Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Key Techniques in Microbiology

Key Techniques in Microbiology

Aseptic techniques prevent contamination, ensure experimental accuracy, and protect researchers and microbial cultures. These techniques are essential in clinical, industrial, and research settings where sterility is required.Maintaining Sterility in Laboratory PracticesScientists maintain sterility by sterilizing tools with heat or chemicals, disinfecting work surfaces, and handling cultures in controlled environments. Working near an open flame or within a laminar flow hood reduces the risk...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

You might also read

Related Articles

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

Sort by

Same author

Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.

bioRxiv : the preprint server for biology·2026

Same author

Highly sensitive and wide-range non-contact fluorescent thermometry based on well-defined Cs<sub>2</sub>ZrCl<sub>6</sub>:Bi perovskite nanocrystals.

Chemical communications (Cambridge, England)·2026

Same author

The oral microbiome is associated with the diagnosis, prognosis and radiotherapy sensitivity of esophageal cancer.

Journal of translational medicine·2026

Same author

Spatiotemporal neural dynamics of Chinese word form processing: An SEEG study.

Cognitive neuropsychology·2026

Same author

Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals <i>Lactobacillus crispatus</i> accessory genes associated with cervical dysplasia.

mSystems·2026

Same author

Glucuronidation metabolomic fingerprinting to map host-microbe metabolism.

Nature communications·2026

Same journal

Correction: Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.

Microbiome·2026

Same journal

Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.

Microbiome·2026

Same journal

Population-based characterisation of child and adolescent oral bacterial microbiomes.

Microbiome·2026

Same journal

Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.

Microbiome·2026

Same journal

IL-17A deficiency in HLA-DR3 transgenic mice enriches beneficial Prevotella species in gut to promote Tregs and reduce CNS autoimmunity.

Microbiome·2026

Same journal

Whole metagenome sequencing: not deep enough for complete microbial function recovery.

Microbiome·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 3, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Optimizing methods and dodging pitfalls in microbiome research.

Dorothy Kim¹, Casey E Hofstaedter¹, Chunyu Zhao¹

¹Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.

|May 7, 2017

Summary

This summary is machine-generated.

This study offers practical guidance for microbiome research, detailing experimental design best practices and common pitfalls. It aims to help scientists avoid errors and improve the reliability of their microbiome studies.

Keywords:

16S rRNA gene Best practices Environmental contamination Metagenomics Methods Shotgun metagenomics Study design

More Related Videos

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

Related Experiment Videos

Last Updated: Mar 3, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Human microbiome research offers significant health insights but is prone to experimental artifacts.
Identifying and mitigating these artifacts is crucial for reliable study outcomes.

Purpose of the Study:

To provide researchers with optimized experimental design strategies for microbiome studies.
To highlight common pitfalls and offer solutions for enhancing experimental robustness.

Main Methods:

Review of best practices in experimental design, including confounder identification (age, diet, etc.).
Guidance on sample storage, and the design and analysis of positive and negative controls.
Strategies for controlling multiple comparisons and comparing discovery/validation cohorts.

Main Results:

Identification of key experimental confounders in microbiome research.
Recommendations for sample handling and the critical role of controls.
Methods to improve the reproducibility and accuracy of microbiome data.

Conclusions:

Implementing these experimental tactics can significantly improve the efficiency and reduce errors in microbiome research.
Adherence to best practices ensures more reliable and impactful scientific discoveries in the field.