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

You might also read

Related Articles

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

Sort by
Same author

Enhancing All-Solid-State Batteries Performance Through Thickness Control and Surface Passivation of Thermally Evaporated Lithium Metal Anodes.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

STING agonist protects against exacerbation of schistosome egg-induced immunopathology.

PLoS pathogens·2026
Same author

Drug-eluting bead TACE improves the efficacy of HAIC combined with molecular-targeted therapy and anti-PD-1 immunotherapy in large hepatocellular carcinoma with inferior vena cava and/or right atrium tumor thrombus: a multicenter retrospective cohort study.

BMC cancer·2026
Same author

Core-shell commensal biocapsules for <i>in situ</i> gut microbiome engineering.

Bioactive materials·2026
Same author

Cervicovaginal Microbiota and Biogenic Amine Metabolic Shifts in HPV-Associated Cervical Disease.

Cancers·2026
Same author

Multi-cohort comparative analysis of salivary microbiotas reveals rural Ethiopians harbor a distinct composition correlated with lower esophageal cancer prevalence.

mSystems·2026

Related Experiment Video

Updated: Sep 19, 2025

Automated and High-throughput Microbial Monoclonal Cultivation and Picking Using the Single-cell Microliter-droplet Culture Omics System
10:16

Automated and High-throughput Microbial Monoclonal Cultivation and Picking Using the Single-cell Microliter-droplet Culture Omics System

Published on: March 14, 2025

755

Microbiome Single Cell Atlases Generated with a Commercial Instrument.

Xiangpeng Li1,2, Linfeng Xu2, Benjamin Demaree2

  • 1Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|June 4, 2025
PubMed
Summary

EASi-seq enables high-quality single-cell genomic sequencing for microbial communities. This new method allows detailed microbiome analysis and discovery of species subpopulations using accessible technology.

Keywords:
microbiomemicrobiome single cell atlasesmicrofluidicssingle cell sequencing

More Related Videos

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

29.7K
Characterizing Microbiome Dynamics &#8211; Flow Cytometry Based Workflows from Pure Cultures to Natural Communities
09:57

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

12.1K

Related Experiment Videos

Last Updated: Sep 19, 2025

Automated and High-throughput Microbial Monoclonal Cultivation and Picking Using the Single-cell Microliter-droplet Culture Omics System
10:16

Automated and High-throughput Microbial Monoclonal Cultivation and Picking Using the Single-cell Microliter-droplet Culture Omics System

Published on: March 14, 2025

755
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

29.7K
Characterizing Microbiome Dynamics &#8211; Flow Cytometry Based Workflows from Pure Cultures to Natural Communities
09:57

Characterizing Microbiome Dynamics – Flow Cytometry Based Workflows from Pure Cultures to Natural Communities

Published on: July 12, 2018

12.1K

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Single-cell sequencing is crucial for dissecting complex biological systems, but microbial applications lag behind mammalian studies.
  • Existing methods for microbial single-cell analysis are limited, hindering comprehensive microbiome research.

Purpose of the Study:

  • To present EASi-seq (Easily Accessible Single microbe sequencing), a novel method for efficient single-cell microbial genome sequencing.
  • To enable detailed genomic analysis of individual microbes within complex microbiomes.

Main Methods:

  • Adapted the commercial Mission Bio Tapestri instrument's single-cell workflow for microbial samples.
  • Developed a companion bioinformatics pipeline for genome clustering, assembly, and annotation.
  • Integrated metagenomic contigs with EASi-seq data to enhance coverage and reduce bias.

Main Results:

  • EASi-seq allows sequencing of tens of thousands of individual microbes per run.
  • Generated detailed genomic atlases for human and environmental microbiomes.
  • Demonstrated improved whole genome assembly, strain identification, and taxonomic classification.

Conclusions:

  • EASi-seq provides a simple, efficient, and accessible platform for high-quality single-cell genomic sequencing of microbiomes.
  • This method unlocks new opportunities for discovering and analyzing microbial species subpopulations.