Human gut bacteria contain acquired interbacterial defence systems

Adaptive Evolution within Gut Microbiomes of Healthy People

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The Biology of CRISPR-Cas: Backward and Forward

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(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Bacterial antagonism in host-associated microbial communities

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Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins

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Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes

(2017) Margaret I. Steele et al.   mBio

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria

(2017) John C Whitney et al.   eLife

Sequential displacement of Type VI Secretion System effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae

(2017) Paul C. Kirchberger et al.   Scientific Reports

Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements

(2016) Michael J. Coyne et al.   BMC GENOMICS

Strain competition restricts colonization of an enteric pathogen and prevents colitis

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Human symbionts inject and neutralize antibacterial toxins to persist in the gut

(2016) Aaron G. Wexler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis

(2016) Ohad Manor et al.   Scientific Reports

Assessing the Unseen Bacterial Diversity in Microbial Communities

(2015) Alejandro Caro-Quintero et al.   Genome Biology and Evolution

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(2015) Duy Tin Truong et al.   NATURE METHODS

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism

(2014) Alistair B. Russell et al.   Cell Host & Microbe

Human Gut Microbes Use Multiple Transporters to Distinguish Vitamin B12 Analogs and Compete in the Gut

(2014) Patrick H. Degnan et al.   Cell Host & Microbe

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Escherichia coli Dysbiosis Correlates With Gastrointestinal Dysfunction in Children With Cystic Fibrosis

(2013) Lucas R. Hoffman et al.   CLINICAL INFECTIOUS DISEASES

Haemolysin Coregulated Protein Is an Exported Receptor and Chaperone of Type VI Secretion Substrates

(2013) Julie M. Silverman et al.   MOLECULAR CELL

Competition sensing: the social side of bacterial stress responses

(2013) Daniel M. Cornforth et al.   NATURE REVIEWS MICROBIOLOGY

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

(2012) Dapeng Zhang et al.   Biology Direct

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification of Functional Toxin/Immunity Genes Linked to Contact-Dependent Growth Inhibition (CDI) and Rearrangement Hotspot (Rhs) Systems

(2011) Stephen J. Poole et al.   PLoS Genetics

A Type VI Secretion System of Pseudomonas aeruginosa Targets a Toxin to Bacteria

(2010) Rachel D. Hood et al.   Cell Host & Microbe

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

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Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

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