The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome

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

(2020) Tayte P. Campbell et al.   ISME Journal

Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model

(2020) Barry Rockx et al.   SCIENCE

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms

(2020) Jian Sun et al.   Nature Communications

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

(2020) Tanya M. Monaghan et al.   Gut Microbes

Family livestock waste: An ignored pollutant resource of antibiotic resistance genes

(2020) Yanru Gu et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Rotavirus is associated with decompensated diarrhea among young rhesus macaques (Macaca mulatta )

(2019) Kuo-Yang Wang et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

(2019) Samuel T. Westreich et al.   Microbiome

Probiotic Lactobacillus casei: Effective for Managing Childhood Diarrhea by Altering Gut Microbiota and Attenuating Fecal Inflammatory Markers

(2019) Hung-Hsiang Lai et al.   Nutrients

Lactobacillus fermentum and Lactobacillus plantarum increased gut microbiota diversity and functionality, and mitigated Enterobacteriaceae, in a mouse model

(2019) C. Linninge et al.   Beneficial Microbes

In vitro colonic fermentation of dietary fibers: Fermentation rate, short-chain fatty acid production and changes in microbiota

(2019) Miaomiao Wang et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Gut resistomes, microbiota and antibiotic residues in Chinese patients undergoing antibiotic administration and healthy individuals

(2019) Yujing Duan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Dynamics of bacterial composition and the fate of antibiotic resistance genes and mobile genetic elements during the co-composting with gentamicin fermentation residue and lovastatin fermentation residue

(2018) Yuanwang Liu et al.   BIORESOURCE TECHNOLOGY

Understanding the adhesion mechanism of a mucin binding domain from Lactobacillus fermentum and its role in enteropathogen exclusion

(2018) Maitrayee Chatterjee et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

(2018) Katherine R. Amato et al.   ISME Journal

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Role of Lactobacillus reuteri in Human Health and Diseases

(2018) Qinghui Mu et al.   Frontiers in Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets

(2018) Boshuai Liu et al.   Frontiers in Microbiology

Species-level functional profiling of metagenomes and metatranscriptomes

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

Gut microbiota functions: metabolism of nutrients and other food components

(2017) Ian Rowland et al.   EUROPEAN JOURNAL OF NUTRITION

Probiotic roles ofLactobacillussp. in swine: insights from gut microbiota

(2017) V.D.V. Valeriano et al.   JOURNAL OF APPLIED MICROBIOLOGY

Gut microbiota-mediated protection against diarrheal infections

(2017) Stefanie L. Vogt et al.   JOURNAL OF TRAVEL MEDICINE

Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea

(2017) Beatrix Kapusinszky et al.   JOURNAL OF VIROLOGY

Subspecies in the global human gut microbiome

(2017) Paul I Costea et al.   Molecular Systems Biology

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Rhesus monkeys for a nonhuman primate model of cytomegalovirus infections

(2017) Hannah L Itell et al.   Current Opinion in Virology

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

(2017) Francesco Asnicar et al.   mSystems

Generation of a Nonhuman Primate Model of Severe Combined Immunodeficiency Using Highly Efficient Genome Editing

(2016) Kenya Sato et al.   Cell Stem Cell

Captivity humanizes the primate microbiome

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

Mining metagenomic whole genome sequences revealed subdominant but constantLactobacilluspopulation in the human gut microbiota

(2016) Maddalena Rossi et al.   Environmental Microbiology Reports

Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis

(2016) Wenjun Liu et al.   Scientific Reports

Bovine mastitis may be associated with the deprivation of gut Lactobacillus

(2016) C. Ma et al.   Beneficial Microbes

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

(2016) Emily Vogtmann et al.   PLoS One

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

(2015) Simone Rampelli et al.   CURRENT BIOLOGY

Etiology of diarrhea among children under the age five in China: Results from a five-year surveillance

(2015) Jianxing Yu et al.   JOURNAL OF INFECTION

Tackling antibiotic resistance: the environmental framework

(2015) Thomas U. Berendonk et al.   NATURE REVIEWS MICROBIOLOGY

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

(2015) K. Z. Coyte et al.   SCIENCE

Subsistence strategies in traditional societies distinguish gut microbiomes

(2015) Alexandra J. Obregon-Tito et al.   Nature Communications

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Cross-talk between probiotic lactobacilli and host immune system

(2014) T.S. Kemgang et al.   JOURNAL OF APPLIED MICROBIOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Gut Microbiota-Derived Short-Chain Fatty Acids, T Cells, and Inflammation

(2014) Chang H. Kim et al.   Immune Network

Familial aggregation of chronic diarrhea disease (CDD) in rhesus macaques (Macaca mulatta)

(2013) Sree Kanthaswamy et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Risk Factor Analysis May Provide Clues to Diarrhea Prevention in Outdoor-Housed Rhesus Macaques (Macaca mulatta)

(2013) KAMM PRONGAY et al.   AMERICAN JOURNAL OF PRIMATOLOGY

Bacterial and viral etiology of childhood diarrhea in Ouagadougou, Burkina Faso

(2013) Isidore Juste O Bonkoungou et al.   BMC Pediatrics

Epidemiological Interpretation of Studies Examining the Effect of Antibiotic Usage on Resistance

(2013) V. Schechner et al.   CLINICAL MICROBIOLOGY REVIEWS

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

Climate Change is Likely to Worsen the Public Health Threat of Diarrheal Disease in Botswana

(2013) Kathleen Alexander et al.   International Journal of Environmental Research and Public Health

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

The non-human primate model of tuberculosis

(2012) D. Kaushal et al.   JOURNAL OF MEDICAL PRIMATOLOGY

High incidence of rhesus enteric calicivirus infections and diarrhea in captive juvenile macaques: a likely association

(2012) Tibor Farkas et al.   JOURNAL OF MEDICAL PRIMATOLOGY

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli 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

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Carbapenem resistance in Enterobacteriaceae: here is the storm!

(2012) Patrice Nordmann et al.   TRENDS IN MOLECULAR MEDICINE

Investigation of the prevalence of tetQ, tetX and tetX1 genes in Bacteroides strains with elevated tigecycline minimum inhibitory concentrations

(2011) Noémi Anikó Bartha et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Lactobacillus Adhesion to Mucus

(2011) Maxwell L. Van Tassell et al.   Nutrients

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Role of Colonic Short-Chain Fatty Acid Transport in Diarrhea

(2010) Henry J. Binder   Annual Review of Physiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Evaluation of the use of coconut to treat chronic diarrhea in rhesus macaques (Macaca mulatta)

(2010) J.L. Wilk et al.   JOURNAL OF MEDICAL PRIMATOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inhibition of Fungi and Gram-Negative Bacteria by Bacteriocin BacTN635 Produced by Lactobacillus plantarum sp. TN635

(2009) Slim Smaoui et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

The tetracycline resistome

(2009) Maulik Thaker et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Investigation of  the faecal microbiota associated with canine chronic diarrhoea

(2009) Jie Jia et al.   FEMS MICROBIOLOGY ECOLOGY

Human-derived probiotic Lactobacillus reuteri demonstrate antimicrobial activities targeting diverse enteric bacterial pathogens

(2008) Jennifer K. Spinler et al.   ANAEROBE

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE