Keystone taxa as drivers of microbiome structure and functioning

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes

(2017) Emily B. Graham et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2017) Alexandre Jousset et al.   ISME Journal

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Plant cultivars imprint the rhizosphere bacterial community composition and association networks

(2017) Yuji Jiang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil

(2017) Honggui Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research

(2017) Claire E. Stanley et al.   TRENDS IN MICROBIOLOGY

Soil C and N as causal factors of spatial variation in extracellular enzyme activity across grassland-woodland ecotones

(2016) Samiran Banerjee et al.   APPLIED SOIL ECOLOGY

Network-based metabolic analysis and microbial community modeling

(2016) Cesar Cardona et al.   CURRENT OPINION IN MICROBIOLOGY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types

(2016) Yang Ji et al.   ENVIRONMENTAL MICROBIOLOGY

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine

(2016) Yuanqing Chao et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap

(2016) Jarishma K. Gokul et al.   MOLECULAR ECOLOGY

Network analysis reveals seasonal variation of co-occurrence correlations between Cyanobacteria and other bacterioplankton

(2016) Dayong Zhao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns

(2016) Shuo Jiao et al.   SOIL BIOLOGY & BIOCHEMISTRY

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts

(2016) George Hajishengallis et al.   TRENDS IN MICROBIOLOGY

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

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

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

(2016) Haifeng Geng et al.   Frontiers in Microbiology

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure

(2015) Richard Hill et al.   ENVIRONMENTAL MICROBIOLOGY

Determinants of bacterial communities in Canadian agroforestry systems

(2015) Samiran Banerjee et al.   ENVIRONMENTAL MICROBIOLOGY

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

(2015) David J Eldridge et al.   ISME Journal

Tritagonist as a new term for uncharacterised microorganisms in environmental systems

(2015) Florian M Freimoser et al.   ISME Journal

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests

(2015) Junjun Ding et al.   MOLECULAR ECOLOGY

Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract

(2015) Sushma Kommineni et al.   NATURE

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

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

Mycorrhizal ecology and evolution: the past, the present, and the future

(2015) Marcel G. A. van der Heijden et al.   NEW PHYTOLOGIST

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

(2015) Pål Trosvik et al.   Microbiome

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape

(2014) Meredith M. Curtis et al.   Cell Host & Microbe

Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice

(2014) Jingjing Wang et al.   ISME Journal

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Recently identified microbial guild mediates soil N2O sink capacity

(2014) Christopher M. Jones et al.   Nature Climate Change

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

(2014) David Berry et al.   Frontiers in Microbiology

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes

(2013) Trista J Vick-Majors et al.   ISME Journal

On-chip microbial culture for the specific detection of very low levels of bacteria

(2013) Sihem Bouguelia et al.   LAB ON A CHIP

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Extending the concept of keystone species to communities and ecosystems

(2012) Nicolas Mouquet et al.   ECOLOGY LETTERS

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Microbial control over carbon cycling in soil

(2012) Joshua P. Schimel et al.   Frontiers in Microbiology

Structural equation modeling in the plant sciences: An example using yield components in oat

(2011) Eric Lamb et al.   CANADIAN JOURNAL OF PLANT SCIENCE

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

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Intestinal homeostasis and its breakdown in inflammatory bowel disease

(2011) Kevin J. Maloy et al.   NATURE

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Intestinal Bacteria and the Regulation of Immune Cell Homeostasis

(2010) David A. Hill et al.   Annual Review of Immunology

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

On the specification of structural equation models for ecological systems

(2010) James B. Grace et al.   ECOLOGICAL MONOGRAPHS

Structure of the human gastric bacterial community in relation to Helicobacter pylori status

(2010) Ana Maldonado-Contreras et al.   ISME Journal

A ‘rare biosphere’ microorganism contributes to sulfate reduction in a peatland

(2010) Michael Pester et al.   ISME Journal

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

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

(2009) M. Hamady et al.   GENOME RESEARCH

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses

(2009) Shaoguang Wu et al.   NATURE MEDICINE

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

A trap for in situ cultivation of filamentous actinobacteria

(2008) Ekaterina Gavrish et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Culture-Independent Assessment of Rhizobiales-Related Alphaproteobacteria and the Diversity of Methylobacterium in the Rhizosphere and Rhizoplane of Transgenic Eucalyptus

(2008) Fernando Dini Andreote et al.   MICROBIAL ECOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

A single-cell view on the ecophysiology of anaerobic phototrophic bacteria

(2008) N. Musat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA