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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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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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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Microorganisms play a fundamental role in vaccine development, gene therapy, and therapeutic production. Their biological properties are harnessed to advance medicine and public health. Beyond immunization, microorganisms contribute to gut health, antibiotic synthesis, and genetic disease treatment.Live Attenuated and Inactivated VaccinesLive attenuated vaccines, such as the measles, mumps, and rubella (MMR) vaccine, utilize weakened forms of pathogens to closely resemble natural infections.
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Microorganisms play a pivotal role in maintaining ecosystem balance by recycling essential elements such as carbon, nitrogen, and phosphorus, as well as supporting processes like bioremediation, wastewater treatment, and biofuel production.Microbes in Elemental CyclesIn the carbon cycle, microorganisms decompose organic matter, releasing carbon dioxide via aerobic respiration. This carbon dioxide is subsequently used by photosynthetic organisms to synthesize organic compounds, closing the...
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Related Experiment Video

Updated: Jul 12, 2025

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
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SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.

Thomas S B Schmidt1, Anthony Fullam1, Pamela Ferretti1

  • 1Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

Nucleic Acids Research
|October 28, 2023
PubMed
Summary
This summary is machine-generated.

SPIRE is a new resource integrating microbial data from nearly 100,000 metagenomic samples. It provides access to millions of microbial genomes and functional annotations, enhancing microbiome research.

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Related Experiment Videos

Last Updated: Jul 12, 2025

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomic data is rapidly accumulating but often fragmented across different databases and formats.
  • Siloed data hinders comprehensive analysis of microbial diversity and function across various environments.

Purpose of the Study:

  • To present SPIRE, a Searchable Planetary-scale mIcrobiome REsource, integrating diverse metagenomic data.
  • To provide a unified platform for exploring microbial communities across habitats, geography, and phylogeny.

Main Methods:

  • Integration of 99,146 metagenomic samples from 739 studies with manual curation.
  • Processing 16 Tbp of metagenomic data to generate 1.16 million medium/high-quality metagenome-assembled genomes (MAGs).
  • Development of novel species-level clusters and integration with custom mOTUs database for taxonomic profiling.

Main Results:

  • SPIRE resource created, comprising 35 billion protein sequences and 1.16 million MAGs.
  • 92,134 novel species-level clusters identified, many unclassified by current tools.
  • Resource offers functional annotations and crosslinks to biological databases.

Conclusions:

  • SPIRE significantly enhances accessibility and searchability of planetary-scale microbiome data.
  • Facilitates deeper understanding of microbial diversity, function, and evolution across diverse ecosystems.
  • Provides a valuable, integrated resource for the scientific community via http://spire.embl.de.