Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

Can rumen bacteria communicate to each other?

(2020) Mi-Young Won et al.   Microbiome

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture

(2020) Max M. Villa et al.   mSystems

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip

(2019) Sasan Jalili-Firoozinezhad et al.   Nature Biomedical Engineering

Microbial Interaction Network Inference in Microfluidic Droplets

(2019) Ryan H. Hsu et al.   Cell Systems

Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant

(2019) Zachariah DeFilipp et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Current trends of human infections and antibiotic resistance of the genus Shewanella

(2017) K. Yousfi et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

(2017) David M Needham et al.   ISME Journal

Moving beyond microbiome-wide associations to causal microbe identification

(2017) Neeraj K. Surana et al.   NATURE

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

(2017) Supratim Mukherjee et al.   NATURE BIOTECHNOLOGY

Gut microbiota and IBD: causation or correlation?

(2017) Josephine Ni et al.   Nature Reviews Gastroenterology & Hepatology

Printed droplet microfluidics for on demand dispensing of picoliter droplets and cells

(2017) Russell H. Cole et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characteristics of N-Acylhomoserine Lactones Produced by Hafnia alvei H4 Isolated from Spoiled Instant Sea Cucumber

(2017) Hong-Man Hou et al.   SENSORS

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates

(2016) Cheng-Ying Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Droplet microfluidics for microbiology: techniques, applications and challenges

(2016) Tomasz S. Kaminski et al.   LAB ON A CHIP

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

Systematic Review: Adverse Events of Fecal Microbiota Transplantation

(2016) Sinan Wang et al.   PLoS One

The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community

(2015) Meghan Wymore Brand et al.   ILAR JOURNAL

Accurate microfluidic sorting of droplets at 30 kHz

(2015) Adam Sciambi et al.   LAB ON A CHIP

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

(2015) Hyun Jung Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Monodisperse Emulsion Drop Microenvironments for Bacterial Biofilm Growth

(2015) Connie B. Chang et al.   Small

Harnessing the landscape of microbial culture media to predict new organism–media pairings

(2015) Matthew A. Oberhardt et al.   Nature Communications

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Microfluidic organs-on-chips

(2014) Sangeeta N Bhatia et al.   NATURE BIOTECHNOLOGY

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa

(2014) Liang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PNAS Plus: From the Cover: Oligotyping analysis of the human oral microbiome

(2014) A. M. Eren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time image processing for label-free enrichment of Actinobacteria cultivated in picolitre droplets

(2013) Emerson Zang et al.   LAB ON A CHIP

Single-cell analysis and sorting using droplet-based microfluidics

(2013) Linas Mazutis et al.   Nature Protocols

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Bacteria–surface interactions

(2013) Hannah H. Tuson et al.   Soft Matter

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Rapid screening of antibiotic toxicity in an automated microdroplet system

(2012) Krzysztof Churski et al.   LAB ON A CHIP

Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow

(2012) Hyun Jung Kim et al.   LAB ON A CHIP

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

(2012) Anthony A. Fodor et al.   PLoS One

In VitroActivities of CB-183,315, Vancomycin, and Metronidazole against 556 Strains of Clostridium difficile, 445 Other Intestinal Anaerobes, and 56 Enterobacteriaceae Species

(2011) Diane M. Citron et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities

(2011) Jihyang Park et al.   PLoS One

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of resistance genes and susceptibility patterns in Bacteroides and Parabacteroides strains

(2010) Renata F. Boente et al.   ANAEROBE

High-throughput injection with microfluidics using picoinjectors

(2010) A. R. Abate et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microfluidic Confinement of Single Cells of Bacteria in Small Volumes Initiates High-Density Behavior of Quorum Sensing and Growth and Reveals Its Variability

(2009) James Q. Boedicker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

SlipChip

(2009) Wenbin Du et al.   LAB ON A CHIP

Wolbachia as a bacteriocyte-associated nutritional mutualist

(2009) T. Hosokawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pillar-induced droplet merging in microfluidic circuits

(2008) Xize Niu et al.   LAB ON A CHIP