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

Antibiotic Selection00:57

Antibiotic Selection

52.1K
Overview
52.1K

You might also read

Related Articles

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

Sort by
Same author

Frailty may confound the association between MASLD and cardiovascular mortality in people with cardiometabolic risk factors.

Cardiovascular diabetology·2026
Same author

Pangenome-based structural variant imputation enables large-scale genotype-phenotype studies in dairy cattle.

Nature communications·2026
Same author

Overexpression of <i>PtrPIP2:4</i> Accelerates Adventitious Root Emergence, Promotes Adventitious Root Elongation, and Increases Lateral Root Number in Poplar.

Plants (Basel, Switzerland)·2026
Same author

Combined Developmental Toxicity of Ecologically Relevant Concentrations of the PFOS Alternative F-53B and Hexavalent Chromium in Zebrafish, Danio rerio.

Toxics·2026
Same author

Caecum transcriptome and associated microbial community in young calves with artificial dosing of rumen content obtained from an adult cow.

Journal of animal science and technology·2026
Same author

Molecular Analysis of a New Alphapartitivirus from Rhizoctonia solani AG-4 HG III Isolate Rs292.

Current microbiology·2026

Related Experiment Video

Updated: May 20, 2025

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach
12:32

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Published on: December 14, 2019

13.9K

Pipeline for Antimicrobial Resistance Gene Quantification from Host Tissue.

Levi M Svaren1, Wenli Li1

  • 1USDA, Agricultural Research Service, Madison, Wisconsin.

Current Protocols
|March 27, 2025
PubMed
Summary

A new bioinformatics workflow quantifies antimicrobial resistance (AMR) genes in food animal gut microbiomes. This tool helps track AMR spread through the food chain, protecting animal and human health.

Keywords:
antimicrobial resistancegut tissue RNA sequencingsingle nucleotide polymorphismstranscript quantification

More Related Videos

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
09:13

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Published on: January 13, 2016

8.0K
Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
08:58

Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes

Published on: March 3, 2023

6.2K

Related Experiment Videos

Last Updated: May 20, 2025

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach
12:32

Quantification of Plasmid-Mediated Antibiotic Resistance in an Experimental Evolution Approach

Published on: December 14, 2019

13.9K
Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
09:13

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Published on: January 13, 2016

8.0K
Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
08:58

Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes

Published on: March 3, 2023

6.2K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Food Safety

Background:

  • Antimicrobial use in food animals drives antimicrobial resistance (AMR), threatening animal and human health.
  • Understanding AMR gene abundance in food animal gut resistomes is crucial for mitigation but currently lacks sufficient data.
  • Existing Gut Tissue RNA Sequencing (GTRS) methods primarily focus on host data, neglecting microbial AMR analysis.

Purpose of the Study:

  • To develop and present a straightforward bioinformatics workflow for quantifying antimicrobial resistance (AMR) genes in food animal gut microbiomes.
  • To enable the examination of AMR gene expression and abundance using GTRS data.
  • To facilitate the study of host-microbe interactions related to AMR.

Main Methods:

  • A novel bioinformatics pipeline using common command-line tools to analyze GTRS data.
  • Filtering host-derived reads to focus on microbial transcripts.
  • Quantification of AMR gene transcripts, differential gene expression analysis, and single-nucleotide polymorphism (SNP) analysis.

Main Results:

  • Successful implementation of a user-friendly pipeline for analyzing microbial AMR from GTRS data.
  • Enables quantification of AMR gene expression and identification of genetic variations.
  • Provides results ready for integration into scientific reports and publications.

Conclusions:

  • The developed workflow effectively addresses the gap in analyzing microbial AMR from GTRS data in food animals.
  • This tool is essential for monitoring and mitigating AMR spread within the food chain.
  • Facilitates a deeper understanding of AMR dynamics in animal agriculture and its public health implications.