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

Two-Dimensional Microscopy in Microbiology01:29

Two-Dimensional Microscopy in Microbiology

1.8K
Two-dimensional (2D) microscopy encompasses a range of optical techniques that capture images within a single focal plane, offering detailed representations of microscopic structures. These techniques are essential in biological and medical research, enabling the visualization of cellular and subcellular structures with different levels of contrast and specificity.There are several major types of 2D microscopy, each with strengths and applications.Bright-Field MicroscopyBright-field microscopy...
1.8K
Three-Dimensional Microscopy in Microbiology01:28

Three-Dimensional Microscopy in Microbiology

903
Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...
903
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

834
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
834
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

58
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
58

You might also read

Related Articles

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

Sort by
Same author

Toward precision microbiome therapeutics: From black box to blueprint.

Cell host & microbe·2026
Same author

Hexanoic acid production from lignocellulosic hydrolysates via simultaneous glucose-xylose utilization by carbon catabolite repression-relaxed Clostridium sp. JS66 with in situ adsorption.

Bioresource technology·2026
Same author

Toward life with a 19-amino acid alphabet through generative artificial intelligence design.

Science (New York, N.Y.)·2026
Same author

Publisher Correction: Macro-level determinants of nature connectedness: An exploratory analysis of 61 countries.

Ambio·2026
Same author

MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.

Microbiome·2025
Same author

Colibactin-producing <i>E. coli</i> promote carcinogenesis of gastroesophageal adenocarcinoma and simultaneously induce autophagy and differentiation.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: Apr 28, 2026

Characterizing Microbiome Dynamics &#8211; Flow Cytometry Based Workflows from Pure Cultures to Natural Communities
09:57

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

11.9K

MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.

Gurdip Uppal, Guillaume K Urtecho, Miles Richardson

    Biorxiv : the Preprint Server for Biology
    |December 16, 2024
    PubMed
    Summary

    We developed MCSPACE, an AI tool to analyze complex gut microbiome data. It reveals microbial community structures and dynamics over time, aiding in understanding host-microbial interactions.

    More Related Videos

    High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression
    12:52

    High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression

    Published on: April 18, 2021

    4.7K
    Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
    09:31

    Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

    Published on: July 9, 2021

    7.9K

    Related Experiment Videos

    Last Updated: Apr 28, 2026

    Characterizing Microbiome Dynamics &#8211; Flow Cytometry Based Workflows from Pure Cultures to Natural Communities
    09:57

    Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

    Published on: July 12, 2018

    11.9K
    High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression
    12:52

    High-Throughput Live Imaging of Microcolonies to Measure Heterogeneity in Growth and Gene Expression

    Published on: April 18, 2021

    4.7K
    Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
    09:31

    Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

    Published on: July 9, 2021

    7.9K

    Area of Science:

    • Microbiome research
    • Computational biology
    • Systems biology

    Background:

    • High-throughput sequencing enables large-scale microbiome analysis.
    • Microbiome co-localization data present unique challenges due to high dimensionality and noise.
    • Understanding gut microbiome spatial structuring is crucial for host-microbial ecosystem function.

    Purpose of the Study:

    • To develop a probabilistic AI method (MCSPACE) for inferring spatially coherent microbial assemblages from co-localization data.
    • To characterize microbial dynamics over time and responses to perturbations.
    • To provide an open-source tool for microbiome biogeography research.

    Main Methods:

    • Development of MCSPACE, a probabilistic AI method for microbiome co-localization data analysis.
    • Generation of a large-scale longitudinal microbiome co-localization dataset in mice subjected to dietary perturbations.
    • Benchmarking MCSPACE against existing methods using murine and human longitudinal datasets.

    Main Results:

    • MCSPACE successfully infers spatially coherent microbial assemblages and their dynamics.
    • The method demonstrates superior performance compared to existing approaches.
    • Identification of temporally persistent and dynamic microbial assemblages in the human gut.
    • Revealed shifts in murine gut microbial assemblages induced by specific dietary components.

    Conclusions:

    • MCSPACE is a powerful tool for elucidating microbiome biogeography and spatiotemporal structuring.
    • The method provides insights into the role of spatial relationships in host-microbial ecosystems.
    • MCSPACE is available as an open-source software tool for the research community.