Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia

The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems

(2018) Lucette Flandroy et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Life history and eco-evolutionary dynamics in light of the gut microbiota

(2017) Emilie Macke et al.   OIKOS

Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria

(2017) Emilie Macke et al.   Nature Communications

Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments

(2016) Maureen Berg et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Daphnia as a refuge for an antibiotic resistance gene in an experimental freshwater community

(2016) Ester M. Eckert et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Gut Microbiotas and Host Evolution: Scaling Up Symbiosis

(2016) Michael Shapira   TRENDS IN ECOLOGY & EVOLUTION

Strain-level dissection of the contribution of the gut microbiome to human metabolic disease

(2016) Chenhong Zhang et al.   Genome Medicine

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution

(2015) Andreas Brune et al.   Annual Review of Microbiology

Gut Microbiota Orchestrates Energy Homeostasis during Cold

(2015) Claire Chevalier et al.   CELL

Bacteria-Mediated Effects of Antibiotics on Daphnia Nutrition

(2015) Elena Gorokhova et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

(2015) Chris CR Smith et al.   ISME Journal

Food availability affects the strength of mutualistic host–microbiota interactions in Daphnia magna

(2015) Martijn Callens et al.   ISME Journal

Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents

(2015) Scott F. Gilbert et al.   NATURE REVIEWS GENETICS

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean,Daphnia magna

(2015) Saranya Peerakietkhajorn et al.   Environmental Microbiology Reports

Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee

(2015) Javier A. Ceja-Navarro et al.   Nature Communications

The Hologenome Concept: Helpful or Hollow?

(2015) Nancy A. Moran et al.   PLOS BIOLOGY

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host

(2014) Ji-Hyun Yun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Water fleas require microbiota for survival, growth and reproduction

(2014) Marilou P Sison-Mangus et al.   ISME Journal

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

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

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

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

Gut–brain axis: how the microbiome influences anxiety and depression

(2013) Jane A. Foster et al.   TRENDS IN NEUROSCIENCES

Concentration-dependent activity in natural environments

(2013) Steve P. Bernier et al.   Frontiers in Microbiology

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Host Cell Autophagy Activated by Antibiotics Is Required for Their Effective Antimycobacterial Drug Action

(2012) Jwa-Jin Kim et al.   Cell Host & Microbe

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

(2012) B. E. Miner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Midgut Microbiota of the Malaria Mosquito Vector Anopheles gambiae and Interactions with Plasmodium falciparum Infection

(2012) Anne Boissière et al.   PLoS Pathogens

Disruption of the Termite Gut Microbiota and Its Prolonged Consequences for Fitness

(2011) Rebeca B. Rosengaus et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Reductive Evolution of Bacterial Genome in Insect Gut Environment

(2011) Naruo Nikoh et al.   Genome Biology and Evolution

Composition and Stability of the Microbial Community inside the Digestive Tract of the Aquatic Crustacean Daphnia magna

(2011) Heike M. Freese et al.   MICROBIAL ECOLOGY

Local and regional factors influencing bacterial community assembly

(2011) Eva S. Lindström et al.   Environmental Microbiology Reports

PCR-based community structure studies of Bacteria associated with eukaryotic organisms: A simple PCR strategy to avoid co-amplification of eukaryotic DNA

(2010) Ingrid Bakke et al.   JOURNAL OF MICROBIOLOGICAL METHODS

From Structure to Function: the Ecology of Host-Associated Microbial Communities

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

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

(2009) D. A. Antonopoulos et al.   INFECTION AND IMMUNITY