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

Oxygen Requirements and Growth Patterns01:29

Oxygen Requirements and Growth Patterns

1.0K
Microorganisms exhibit diverse oxygen requirements and growth patterns driven by their metabolic strategies and environmental adaptations. Oxygen, while essential for many organisms, can also be toxic under certain conditions, shaping how microorganisms grow and survive.Oxygen Requirements of MicroorganismsMicroorganisms are classified based on their ability to use or tolerate oxygen:● Obligate aerobes like Mycobacterium tuberculosis need oxygen for energy production, as it serves as the...
1.0K
Microbial Fermentation01:23

Microbial Fermentation

1.1K
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...
1.1K
Microbial Growth Measurement: Indirect Methods01:27

Microbial Growth Measurement: Indirect Methods

1.2K
Estimating microbial growth is essential for understanding population dynamics and environmental adaptations. Indirect methods provide valuable insights by measuring parameters such as turbidity, metabolic activity, and biomass, enabling efficient and reproducible assessments.During exponential growth, microbial cells scatter light proportionally to their biomass, a principle used in turbidity measurements. About one million cells per milliliter produce detectable scattering, which a...
1.2K
Microbial Growth Measurement: Direct Methods01:23

Microbial Growth Measurement: Direct Methods

1.3K
Direct methods for measuring microbial populations in a culture are essential tools in microbiology, providing quantitative data for various applications. Among these, microscopic counts, plate counts, and serial dilution are widely used techniques, each with unique principles and applications.Microscopic CountsMicroscopic counting involves the use of a Petroff-Hausser chamber, a specialized microscope slide with a grid and defined depth. By observing a liquid culture under a microscope,...
1.3K
Anoxygenic Phototrophic Bacteria01:28

Anoxygenic Phototrophic Bacteria

594
Anoxygenic phototrophic bacteria are a diverse group of microorganisms that perform photosynthesis without producing oxygen. They primarily include purple sulfur bacteria, purple nonsulfur bacteria, green sulfur bacteria, and green nonsulfur bacteria. These bacteria are classified into the Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Chlorobi, and Chloroflexi lineages, each with distinct physiological and ecological adaptations.Purple sulfur bacteria belong to the...
594
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

9.7K
Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
9.7K

You might also read

Related Articles

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

Sort by
Same author

A fluorous-phase oxygen optical nanosensor for mitigating redox-active microbial metabolite interference.

The Analyst·2026
Same author

Nitric Oxide Tunes Secreted Metabolite Bioactivity.

Molecular microbiology·2026
Same author

Alkamines reveal a hidden layer of steroid and drug metabolism.

bioRxiv : the preprint server for biology·2026
Same author

Redox-dependent lipophilicity of phenazine metabolites is modulated by intramolecular hydrogen bonds and controls their biological distribution.

bioRxiv : the preprint server for biology·2026
Same author

Inferring Local Protein Structural Similarity from Sequence Alone.

Journal of chemical information and modeling·2026
Same author

Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness.

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

Related Experiment Video

Updated: Dec 16, 2025

Author Spotlight: Oxygen-Independent Assays to Measure Mitochondrial Function in Mammals
05:59

Author Spotlight: Oxygen-Independent Assays to Measure Mitochondrial Function in Mammals

Published on: May 19, 2023

2.6K

Annotation-free prediction of microbial dioxygen utilization.

Avi I Flamholz1, Joshua E Goldford2, Philippa A Richter2

  • 1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.

Msystems
|September 4, 2024
PubMed
Summary

Predicting microbial oxygen needs from DNA sequences is now possible using annotation-free methods. These rapid genomic analyses reveal microbial community composition and environmental oxygen levels.

Keywords:
biogeochemistrygenome analysismachine learningoxygenphysiology

More Related Videos

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition
08:31

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition

Published on: October 3, 2018

8.5K
Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology
10:43

Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

Published on: November 5, 2014

25.7K

Related Experiment Videos

Last Updated: Dec 16, 2025

Author Spotlight: Oxygen-Independent Assays to Measure Mitochondrial Function in Mammals
05:59

Author Spotlight: Oxygen-Independent Assays to Measure Mitochondrial Function in Mammals

Published on: May 19, 2023

2.6K
Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition
08:31

Anaerobic Protein Purification and Kinetic Analysis via Oxygen Electrode for Studying DesB Dioxygenase Activity and Inhibition

Published on: October 3, 2018

8.5K
Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology
10:43

Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

Published on: November 5, 2014

25.7K

Area of Science:

  • Microbiology and Genomics
  • Bioinformatics and Computational Biology

Background:

  • Distinguishing aerobic (oxygen-requiring) from anaerobic (non-oxygen-requiring) microbes is challenging using genomic data alone, as many microbes utilize oxygen for detoxification.
  • Aerobes typically possess larger genomes with specific oxygen-utilizing enzymes, offering clues for prediction.
  • Current prediction methods often rely on computationally intensive genome annotation.

Purpose of the Study:

  • To develop and validate annotation-free methods for accurately predicting microbial oxygen utilization directly from genomic sequences.
  • To assess the performance of sequence content-based models compared to annotation-based approaches.
  • To explore the utility of these rapid prediction methods for analyzing microbial communities in natural environments.

Main Methods:

  • Developed and evaluated machine learning models based on genomic sequence content, specifically amino acid trimers (triplets).
  • Compared the accuracy of annotation-free models with traditional annotation-based classifiers for ternary classification of microbial oxygen utilization.
  • Applied the developed models to analyze microbial community composition in the Earth Microbiome Project and a Black Sea oxygen gradient dataset.

Main Results:

  • Annotation-free models using amino acid trimers achieved prediction accuracy comparable to intensive annotation-based methods (approximately 80%).
  • Amino acid trimers effectively encode information about protein composition and microbial phylogeny, enabling accurate predictions.
  • Analysis of the Black Sea dataset revealed a quantitative correlation between microbial community composition and local oxygen levels.

Conclusions:

  • Annotation-free genomic analysis provides a rapid and accurate method for predicting microbial oxygen utilization.
  • These methods can be used to infer microbial physiology and environmental conditions from DNA sequencing data.
  • DNA sequencing data, analyzed with these statistical methods, can serve as a sensor for key environmental features like oxygen concentration.