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

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

137
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...
137
Microbial Classification System01:24

Microbial Classification System

182
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
182
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.5K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
11.5K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

99
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
99
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.1K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.1K
Next-generation Sequencing03:00

Next-generation Sequencing

92.6K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
92.6K

You might also read

Related Articles

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

Sort by
Same author

Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture.

ISME communications·2026
Same author

Timing Is Everything: The Effect of Exposure to Pollution on Wildlife Gut Microbiota Is Contingent on Season.

Molecular ecology·2026
Same author

The gut microbiota and sleep in infants: a focus on diurnal rhythmicity patterns.

Gut microbes reports·2026
Same author

Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota.

Gut microbes reports·2026
Same author

HighALPS: ultra-high-throughput marker-gene amplicon library preparation and sequencing on the Illumina NextSeq and NovaSeq Platforms.

mSystems·2026
Same author

FAIRer DNA sequence data with q2-ena-uploader: a QIIME 2 plugin for data deposition in the European Nucleotide Archive.

Microbiology resource announcements·2026

Related Experiment Video

Updated: Sep 11, 2025

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

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

Published on: August 25, 2018

13.0K

Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.

Lina Kim1, Anton Lavrinienko1, Zuzana Sebechlebska1

  • 1Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland.

Nucleic Acids Research
|August 18, 2025
PubMed
Summary

Microbiome research faces challenges with data sharing and metadata standardization. A new badge system and automated tool reveal that many studies lack sufficient data availability and consistent metadata, hindering reproducibility.

More Related Videos

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
08:05

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

Published on: March 19, 2018

19.8K
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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

Published on: October 15, 2019

29.4K

Related Experiment Videos

Last Updated: Sep 11, 2025

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

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

Published on: August 25, 2018

13.0K
Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
08:05

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

Published on: March 19, 2018

19.8K
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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

Published on: October 15, 2019

29.4K

Area of Science:

  • Life sciences
  • Microbiome research
  • Bioinformatics

Background:

  • Microbiome research is rapidly expanding and relies heavily on data.
  • Existing policies for sharing microbiome sequence data and metadata exist, but compliance is inconsistent.
  • Standardized metadata is crucial for harmonizing and comparing data across studies.

Purpose of the Study:

  • To propose a tiered badge system for evaluating data/metadata sharing compliance in microbiome research.
  • To develop an automated tool for assessing adherence to data reporting standards in publications.
  • To promote open research data best practices within the microbiome community.

Main Methods:

  • Developed a two-tiered badge system to evaluate data and metadata sharing.
  • Created an automated tool to assess reporting standards for amplicon and metagenome sequence data.
  • Systematically evaluated 2929 publications in human gut microbiome research and 370 case studies in soil and gut microbiota.

Main Results:

  • Nearly half of the evaluated publications failed to meet minimum standards for sequence data availability.
  • Inconsistent metadata reporting presents a significant obstacle to data harmonization and cross-study comparisons.
  • The study identified the ineffectiveness of current data availability statements and the lack of standardized metadata.

Conclusions:

  • Improved practices and infrastructure are needed to lower barriers to data submission and enhance reproducibility in microbiome research.
  • The proposed tiered badge framework aims to encourage discussion on data sharing and facilitate data reuse.
  • Adoption of the badge system can support Findable, Accessible, Interoperable, and Reusable (FAIR) data principles in microbiome science.