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Protists are diverse eukaryotic microorganisms that lack the specialized tissues of plants and animals and the chitinous cell walls of fungi. Their early divergence within Eukarya resulted in structural, functional, and ecological diversity. They are classified into supergroups such as Archaeplastida, Excavata, Amoebozoa, Rhizaria, Alveolata, and Stramenopiles, determined through genetic analysis and structural similarities.Structural and Functional AdaptationsProtists have various adaptations...
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Alveolates are a group of organisms recognized by the presence of alveoli, which are cytoplasmic sacs located beneath the cell membrane. While their function remains uncertain, alveoli may help regulate water balance by controlling how much water enters and leaves the cell. In dinoflagellates, these structures may serve as armor plates. There are three major types of alveolates: ciliates, which move using cilia; dinoflagellates, which use flagella for movement; and apicomplexans, which are...
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Excavata is a diverse group of protists that includes both chemoorganotrophic and phototrophic species, with some thriving in anaerobic environments. Among the key groups within Excavata are diplomonads and parabasalids, which are flagellated protists that lack mitochondria and chloroplasts. These microorganisms typically inhabit anoxic environments, such as the intestines of animals, where they exist either symbiotically or as parasites, relying on fermentation for energy production. Some...
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Amoebozoa represent a diverse group of terrestrial and aquatic protists that utilize lobe-shaped pseudopodia for locomotion and feeding. This characteristic differentiates them from the Rhizaria, which possess threadlike pseudopodia. The primary classifications within Amoebozoa include gymnamoebas, entamoebas, and the plasmodial and cellular slime molds. Phylogenetic evidence indicates that Amoebozoa diverged from a lineage that ultimately gave rise to fungi and animals.Gymnamoebas and...
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Rhizaria are a diverse group of unicellular protists characterized by their threadlike cytoplasmic extensions known as pseudopodia. These structures aid in both locomotion and feeding, giving Rhizaria an amoeboid appearance. Their amoeboid morphology once led to taxonomic confusion, but molecular phylogenetics has clarified their evolutionary placement and emphasized their shared use of pseudopodia despite divergent lineages.This clade comprises diverse lineages such as Chlorarachniophyta,...
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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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Database Release: PPSDB, a Linked Open Data Knowledge Base for Protist-Prokaryote Symbioses.

Brandon K B Seah1

  • 1Thünen Institute for Biodiversity, Braunschweig, Germany.

The Journal of Eukaryotic Microbiology
|October 10, 2025
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Summary

A new Protist-Prokaryote Symbiosis Database (PPSDB) organizes knowledge on microbial eukaryote and prokaryote interactions. This structured database aids researchers by integrating diverse data and enabling advanced queries on symbiosis.

Keywords:
FAIRSPARQLWikibase.cloudknowledge graphsemantic web

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Area of Science:

  • Microbiology
  • Eukaryotic Biology
  • Symbiosis Research

Background:

  • Symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) are crucial for ecological and evolutionary processes.
  • A comprehensive overview of the diversity and literature on these interactions is challenging to maintain.

Purpose of the Study:

  • To present the Protist-Prokaryote Symbiosis Database (PPSDB), a manually curated knowledge base.
  • To address challenges in managing and accessing data on protist-prokaryote symbiosis.

Main Methods:

  • Manual curation of 1146 interaction statements from 443 publications.
  • Annotation of biological taxonomy, anatomical localization, and analytical methods.
  • Mapping data to external databases and ontologies (e.g., Wikidata, NCBI Taxonomy, Gene Ontology).
  • Development of a data model to handle incomplete information and inconsistent taxon concepts.
  • Utilizing a Wikibase software platform for extensibility and programmatic access.

Main Results:

  • The PPSDB contains 1146 curated interaction statements.
  • The database integrates taxonomic, localization, and methodological data.
  • The data model and platform are designed to handle data inconsistencies and are extensible.
  • The database enables programmatic access and semantic queries.

Conclusions:

  • The PPSDB provides a structured, queryable knowledge base for protist-prokaryote symbiosis.
  • The database design offers a model for similar data integration projects.
  • PPSDB facilitates a deeper understanding of microbial symbiotic interactions.