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

Making the Most of “Omics” for Symbiosis Research

(2016) J Chaston et al.   BIOLOGICAL BULLETIN

Multiorganismal Insects: Diversity and Function of Resident Microorganisms

(2015) Angela E. Douglas   Annual Review of Entomology

The Gut Microbial Endocrine Organ: Bacterially Derived Signals Driving Cardiometabolic Diseases

(2015) J. Mark Brown et al.   Annual Review of Medicine

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

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

(2015) Jun Wang et al.   Nature Communications

Social networks predict gut microbiome composition in wild baboons

(2015) Jenny Tung et al.   eLife

Insect behaviour and the microbiome

(2015) Zenobia Lewis et al.   Current Opinion in Insect Science

The Importance of Microbes in Animal Development: Lessons from the Squid-Vibrio Symbiosis

(2014) Margaret J. McFall-Ngai   Annual Review of Microbiology

Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One

(2014) James T. Van Leuven et al.   CELL

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

(2014) Ohad Manor et al.   Cell Metabolism

The cryptic role of biodiversity in the emergence of host-microbial mutualisms

(2014) Pradeep Pillai et al.   ECOLOGY LETTERS

Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

(2014) Maggie R. Wagner et al.   ECOLOGY LETTERS

Clostridium difficile and the microbiota

(2014) Anna M. Seekatz et al.   JOURNAL OF CLINICAL INVESTIGATION

The microbiome revolution

(2014) Martin J. Blaser   JOURNAL OF CLINICAL INVESTIGATION

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

(2014) Daniel I. Bolnick et al.   MOLECULAR ECOLOGY

Does evolutionary theory need a rethink?

(2014) Kevin Laland et al.   NATURE

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

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

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

(2014) S. W. Kembel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics and host specialization of honey bee and bumble bee gut symbionts

(2014) W. K. Kwong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Partner choice and fidelity stabilize coevolution in a Cretaceous-age defensive symbiosis

(2014) M. Kaltenpoth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional and phylogenetic assembly of microbial communities in the human microbiome

(2014) Afrah Shafquat et al.   TRENDS IN MICROBIOLOGY

Symbiosis as a General Principle in Eukaryotic Evolution

(2014) A. E. Douglas   Cold Spring Harbor Perspectives in Biology

Divining the Essence of Symbiosis: Insights from the Squid-Vibrio Model

(2014) Margaret McFall-Ngai   PLOS BIOLOGY

Holobiont–Holobiont Interactions: Redefining Host–Parasite Interactions

(2014) Nolwenn Marie Dheilly   PLoS Pathogens

Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?

(2014) Roman M. Stilling et al.   Frontiers in Cellular and Infection Microbiology

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

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

Symbiote transmission and maintenance of extra-genomic associations

(2014) Benjamin M. Fitzpatrick   Frontiers in Microbiology

Microbial impacts on insect evolutionary diversification: from patterns to mechanisms

(2014) Fabrice Vavre et al.   Current Opinion in Insect Science

Microbial secondary metabolites and their impacts on insect symbioses

(2014) Jonathan L Klassen   Current Opinion in Insect Science

A holobiont birth narrative: the epigenetic transmission of the human microbiome

(2014) Scott F. Gilbert   Frontiers in Genetics

The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission

(2013) Dieter Ebert   Annual Review of Ecology Evolution and Systematics

Cytonuclear Genomic Interactions and Hybrid Breakdown

(2013) Ronald S. Burton et al.   Annual Review of Ecology Evolution and Systematics

The world within: Quantifying the determinants and outcomes of a host's microbiome

(2013) Elizabeth T. Borer et al.   BASIC AND APPLIED ECOLOGY

Previously unrecognized stages of species-specific colonization in the mutualism betweenXenorhabdusbacteria andSteinernemanematodes

(2013) John M. Chaston et al.   CELLULAR MICROBIOLOGY

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

(2013) Sharon Greenblum et al.   CURRENT OPINION IN BIOTECHNOLOGY

Omics approaches to study host–microbiota interactions

(2013) Peter van Baarlen et al.   CURRENT OPINION IN MICROBIOLOGY

Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective

(2013) Emma Allen-Vercoe   CURRENT OPINION IN MICROBIOLOGY

Under niche construction: an operational bridge between ecology, evolution, and ecosystem science

(2013) Blake Matthews et al.   ECOLOGICAL MONOGRAPHS

Exploring host-microbiota interactions in animal models and humans

(2013) A. D. Kostic et al.   GENES & DEVELOPMENT

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila

(2013) Bertsy Goic et al.   NATURE IMMUNOLOGY

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiotic bacteria appear to mediate hyena social odors

(2013) K. R. Theis 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

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Niche Construction Theory: A Practical Guide for Ecologists

(2013) John Odling-Smee et al.   QUARTERLY REVIEW OF BIOLOGY

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

(2013) R. M. Brucker et al.   SCIENCE

Wolbachia: Can we save lives with a great pandemic?

