Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

The Host Shapes the Gut Microbiota via Fecal MicroRNA

(2016) Shirong Liu et al.   Cell Host & Microbe

Host Selection of Microbiota via Differential Adhesion

(2016) Kirstie McLoughlin et al.   Cell Host & Microbe

Quantification of cerivastatin toxicity supports organismal performance assays as an effective tool during pharmaceutical safety assessment

(2016) Shannon M. Gaukler et al.   Evolutionary Applications

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

(2016) Chenhong Zhang et al.   ISME Journal

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

An optimized approach to germ-free rearing in the jewel waspNasonia

(2016) J. Dylan Shropshire et al.   PeerJ

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

(2016) Kevin R. Theis et al.   mSystems

Host Genetic Control of the Microbiota Mediates the Drosophila Nutritional Phenotype

(2015) John M. Chaston et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets

(2015) Kevin D. Kohl et al.   ENVIRONMENTAL MICROBIOLOGY

Genetic and environmental control of host-gut microbiota interactions

(2015) Elin Org et al.   GENOME RESEARCH

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

What IsPeromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification

(2015) Roy N. Platt et al.   JOURNAL OF MAMMALOGY

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

(2015) Xue Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking heritability of the microbiome

(2015) Edward J. van Opstal et al.   SCIENCE

Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts

(2015) Kristen E. Murfin et al.   mBio

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome

(2015) Jun Wang et al.   Nature Communications

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

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

The Cockroach Origin of the Termite Gut Microbiota: Patterns in Bacterial Community Structure Reflect Major Evolutionary Events

(2014) Carsten Dietrich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Intra- and Interindividual Variations Mask Interspecies Variation in the Microbiota of Sympatric Peromyscus Populations

(2014) Nielson T. Baxter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut

(2014) Henning Seedorf et al.   CELL

Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity

(2014) Amandine Everard et al.   ISME Journal

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

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

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

(2014) D. E. Neafsey et al.   SCIENCE

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges

(2014) Cole G. Easson et al.   Frontiers in Microbiology

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

Biphasic assembly of the murine intestinal microbiota during early development

(2013) Ida Gisela Pantoja-Feliciano et al.   ISME Journal

The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis

(2013) Adam C-N Wong et al.   ISME Journal

Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

(2013) Jon G. Sanders et al.   MOLECULAR ECOLOGY

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

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

Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment

(2013) Fabian Staubach et al.   PLoS One

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

(2013) S. Franzenburg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

(2013) P. C. Kashyap et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia

(2013) R. M. Brucker et al.   SCIENCE

Mom Knows Best: The Universality of Maternal Microbial Transmission

(2013) Lisa J. Funkhouser et al.   PLOS BIOLOGY

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography

(2012) CALEB D. PHILLIPS et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

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

Speciation by symbiosis

(2012) Robert M. Brucker et al.   TRENDS IN ECOLOGY & EVOLUTION

A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals

(2012) Rosanna A Alegado et al.   eLife

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Python for Scientists and Engineers

(2011) K. Jarrod Millman et al.   COMPUTING IN SCIENCE & ENGINEERING

THE ROLES OF HOST EVOLUTIONARY RELATIONSHIPS (GENUS: NASONIA) AND DEVELOPMENT IN STRUCTURING MICROBIAL COMMUNITIES

(2011) Robert M. Brucker et al.   EVOLUTION

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

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

(2011) B. D. Muegge et al.   SCIENCE

Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling

(2011) S. C. Shin et al.   SCIENCE

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

(2011) James Angus Chandler et al.   PLoS Genetics

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Intestinal alkaline phosphatase preserves the normal homeostasis of gut microbiota

(2010) M. S. Malo et al.   GUT

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

The evolution of burrowing behaviour in deer mice (genus Peromyscus)

(2009) Jesse N. Weber et al.   ANIMAL BEHAVIOUR

Quantifying Adaptive Evolution in the Drosophila Immune System

(2009) Darren J. Obbard et al.   PLoS Genetics

Grammar-based distance in progressive multiple sequence alignment

(2008) David J Russell et al.   BMC BIOINFORMATICS

Strain-specific priming of resistance in the red flour beetle, Tribolium castaneum

(2008) O. Roth et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE