Applying the core microbiome to understand host-microbe systems

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

(2020) Se Jin Song et al.   mBio

Trophic level mediates soil microbial community composition and function

(2020) Jane M. Lucas et al.   SOIL BIOLOGY & BIOCHEMISTRY

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection

(2019) Eric M. Velazquez et al.   Nature Microbiology

Rare gut microbiota associated with breeding success, hormone metabolites and ovarian cycle phase in the critically endangered eastern black rhino

(2019) Rachael E. Antwis et al.   Microbiome

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

(2019) Serena Sanna et al.   NATURE GENETICS

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Not all animals need a microbiome

(2019) Tobin J Hammer et al.   FEMS MICROBIOLOGY LETTERS

Understanding Competition and Cooperation within the Mammalian Gut Microbiome

(2019) Katharine Z. Coyte et al.   CURRENT BIOLOGY

Spatial patterns of fungal endophytes in a subtropical montane rainforest of northern Taiwan

(2019) Daniel Thomas et al.   Fungal Ecology

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

(2019) Nicholas D. Youngblut et al.   Nature Communications

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish

(2019) Fotini Kokou et al.   Nature Microbiology

Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere

(2019) Charlotte I. Carlström et al.   Nature Ecology & Evolution

Abdominal microbial communities in ants depend on colony membership rather than caste and are linked to colony productivity

(2019) Francisca H. I. D. Segers et al.   Ecology and Evolution

Gut microbiota structure differs between honeybees in winter and summer

(2019) Lucie Kešnerová et al.   ISME Journal

Evidence for a multi-level trophic organization of the human gut microbiome

(2019) Tong Wang et al.   PLoS Computational Biology

Seasonal shifts in the insect gut microbiome are concurrent with changes in cold tolerance and immunity

(2018) Laura V. Ferguson et al.   FUNCTIONAL ECOLOGY

Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota

(2018) H. Pieter J. van Veelen et al.   ISME Journal

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

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

The impact of bacteriophages on phyllosphere bacterial abundance and composition

(2018) Norma M. Morella et al.   MOLECULAR ECOLOGY

Introduction: The host-associated microbiome: Pattern, process and function

(2018) Laura Wegener Parfrey et al.   MOLECULAR ECOLOGY

Rates of gut microbiome divergence in mammals

(2018) Alex H. Nishida et al.   MOLECULAR ECOLOGY

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Gut microbiota utilize immunoglobulin A for mucosal colonization

(2018) G. P. Donaldson et al.   SCIENCE

Functional Genomics of Host–Microbiome Interactions in Humans

(2018) Francesca Luca et al.   TRENDS IN GENETICS

Defining microbiome function

(2018) Jonathan L. Klassen   Nature Microbiology

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

(2018) M. Lisandra Zepeda Mendoza et al.   Nature Ecology & Evolution

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

The gut microbiome as a driver of individual variation in cognition and functional behaviour

(2018) Gabrielle L. Davidson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Macroecology to Unite All Life, Large and Small

(2018) Ashley Shade et al.   TRENDS IN ECOLOGY & EVOLUTION

Can we predict keystones?

(2018) Lisa Röttjers et al.   NATURE REVIEWS MICROBIOLOGY

Microbiome-assisted carrion preservation aids larval development in a burying beetle

(2018) Shantanu P. Shukla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Upper Limit on the Functional Fraction of the Human Genome

(2017) Dan Graur   Genome Biology and Evolution

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons

(2017) Laura E. Grieneisen et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

Effects of host species and environment on the skin microbiome of Plethodontid salamanders

(2017) Carly R. Muletz Wolz et al.   JOURNAL OF ANIMAL ECOLOGY

Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring

(2017) Shantanu P. Shukla et al.   MOLECULAR ECOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery

(2017) Derrick M Chu et al.   NATURE MEDICINE

The resilience of the intestinal microbiota influences health and disease

(2017) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas

(2017) Qi Wu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Defining the Core Microbiome in Corals’ Microbial Soup

(2017) Alejandra Hernandez-Agreda et al.   TRENDS IN MICROBIOLOGY

Let the Core Microbiota Be Functional

(2017) Philippe Lemanceau et al.   TRENDS IN PLANT SCIENCE

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

(2017) Yun Kit Yeoh et al.   Nature Communications

The evolution of host-symbiont dependence

(2017) Roberta M. Fisher et al.   Nature Communications

Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels

(2017) Tiantian Ren et al.   Microbiome

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

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

Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

(2016) Kei Hiruma et al.   CELL

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities

(2016) Tiantian Ren et al.   GENE

Phylogenetic organization of bacterial activity

(2016) Ember M Morrissey et al.   ISME Journal

Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits

(2016) Yuliaxis Ramayo-Caldas et al.   ISME Journal

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

(2016) Hsiao-Pei Lu et al.   ISME Journal

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

(2016) Sheerli Kruger Ben Shabat et al.   ISME Journal

A bacterial filter protects and structures the gut microbiome of an insect

(2016) Michele Caroline Lanan et al.   ISME Journal

Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition

(2016) M. Schwarzer et al.   SCIENCE

Gut Microbiotas and Host Evolution: Scaling Up Symbiosis

(2016) Michael Shapira   TRENDS IN ECOLOGY & EVOLUTION

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

(2016) Felix Sommer et al.   Cell Reports

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

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

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

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

Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche

(2016) Sarah M. Kopac et al.   Frontiers in Microbiology

Control of Brain Development, Function, and Behavior by the Microbiome

(2015) Timothy R. Sampson et al.   Cell Host & Microbe

Bacterial predation in a marine host-associated microbiome

(2015) Rory M Welsh et al.   ISME Journal

Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp

(2015) Andres Gomez et al.   ISME Journal

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

(2015) Tracy D Ainsworth et al.   ISME Journal

Microbial response to simulated global change is phylogenetically conserved and linked with functional potential

(2015) Anthony S Amend et al.   ISME Journal

The composition of the zebrafish intestinal microbial community varies across development

(2015) W Zac Stephens et al.   ISME Journal

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities

(2015) Jiachao Zhang et al.   ISME Journal

Marked seasonal variation in the wild mouse gut microbiota

(2015) Corinne F Maurice et al.   ISME Journal

Horizontal gene transfer: building the web of life

(2015) Shannon M. Soucy et al.   NATURE REVIEWS GENETICS

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Temporal patterns of rarity provide a more complete view of microbial diversity

(2015) Ashley Shade et al.   TRENDS IN MICROBIOLOGY

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations

(2015) Zhengsheng Xue et al.   mBio

Distinguishing between "Function" and "Effect" in Genome Biology

(2014) W. F. Doolittle et al.   Genome Biology and Evolution

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra)

(2014) Katherine R. Amato et al.   MICROBIAL ECOLOGY

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

Functional and phylogenetic assembly of microbial communities in the human microbiome

(2014) Afrah Shafquat et al.   TRENDS IN MICROBIOLOGY

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission

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

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

(2013) Kelvin Li et al.   PLoS One

Long-Term Temporal Analysis of the Human Fecal Microbiota Revealed a Stable Core of Dominant Bacterial Species

(2013) Inés Martínez et al.   PLoS One

Restructuring of the amphibian gut microbiota through metamorphosis

(2013) Kevin D. Kohl et al.   Environmental Microbiology Reports

Mom Knows Best: The Universality of Maternal Microbial Transmission

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

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

(2012) Hannah V. Carey et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

(2012) Omry Koren et al.   CELL

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

(2012) Susan M. Huse et al.   PLoS One

Functional diversity within the simple gut microbiota of the honey bee

(2012) P. Engel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement

(2011) George Hajishengallis et al.   Cell Host & Microbe

Beyond the Venn diagram: the hunt for a core microbiome

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Intestinal Microbiota in Healthy Adults: Temporal Analysis Reveals Individual and Common Core and Relation to Intestinal Symptoms

(2011) Jonna Jalanka-Tuovinen et al.   PLoS One

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) B. D. Muegge et al.   SCIENCE

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

(2009) Anders F Andersson et al.   ISME Journal

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE