Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes

The Effects of Captivity on the Mammalian Gut Microbiome

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Next-generation approaches to understand and combat the antibiotic resistome

(2017) Terence S. Crofts et al.   NATURE REVIEWS MICROBIOLOGY

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

Captivity humanizes the primate microbiome

(2016) Jonathan B. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

A diverse intrinsic antibiotic resistome from a cave bacterium

(2016) Andrew C. Pawlowski et al.   Nature Communications

The Prehistory of Antibiotic Resistance

(2016) Julie Perry et al.   Cold Spring Harbor Perspectives in Medicine

Bifidobacteria and Their Role as Members of the Human Gut Microbiota

(2016) Amy O'Callaghan et al.   Frontiers in Microbiology

Social behavior shapes the chimpanzee pan-microbiome

(2016) A. H. Moeller et al.   Science Advances

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons

(2015) Tiantian Ren et al.   ENVIRONMENTAL MICROBIOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Social networks predict gut microbiome composition in wild baboons

(2015) Jenny Tung et al.   eLife

The microbiome of uncontacted Amerindians

(2015) J. C. Clemente et al.   Science Advances

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Persistent gut microbiota immaturity in malnourished Bangladeshi children

(2014) Sathish Subramanian et al.   NATURE

Microbiological effects of sublethal levels of antibiotics

(2014) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Antibiotic resistance—the need for global solutions

(2013) Ramanan Laxminarayan et al.   LANCET INFECTIOUS DISEASES

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes

(2013) Aimée M. Moore et al.   PLoS One

The antibiotic resistance “mobilome”: searching for the link between environment and clinic

(2013) Julie A. Perry et al.   Frontiers in Microbiology

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

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Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Kinda baboons (Papio kindae) and grayfoot chacma baboons (P. ursinus griseipes) hybridize in the Kafue river valley, Zambia

(2010) C.J. Jolly et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Call of the wild: antibiotic resistance genes in natural environments

(2010) Heather K. Allen et al.   NATURE REVIEWS MICROBIOLOGY

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Antibiotic resistance in a very remote Amazonas community

(2008) Alessandro Bartoloni et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotics and Antibiotic Resistance Genes in Natural Environments

(2008) J. L. Martinez   SCIENCE