The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

A great-ape view of the gut microbiome

(2019) Alex H. Nishida et al.   NATURE REVIEWS GENETICS

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

(2019) Francesca De Filippis et al.   Cell Host & Microbe

Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles-A comprehensive literature review

(2019) Gabriela Precup et al.   BRITISH JOURNAL OF NUTRITION

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

(2019) Lydia K. Greene et al.   AMERICAN JOURNAL OF PRIMATOLOGY

African apes coexisting with logging: Comparing chimpanzee ( Pan troglodytes troglodytes ) and gorilla ( Gorilla gorilla gorilla ) resource needs and responses to forestry activities

(2018) David Morgan et al.   BIOLOGICAL CONSERVATION

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes

(2018) Aura Ferreiro et al.   CELL

Pathogen Transmission from Humans to Great Apes is a Growing Threat to Primate Conservation

(2018) Emily Dunay et al.   EcoHealth

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

(2018) Allison L. Hicks et al.   Nature Communications

Defining ICR-Mo, an intrinsic colistin resistance determinant from Moraxella osloensis

(2018) Wenhui Wei et al.   PLoS Genetics

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

(2018) Pablo Tsukayama et al.   mSystems

US Immigration Westernizes the Human Gut Microbiome

(2018) Pajau Vangay et al.   CELL

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

The Effects of Captivity on the Mammalian Gut Microbiome

(2017) Valerie J. McKenzie et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

MCR-2-mediated plasmid-borne polymyxin resistance most likely originates from Moraxella pluranimalium

(2017) Laurent Poirel et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

mcr-1 and mcr-2 (mcr-6.1) variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015

(2017) Manal AbuOun et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

(2017) Andreas Porse et al.   Frontiers in Cellular and Infection Microbiology

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

(2016) Yi-Yun Liu et al.   LANCET INFECTIOUS DISEASES

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla)

(2016) Klára Vlčková et al.   MICROBIAL ECOLOGY

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

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

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

(2016) Andres Gomez et al.   Cell Reports

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome

(2016) Matteo Soverini et al.   Frontiers in Microbiology

The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes

(2015) Kevin J. Forsberg et al.   CHEMISTRY & BIOLOGY

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp

(2015) Andres Gomez et al.   ISME Journal

The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

(2015) Inés Martínez et al.   Cell Reports

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Variable responses of human and non-human primate gut microbiomes to a Western diet

(2015) Katherine R. Amato et al.   Microbiome

The microbiome of uncontacted Amerindians

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

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

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

Lethal aggression in Pan is better explained by adaptive strategies than human impacts

(2014) Michael L. Wilson et al.   NATURE

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Rapid changes in the gut microbiome during human evolution

(2014) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Implementing a low-starch biscuit-free diet in zoo gorillas: The impact on health

(2014) E.H. Less et al.   ZOO BIOLOGY

Gut microbiome of the Hadza hunter-gatherers

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

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

(2013) A. H. Moeller et al.   GENOME RESEARCH

Western diet induces dysbiosis with increasedE coliin CEABAC10 mice,alters host barrier function favouring AIEC colonisation

(2013) Margarita Martinez-Medina et al.   GUT

Comparison of the Distal Gut Microbiota from People and Animals in Africa

(2013) Richard J. Ellis et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

(2013) Michael R. Gillings   Frontiers in Microbiology

Recent decline in suitable environmental conditions for African great apes

(2012) Jessica Junker et al.   DIVERSITY AND DISTRIBUTIONS

Exogenously acquired 16S rRNA methyltransferases found in aminoglycoside-resistant pathogenic Gram-negative bacteria: An update

(2012) Jun-ichi Wachino et al.   DRUG RESISTANCE UPDATES

Colistin: an update on the antibiotic of the 21st century

(2012) Silpak Biswas et al.   Expert Review of Anti-Infective Therapy

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

(2012) J Gregory Caporaso et al.   ISME Journal

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

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

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

Complete genome sequence of Treponema succinifaciens type strain (6091T)

(2011) Cliff Han et al.   Standards in Genomic Sciences

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Aminoglycoside modifying enzymes

(2010) Maria S. Ramirez et al.   DRUG RESISTANCE UPDATES

Role of the gut microbiota in defining human health

(2010) Kei E Fujimura et al.   Expert Review of Anti-Infective Therapy

Origin of the human malaria parasite Plasmodium falciparum in gorillas

(2010) Weimin Liu et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

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

Gastrointestinal Bacterial Transmission among Humans, Mountain Gorillas, and Livestock in Bwindi Impenetrable National Park, Uganda

(2008) INNOCENT B. RWEGO et al.   CONSERVATION BIOLOGY

Pandemic Human Viruses Cause Decline of Endangered Great Apes

(2008) Sophie Köndgen et al.   CURRENT BIOLOGY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Accelerated Human Population Growth at Protected Area Edges

(2008) G. Wittemyer et al.   SCIENCE