(2013) Daniel LePage et al.   TRENDS IN PARASITOLOGY

The capacious hologenome

(2013) Robert M. Brucker et al.   ZOOLOGY

Viral Subversion of the Nuclear Pore Complex

(2013) Valerie Le Sage et al.   Viruses-Basel

Mom Knows Best: The Universality of Maternal Microbial Transmission

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

From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome

(2012) Noah Fierer et al.   Annual Review of Ecology Evolution and Systematics

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

(2012) Hachung Chung et al.   CELL

The microbiome as a human organ

(2012) F. Baquero et al.   CLINICAL MICROBIOLOGY AND INFECTION

Actinobacteria as essential symbionts in firebugs and cotton stainers (Hemiptera, Pyrrhocoridae)

(2012) Hassan Salem et al.   ENVIRONMENTAL MICROBIOLOGY

The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks

(2012) Hadas Hawlena et al.   ISME Journal

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

The interplay between the intestinal microbiota and the brain

(2012) Stephen M. Collins et al.   NATURE REVIEWS MICROBIOLOGY

Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

(2012) John F. Cryan et al.   NATURE REVIEWS NEUROSCIENCE

Murine Gut Microbiota Is Defined by Host Genetics and Modulates Variation of Metabolic Traits

(2012) Autumn M. McKnite et al.   PLoS One

Distinctive Gut Microbiota of Honey Bees Assessed Using Deep Sampling from Individual Worker Bees

(2012) Nancy A. Moran et al.   PLoS One

A Symbiotic View of Life: We Have Never Been Individuals

(2012) Scott F. Gilbert et al.   QUARTERLY REVIEW OF BIOLOGY

Animal Behavior and the Microbiome

(2012) V. O. Ezenwa et al.   SCIENCE

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

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

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Host-Gut Microbiota Metabolic Interactions

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

Speciation by symbiosis

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

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Animal behaviour meets microbial ecology

(2011) Elizabeth A. Archie et al.   ANIMAL BEHAVIOUR

Towards a postmodern synthesis of evolutionary biology

(2011) Eugene V. Koonin   CELL CYCLE

The potter’s wheel: the host’s role in sculpting its microbiota

(2011) Charles L. Bevins et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Our microbial selves: what ecology can teach us

(2011) Antonio Gonzalez et al.   EMBO REPORTS

Towards an Evolutionary Model of Animal-Associated Microbiomes

(2011) Carl J. Yeoman et al.   Entropy

Beyond the Venn diagram: the hunt for a core microbiome

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Robert M. Brucker et al.   EVOLUTION

Horizontal Transmission Rapidly Erodes Disequilibria Between Organelle and Symbiont Genomes

(2011) Yaniv Brandvain et al.   GENETICS

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Inheritance of acquired characters in animals: A historical overview, further evidence and mechanistic explanations

(2011) Y.-S. Liu   ITALIAN JOURNAL OF ZOOLOGY

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

The secret languages of coevolved symbioses: Insights from the Euprymna scolopes–Vibrio fischeri symbiosis

(2011) Margaret McFall-Ngai et al.   SEMINARS IN IMMUNOLOGY

Metaorganisms as the new frontier

(2011) Thomas C.G. Bosch et al.   ZOOLOGY

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

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

(2011) James Angus Chandler et al.   PLoS Genetics

Why bacteria matter in animal development and evolution

(2010) Sebastian Fraune et al.   BIOESSAYS

Systems approaches to microbial communities and their functioning

(2010) Wilfred FM Röling et al.   CURRENT OPINION IN BIOTECHNOLOGY

Plant immune system incompatibility and the distribution of enemies in natural hybrid zones

(2010) M Brian Traw et al.   CURRENT OPINION IN PLANT BIOLOGY

The intestinal microbiome: A separate organ inside the body with the metabolic potential to influence the bioactivity of botanicals

(2010) Sam Possemiers et al.   FITOTERAPIA

Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola

(2010) A. C. C. Wilson et al.   INSECT MOLECULAR BIOLOGY

Multilevel and kin selection in a connected world

(2010) Michael J. Wade et al.   NATURE

Endogenous non-retroviral RNA virus elements in mammalian genomes

(2010) Masayuki Horie et al.   NATURE

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

(2010) A. K. Benson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Commensal bacteria play a role in mating preference of Drosophila melanogaster

(2010) G. Sharon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of animals and plants via symbiosis with microorganisms

(2010) Eugene Rosenberg et al.   Environmental Microbiology Reports

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

Infectious Speciation Revisited: Impact of Symbiont-Depletion on Female Fitness and Mating Behavior of Drosophila paulistorum

(2010) Wolfgang J. Miller et al.   PLoS Pathogens

Is evolution Darwinian or/and Lamarckian?

(2009) Eugene V Koonin et al.   Biology Direct

The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework

(2009) Eugene Rosenberg et al.   ENVIRONMENTAL MICROBIOLOGY

SPECIATION DUE TO HYBRID NECROSIS IN PLANT-PATHOGEN MODELS

(2009) Iaroslav Ispolatov et al.   EVOLUTION

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

(2009) Gabriele Berg et al.   FEMS MICROBIOLOGY ECOLOGY

The microbial dimension in insect nutritional ecology

(2009) A. E. Douglas   FUNCTIONAL ECOLOGY

Clostridium difficile infection: new developments in epidemiology and pathogenesis

(2009) Maja Rupnik et al.   NATURE REVIEWS MICROBIOLOGY

Beyond society: the evolution of organismality

(2009) D. C. Queller et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Quantifying Adaptive Evolution in the Drosophila Immune System

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

Molecular Determinants of a Symbiotic Chronic Infection

(2008) Katherine E. Gibson et al.   Annual Review of Genetics

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY

Worlds within worlds: evolution of the vertebrate gut microbiota

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

Is meconium from healthy newborns actually sterile?

(2008) Esther Jiménez et al.   RESEARCH IN MICROBIOLOGY