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

69
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,...
69
Mutations in Microorganisms01:18

Mutations in Microorganisms

55
Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
55
Amino Acid Catabolism01:18

Amino Acid Catabolism

118
Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
118
Synthetic Biology02:55

Synthetic Biology

4.9K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
4.9K

You might also read

Related Articles

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

Sort by
Same author

scDifformer: diffusion-based post-training for virtual cell modeling across large-scale single-cell data.

Nucleic acids research·2026
Same author

Transcriptome study of <i>Talaromyces verruculosus</i> TS63-9 for pectin-degrading CAZymes.

Microbiology spectrum·2026
Same author

Complete plastid genome and phylogenetic analysis of <i>Hypericum wightianum</i> (Hypericaceae).

Mitochondrial DNA. Part B, Resources·2026
Same author

Existential distress and social alienation in adolescents with allergic rhinitis: the serial mediating roles of psychological inflexibility and experiential avoidance.

Frontiers in public health·2026
Same author

Exploiting Biomacromolecular Oligomerization for Next-Generation Pesticide Discovery: Challenges and Perspectives.

Journal of agricultural and food chemistry·2026
Same author

Warehouse Fire Detection System Based on Multi-Sensor Information Fusion.

Sensors (Basel, Switzerland)·2026

Related Experiment Video

Updated: Aug 20, 2025

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

19.6K

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes.

Jinfang Zheng1, Boyang Hu2, Xinpeng Zhang1

  • 1Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA.

Nucleic Acids Research
|November 18, 2022
PubMed
Summary

The updated dbCAN-seq database now includes over 169,000 carbohydrate-active enzyme gene clusters from microbial genomes. It predicts glycan substrates for these clusters, aiding microbiome research.

More Related Videos

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

6.9K
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

18.5K

Related Experiment Videos

Last Updated: Aug 20, 2025

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
09:29

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

Published on: May 15, 2019

19.6K
MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
08:34

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

6.9K
Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

18.5K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Carbohydrate-active enzymes (CAZymes) are crucial for microbial communities in diverse environments.
  • Metagenome-assembled genomes (MAGs) have expanded our understanding of microbial functions.
  • Databases like dbCAN-seq are essential for analyzing CAZyme diversity and function.

Purpose of the Study:

  • To update the dbCAN-seq database with new data and features for analyzing CAZymes in microbiomes.
  • To infer and highlight glycan substrates for CAZyme gene clusters (CGCs).
  • To improve data accessibility and visualization for researchers.

Main Methods:

  • Incorporated approximately 498,000 CAZymes and 169,000 CGCs from 9,421 MAGs across four ecological niches.
  • Utilized dbCAN-PUL homology search and eCAMI subfamily majority voting to predict glycan substrates for CGCs.
  • Redesigned the CGC page for enhanced visualization and added a statistics page for data organization.

Main Results:

  • The updated database contains a substantial number of CAZymes and CGCs from various microbiomes.
  • Glycan substrates were predicted for 24.54% of CGCs using two novel approaches.
  • New features include graphical displays, alignment tools, and organized statistical data.

Conclusions:

  • The updated dbCAN-seq database provides valuable insights into predicted glycan substrates for microbial CGCs.
  • This resource facilitates the study of carbohydrate metabolism in complex microbial communities.
  • Future work will integrate substrate prediction into the dbCAN2 web server.