Metagenomic engineering of the mammalian gut microbiome in situ

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

(2018) Jennifer A. N. Brophy et al.   Nature Microbiology

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

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

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

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract

(2015) Sushma Kommineni et al.   NATURE

CRISPR-Cas immunity in prokaryotes

(2015) Luciano A. Marraffini   NATURE

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating

(2015) Páraic Ó Cuív et al.   Scientific Reports

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

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

(2014) Uli Klümper et al.   ISME Journal

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

Defining the Bacteroides Ribosomal Binding Site

(2013) Udo Wegmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

(2011) N. Saeidi et al.   Molecular Systems Biology

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

Reversible Microbial Colonization of Germ-Free Mice Reveals the Dynamics of IgA Immune Responses

(2010) S. Hapfelmeier et al.   SCIENCE