What can microfluidics do for human microbiome research?

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota

(2020) Rieka Chijiiwa et al.   Microbiome

Developing a new class of engineered live bacterial therapeutics to treat human diseases

(2020) Mark R. Charbonneau et al.   Nature Communications

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

(2020) Sydney B. Blattman et al.   Nature Microbiology

What is new and relevant for sequencing-based microbiome research? A minireview

(2019) Alena M. Fricker et al.   Journal of Advanced Research

Priorities for the next 10 years of human microbiome research

(2019) Lita Proctor   NATURE

Exploring the emerging role of the microbiome in cancer immunotherapy

(2019) Jessica Fessler et al.   Journal for ImmunoTherapy of Cancer

Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics

(2019) Xing Shi et al.   mSystems

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

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

Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity

(2019) Yuguang Liu et al.   ANALYTICAL CHEMISTRY

Experimental Microbiomes: Models Not to Scale

(2019) Marc G. Chevrette et al.   mSystems

An Organ-On-A-Chip Engineered Platform to Study the Microbiota–Gut–Brain Axis in Neurodegeneration

(2019) Manuela Teresa Raimondi et al.   TRENDS IN MOLECULAR MEDICINE

An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface

(2019) Raehyun Kim et al.   Biofabrication

Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health

(2019) Aimée Parker et al.   Gut Microbes

Microfluidic Technologies for cfDNA Isolation and Analysis

(2019) Xu et al.   Micromachines

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods

(2018) Dongxue Zhang et al.   ANALYTICAL CHEMISTRY

The Influence of the Gut Microbiome on Cancer, Immunity, and Cancer Immunotherapy

(2018) Vancheswaran Gopalakrishnan et al.   CANCER CELL

The Human Gut Microbiome: From Association to Modulation

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

A multi-chamber microfluidic intestinal barrier model using Caco-2 cells for drug transport studies

(2018) Hsih-Yin Tan et al.   PLoS One

Salivary Exosome and Cell-Free DNA for Cancer Detection

(2018) Kyung-A Hyun et al.   Micromachines

Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis

(2018) Nan Zhou et al.   MicrobiologyOpen

Oral mucosa-on-a-chip to assess layer-specific responses to bacteria and dental materials

(2018) Christopher Rahimi et al.   Biomicrofluidics

Ultrahigh-throughput functional profiling of microbiota communities

(2018) Stanislav S. Terekhov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance

(2018) Aspen T. Reese et al.   mBio

Interconnected Microphysiological Systems for Quantitative Biology and Pharmacology Studies

(2018) Collin D. Edington et al.   Scientific Reports

In situ immune response and mechanisms of cell damage in central nervous system of fatal cases microcephaly by Zika virus

(2018) Raimunda S. S. Azevedo et al.   Scientific Reports

Recent Advances in Body-on-a-Chip Systems

(2018) Jong Hwan Sung et al.   ANALYTICAL CHEMISTRY

Translating microbiome futures

(2018) Gaspar Taroncher-Oldenburg et al.   NATURE BIOTECHNOLOGY

Intestinal barrier dysfunction orchestrates the onset of inflammatory host–microbiome cross-talk in a human gut inflammation-on-a-chip

(2018) Woojung Shin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions between the microbiota, immune and nervous systems in health and disease

(2017) Thomas C Fung et al.   NATURE NEUROSCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

Effective Light Directed Assembly of Building Blocks with Microscale Control

(2017) Ngoc-Duy Dinh et al.   Small

High-throughput automated microfluidic sample preparation for accurate microbial genomics

(2017) Soohong Kim et al.   Nature Communications

Membrane-free culture and real-time barrier integrity assessment of perfused intestinal epithelium tubes

(2017) Sebastiaan J. Trietsch et al.   Nature Communications

Human microbiome signatures of differential colorectal cancer drug metabolism

(2017) Leah Guthrie et al.   npj Biofilms and Microbiomes

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates

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

Gut microbiome and liver diseases

(2016) Herbert Tilg et al.   GUT

Global epidemiology of nonalcoholic fatty liver disease-Meta-analytic assessment of prevalence, incidence, and outcomes

(2016) Zobair M. Younossi et al.   HEPATOLOGY

Sample introduction interface for on-chip nucleic acid-based analysis of Helicobacter pylori from stool samples

(2016) O. Mosley et al.   LAB ON A CHIP

In vitro micro-physiological immune-competent model of the human skin

(2016) Qasem Ramadan et al.   LAB ON A CHIP

Droplet microfluidics for microbiology: techniques, applications and challenges

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

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

(2016) Satyabrata Bag et al.   Scientific Reports

Skin-on-a-chip model simulating inflammation, edema and drug-based treatment

(2016) Maierdanjiang Wufuer et al.   Scientific Reports

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Genetically modified bacteria as a tool to detect microscopic solid tumor masses with triggered release of a recombinant biomarker

(2015) Jan T. Panteli et al.   Integrative Biology

A compartmentalized microfluidic neuromuscular co-culture system reveals spatial aspects of GDNF functions

(2015) E. E. Zahavi et al.   JOURNAL OF CELL SCIENCE

Pumpless microfluidic platform for drug testing on human skin equivalents

(2015) Hasan Erbil Abaci et al.   LAB ON A CHIP

The tantalizing links between gut microbes and the brain

(2015) Peter Andrey Smith   NATURE

Small airway-on-a-chip enables analysis of human lung inflammation and drug responses in vitro

(2015) Kambez H Benam et al.   NATURE METHODS

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

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Microfluidic Isolation of Nucleic Acids

(2014) Sarah J. Reinholt et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Microfluidics Expanding the Frontiers of Microbial Ecology

(2014) Roberto Rusconi et al.   Annual Review of Biophysics

The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro

(2014) Massimo Marzorati et al.   BMC MICROBIOLOGY

Interactions Between the Intestinal Microbiome and Liver Diseases

(2014) Bernd Schnabl et al.   GASTROENTEROLOGY

Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips

(2014) Liang Ma et al.   Integrative Biology

Three-dimensional intestinal villi epithelium enhances protection of human intestinal cells from bacterial infection by inducing mucin expression

(2014) Si Hyun Kim et al.   Integrative Biology

Poor oral hygiene as a risk factor for infective endocarditis–related bacteremia

(2014) Peter B. Lockhart et al.   JOURNAL OF THE AMERICAN DENTAL ASSOCIATION

Fully biodegradable antibacterial hydrogels via thiol–ene “click” chemistry

(2014) Hong Du et al.   Polymer Chemistry

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

Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria

(2014) Felix J. H. Hol et al.   SCIENCE

One drop at a time: toward droplet microfluidics as a versatile tool for single-cell analysis

(2014) Agata Rakszewska et al.   NPG Asia Materials

Exploring host-microbiota interactions in animal models and humans

(2013) A. D. Kostic et al.   GENES & DEVELOPMENT

Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation

(2013) Hyun Jung Kim et al.   Integrative Biology

A novel microfluidic co-culture system for investigation of bacterial cancer targeting

(2013) Jung Woo Hong et al.   LAB ON A CHIP

Interfacial microfluidic transport on micropatterned superhydrophobic textile

(2013) Siyuan Xing et al.   LAB ON A CHIP

Single-cell analysis and sorting using droplet-based microfluidics

(2013) Linas Mazutis et al.   Nature Protocols

Patterning Bacterial Communities on Epithelial Cells

(2013) Mohammed Dwidar et al.   PLoS One

From meta-omics to causality: experimental models for human microbiome research

(2013) Joëlle V Fritz et al.   Microbiome

Development of chip-compatible sample preparation for diagnosis of infectious diseases

(2012) Marion Ritzi-Lehnert   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

(2012) Pieter Van den Abbeele et al.   ISME Journal

Microfluidic designs and techniques using lab-on-a-chip devices for pathogen detection for point-of-care diagnostics

(2012) Amir M. Foudeh 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

A combined micromagnetic-microfluidic device for rapid capture and culture of rare circulating tumor cells

(2012) Joo H. Kang et al.   LAB ON A CHIP

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

(2012) K. Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In tumors Salmonella migrate away from vasculature toward the transition zone and induce apoptosis

(2011) S Ganai et al.   CANCER GENE THERAPY

Proliferation behavior of E. coli in a three-dimensional in vitro tumor model

(2011) Nelita Elliott et al.   Integrative Biology

Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities

(2011) Jihyang Park et al.   PLoS One

Encapsulating Bacteria in Agarose Microparticles Using Microfluidics for High-Throughput Cell Analysis and Isolation

(2010) Ye-Jin Eun et al.   ACS Chemical Biology

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective for Bacteroidetes and Clostridium Cluster IX

(2010) P. Van den Abbeele et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microfluidic dissolved oxygen gradient generator biochip as a useful tool in bacterial biofilm studies

(2010) Maciej Skolimowski et al.   LAB ON A CHIP

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Reconstituting Organ-Level Lung Functions on a Chip

(2010) D. Huh et al.   SCIENCE

Integrated microfluidic devices for combinatorial cell-based assays

(2009) Zeta Tak For Yu et al.   BIOMEDICAL MICRODEVICES

Co-culture of epithelial cells and bacteria for investigating host–pathogen interactions

(2009) Jeongyun Kim et al.   LAB ON A CHIP