Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Biosynthesis in Bacteria01:24

Biosynthesis in Bacteria

411
Biosynthesis in bacteria is a fundamental anabolic process that generates essential macromolecules, including proteins, nucleic acids, lipids, and polysaccharides. These macromolecules are critical for cellular growth, replication, and function. The process is tightly regulated and energetically linked to catabolic pathways to ensure optimal resource utilization.Biosynthetic pathways begin with precursor metabolites such as pyruvate, acetyl-CoA, and glucose-6-phosphate derived from glycolysis,...
411
Microbial Nutrition01:28

Microbial Nutrition

816
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...
816
Other Unique Bacteria01:18

Other Unique Bacteria

288
Magnetic bacteria exhibit a directed movement called magnetotaxis, driven by structures called magnetosomes. These magnetosomes consist of chains of magnetic particles made of either magnetite (Fe₃O₄) or greigite (Fe₃S₄) and are organized in a linear conformation by a protein scaffold within invaginations of the cell membrane. The bacteria align along the north–south magnetic field lines, much like a compass needle. They are typically microaerophilic or anaerobic...
288
Ecological Niches02:02

Ecological Niches

25.7K
All organisms have a position within an ecosystem. The complete set of living and nonliving factors—including food resources, climate, and terrain—that define the position of a given organism are collectively referred to as the organism’s ecological niche.
25.7K
Bacterial Phylum Planctomycetes01:26

Bacterial Phylum Planctomycetes

279
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...
279
Bacterial Phylum Bacteroidota01:26

Bacterial Phylum Bacteroidota

402
The phylum Bacteroidota includes over 700 species classified into four primary orders: Bacteroidales, Cytophagales, Flavobacteriales, and Sphingobacteriales. These gram-negative, non-sporulating rods exhibit saccharolytic capabilities and can be aerobic or fermentative, encompassing obligate aerobes, facultative aerobes, and obligate anaerobes. Many species display gliding motility, though some are nonmotile or use flagella. The genus Bacteroides is well-studied due to its significant role in...
402

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Generalized dynamics of cross-feeding bacteria.

Journal of the Royal Society, Interface·2026
Same author

Functional motifs in food webs and networks.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Behavioral plasticity and the valence of indirect interactions.

Ecology·2025
Same author

Unsupervised pattern and outlier detection for pedestrian trajectories using diffusion maps.

Physica A·2025
Same author

Phase and gain stability for adaptive dynamical networks.

Chaos (Woodbury, N.Y.)·2025
Same author

Cross-feeding creates tipping points in microbiome diversity.

Proceedings of the National Academy of Sciences of the United States of America·2025

Related Experiment Video

Updated: Dec 7, 2025

Monitoring Spatial Segregation in Surface Colonizing Microbial Populations
07:40

Monitoring Spatial Segregation in Surface Colonizing Microbial Populations

Published on: October 29, 2016

11.4K

Mapping the bacterial metabolic niche space.

Ashkaan K Fahimipour1,2, Thilo Gross3,4,5,6

  • 1University of California Davis, Department of Computer Science, 1 Shields Ave, Davis, CA, 95616, USA. ashkaan.fahimipour@noaa.gov.

Nature Communications
|September 28, 2020
PubMed
Summary

Bacterial genomes reveal a metabolic niche space, organizing diverse lifestyles across habitats. This functional map helps understand microbial communities and their ecological roles.

More Related Videos

Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy
07:00

Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy

Published on: October 4, 2024

945
Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.8K

Related Experiment Videos

Last Updated: Dec 7, 2025

Monitoring Spatial Segregation in Surface Colonizing Microbial Populations
07:40

Monitoring Spatial Segregation in Surface Colonizing Microbial Populations

Published on: October 29, 2016

11.4K
Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy
07:00

Microbiota of Attine Ants' Gardens: Visualizing a Microbial Landscape by Scanning Electron Microscopy

Published on: October 4, 2024

945
Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

46.8K

Area of Science:

  • Microbial Ecology
  • Systems Biology
  • Bioinformatics

Background:

  • Increasing availability of bacterial genomes necessitates new approaches to understand microbial lifestyles and ecological roles.
  • The ecological niche is a fundamental concept defining a population's capabilities, persistence, and environmental impact.
  • Understanding the diversity of potential niches is crucial for ecological synthesis.

Purpose of the Study:

  • To map the space of metabolic networks for thousands of bacterial genera.
  • To identify patterns and structures within bacterial metabolic capabilities.
  • To relate metabolic strategies to ecological niches and habitat types.

Main Methods:

  • Utilized manifold learning techniques to analyze metabolic networks.
  • Represented metabolic networks as points in a high-dimensional space.
  • Applied clustering and dimensionality reduction to reveal the structure of metabolic niche space.

Main Results:

  • Identified a metabolic niche space characterized by discrete clusters and branching manifolds.
  • These structures represent distinct bacterial lifestyle strategies across various habitats and hosts.
  • Demonstrated that microbial communities from similar ecosystems occupy characteristic regions within this functional space.

Conclusions:

  • The metabolic niche space provides a framework for understanding bacterial diversity and ecological adaptation.
  • This approach allows for the coarse-graining of microbiomes based on functional niches.
  • The findings offer insights into how bacteria fill ecological niches in different environments.