Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome

Insertional Inactivation of Prevotella intermedia OxyR Results in Reduced Survival with Oxidative Stress and in the Presence of Host Cells

(2021) Mariko Naito et al.   Microorganisms

Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria

(2021) Anthony L. Shiver et al.   Nature Protocols

A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems

(2021) Jing Li et al.   EMBO JOURNAL

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

(2020) Sidhartha R. Sinha et al.   Cell Host & Microbe

Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells

(2020) Clarissa Campbell et al.   NATURE

Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron

(2020) Mao Taketani et al.   NATURE BIOTECHNOLOGY

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

(2020) Masanori Funabashi et al.   NATURE

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

(2020) Phuc Leo H. Vo et al.   NATURE BIOTECHNOLOGY

The microbiome, cancer, and cancer therapy

(2019) Beth A. Helmink et al.   NATURE MEDICINE

Emerging roles of bile acids in mucosal immunity and inflammation

(2019) Mei Lan Chen et al.   Mucosal Immunology

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Longitudinal multi-omics of host–microbe dynamics in prediabetes

(2019) Wenyu Zhou et al.   NATURE

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

(2019) Andrew Maltez Thomas et al.   NATURE MEDICINE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Systematic evasion of the restriction-modification barrier in bacteria

(2019) Christopher D. Johnston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Conjugal Donor Strain for Improved DNA transfer into Clostridium spp.

(2019) Craig Woods et al.   ANAEROBE

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

RiboCas: A Universal CRISPR-Based Editing Tool for Clostridium

(2019) Inés C. Cañadas et al.   ACS Synthetic Biology

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

(2019) Leonor García-Bayona et al.   mBio

Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids

(2019) Paul O. Sheridan et al.   ANAEROBE

Genetic manipulation of wild human gut Bacteroides

(2019) Natasha A. Bencivenga-Barry et al.   JOURNAL OF BACTERIOLOGY

Bile acid metabolites control TH17 and Treg cell differentiation

(2019) Saiyu Hang et al.   NATURE

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis

(2019) Xinyang Song et al.   NATURE

Depletion of microbiome-derived molecules in the host using Clostridium genetics

(2019) Chun-Jun Guo et al.   SCIENCE

Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production

(2018) Jie Zhang et al.   METABOLIC ENGINEERING

Multiplexed CRISPR-Cpf1-Mediated Genome Editing in Clostridium difficile toward the Understanding of Pathogenesis of C. difficile Infection

(2018) Wei Hong et al.   ACS Synthetic Biology

Bile Acids Activated Receptors Regulate Innate Immunity

(2018) Stefano Fiorucci et al.   Frontiers in Immunology

Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi

(2018) Jason M. Peters et al.   Nature Microbiology

Efficient Transcriptional Gene Repression by Type V-A CRISPR-Cpf1 from Eubacterium eligens

(2017) Seong Keun Kim et al.   ACS Synthetic Biology

Multiplex gene regulation by CRISPR-ddCpf1

(2017) Xiaochun Zhang et al.   Cell Discovery

Using CRISPR-Cas9-mediated genome editing to generate C. difficile mutants defective in selenoproteins synthesis

(2017) Kathleen N. McAllister et al.   Scientific Reports

Bile acids and nonalcoholic fatty liver disease: Molecular insights and therapeutic perspectives

(2016) Juan P. Arab et al.   HEPATOLOGY

Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism

(2016) Thomas C. Fung et al.   IMMUNITY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins

(2016) Junho K Hur et al.   NATURE BIOTECHNOLOGY

Restriction modification system analysis and development of in vivo methylation for the transformation of Clostridium cellulovorans

(2015) Xiaorui Yang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange

(2015) Laura R Hmelo et al.   Nature Protocols

Insights into the Role of Erysipelotrichaceae in the Human Host

(2015) Nadeem O. Kaakoush   Frontiers in Cellular and Infection Microbiology

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota

(2015) Mark Mimee et al.   Cell Systems

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Technical guide for genetic advancement of underdeveloped and intractable Clostridium

(2014) Michael E. Pyne et al.   BIOTECHNOLOGY ADVANCES

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

(2014) Nicole Reichardt et al.   ISME Journal

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

(2014) Laurens Kraal et al.   PLoS One

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome

(2013) Shin Yoshimoto et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Inflammatory Bowel Disease

(2010) Arthur Kaser et al.   Annual Review of Immunology

A modular system for Clostridium shuttle plasmids

(2009) John T. Heap et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The Most Conserved Genome Segments for Life Detection on Earth and Other Planets

(2008) Thomas A. Isenbarger et al.   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Clostridium scindens baiCD and baiH genes encode stereo-specific 7α/7β-hydroxy-3-oxo-Δ4-cholenoic acid oxidoreductases☆

(2007) D KANG   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS