A Developing Symbiosis: Enabling Cross-Talk Between Ecologists and Microbiome Scientists

A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome

(2018) Charlotte T C Quigley et al.   JOURNAL OF PHYCOLOGY

Why does the microbiome affect behaviour?

(2018) Katerina V.-A. Johnson et al.   NATURE REVIEWS MICROBIOLOGY

The gut virome of the protochordate model organism, Ciona intestinalis subtype A

(2018) Brittany A. Leigh et al.   VIRUS RESEARCH

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture

(2018) Olav Vadstein et al.   Frontiers in Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Dysbiosis and Its Discontents

(2017) Katarzyna B. Hooks et al.   mBio

An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae)

(2017) Justin P. Shaffer et al.   Frontiers in Microbiology

Stress and stability: applying the Anna Karenina principle to animal microbiomes

(2017) Jesse R. Zaneveld et al.   Nature Microbiology

The microbiome beyond the horizon of ecological and evolutionary theory

(2017) Britt Koskella et al.   Nature Ecology & Evolution

A macroecological theory of microbial biodiversity

(2017) William R. Shoemaker et al.   Nature Ecology & Evolution

Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems

(2016) David G. Bourne et al.   Annual Review of Microbiology

Multi-scale ecological filters shape the crayfish microbiome

(2016) James Skelton et al.   SYMBIOSIS

English translation of Heinrich Anton de Bary’s 1878 speech, ‘Die Erscheinung der Symbiose’ (‘De la symbiose’)

(2016) Nathalie Oulhen et al.   SYMBIOSIS

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

(2016) Andrew W. Brooks et al.   PLOS BIOLOGY

What Is Speciation?

(2016) B. Jesse Shapiro et al.   PLoS Genetics

Disentangling a Holobiont – Recent Advances and Perspectives in Nasonia Wasps

(2016) Jessica Dittmer et al.   Frontiers in Microbiology

Gnotobiotic Rodents: An In Vivo Model for the Study of Microbe–Microbe Interactions

(2016) Rebeca Martín et al.   Frontiers in Microbiology

Low diversity of planktonic bacteria in the tropical ocean

(2016) Mathias Milici et al.   Scientific Reports

Common garden experiments in the genomic era: new perspectives and opportunities

(2015) P de Villemereuil et al.   HEREDITY

Microbes Promote Amino Acid Harvest to Rescue Undernutrition in Drosophila

(2015) Ryuichi Yamada et al.   Cell Reports

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

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

REVIEW: On the species abundance distribution in applied ecology and biodiversity management

(2014) Thomas J. Matthews et al.   JOURNAL OF APPLIED ECOLOGY

Spatial scale resolves the niche versus neutral theory debate

(2014) Jonathan M. Chase   JOURNAL OF VEGETATION SCIENCE

Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development

(2014) Laura B. Martínez-García et al.   NEW PHYTOLOGIST

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

(2013) Alison Morris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Cystic Fibrosis Therapy: A Community Ecology Perspective

(2013) Douglas Conrad et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Global marine bacterial diversity peaks at high latitudes in winter

(2013) Joshua Ladau et al.   ISME Journal

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

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

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

(2013) R. M. Brucker et al.   SCIENCE

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Defining the human microbiome

(2012) Luke K Ursell et al.   NUTRITION REVIEWS

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

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

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Our microbial selves: what ecology can teach us

(2011) Antonio Gonzalez et al.   EMBO REPORTS

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

(2011) Anthony S Amend et al.   ISME Journal

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally

(2011) M. S. Robeson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus

(2010) Jörg Barke et al.   BMC BIOLOGY

A diversity of beta diversities: straightening up a concept gone awry. Part 1. Defining beta diversity as a function of alpha and gamma diversity

(2010) Hanna Tuomisto   ECOGRAPHY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Oral Biofilm Architecture on Natural Teeth

(2010) Vincent Zijnge et al.   PLoS One

A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats

(2009) Benjamin Allen et al.   AMERICAN NATURALIST

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

(2009) J.-B. Raina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relative roles of niche and neutral processes in structuring a soil microbial community

(2009) Alex J Dumbrell et al.   ISME Journal

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

(2009) Leho Tedersoo et al.   MYCORRHIZA

Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans

(2009) V. Schroeckh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global distribution and diversity of coral-associatedArchaeaand their possible role in the coral holobiont nitrogen cycle

(2008) Nachshon Siboni et al.   ENVIRONMENTAL MICROBIOLOGY

Communicability and multipartite structures in complex networks at negative absolute temperatures

(2008) Ernesto Estrada et al.   PHYSICAL REVIEW E

A latitudinal diversity gradient in planktonic marine bacteria

(2008) J. A. Fuhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE