Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

(2019) Pierre Plassart et al.   Scientific Reports

Genomic diversity landscape of the honey bee gut microbiota

(2019) Kirsten M. Ellegaard et al.   Nature Communications

Spatial vs. temporal controls over soil fungal community similarity at continental and global scales

(2019) Colin Averill et al.   ISME Journal

Microbiome genome structure drives function

(2019) Matthew G. Durrant et al.   Nature Microbiology

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

(2019) Xiaoqing Jiang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin

(2019) Ariel Kruger   MICROBIAL ECOLOGY

Environmental filtering: A case of bacterial community assembly in soil

(2019) Yan Yan et al.   SOIL BIOLOGY & BIOCHEMISTRY

A new perspective on functional redundancy and phylogenetic niche conservatism in soil microbial communities

(2019) Yu JIA et al.   PEDOSPHERE

Drivers of microbial community structure in forest soils

(2018) Salvador Lladó et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Why do microbes exhibit weak biogeographic patterns?

(2018) Kyle M. Meyer et al.   ISME Journal

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure

(2018) Kieran A. Bates et al.   Nature Communications

Host genetic variation and its microbiome interactions within the Human Microbiome Project

(2018) Raivo Kolde et al.   Genome Medicine

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs

(2018) Brandon J. Varela et al.   Frontiers in Microbiology

Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny

(2018) Alicia K. Bird et al.   Frontiers in Microbiology

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

(2017) Sarahi L. Garcia et al.   ISME Journal

Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function

(2017) Molly C Bletz 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

Variation in Metabolite Profiles of Amphibian Skin Bacterial Communities Across Elevations in the Neotropics

(2017) Daniel Medina et al.   MICROBIAL ECOLOGY

Biodiversity and species competition regulate the resilience of microbial biofilm community

(2017) Kai Feng et al.   MOLECULAR ECOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Amphibians on the brink

(2017) Deborah S. Bower et al.   SCIENCE

Patterns in the skin microbiota differ in children and teenagers between rural and urban environments

(2017) Jenni Lehtimäki et al.   Scientific Reports

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin

(2017) Daniel Medina et al.   Frontiers in Microbiology

Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei

(2017) Mariel Familiar López et al.   Frontiers in Microbiology

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

(2017) Isabelle Laforest-Lapointe et al.   mSystems

Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge

(2017) Dietrich J. Epp Schmidt et al.   Nature Ecology & Evolution

The Modern Synthesis in the Light of Microbial Genomics

(2016) Austin Booth et al.   Annual Review of Microbiology

The amphibian microbiome: natural range of variation, pathogenic dysbiosis, and role in conservation

(2016) Randall R. Jiménez et al.   BIODIVERSITY AND CONSERVATION

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning

(2016) Manuel Delgado-Baquerizo et al.   JOURNAL OF ECOLOGY

Climate forcing of an emerging pathogenic fungus across a montane multi-host community

(2016) Frances C. Clare et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Inhibitory interactions promote frequent bistability among competing bacteria

(2016) Erik S. Wright et al.   Nature Communications

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

(2016) Pedro Gómez et al.   Nature Communications

Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin

(2016) Andrew H. Loudon et al.   Frontiers in Microbiology

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

Patterns of Local Adaptation in Space and Time among Soil Bacteria

(2015) Susanne A. Kraemer et al.   AMERICAN NATURALIST

First arrived takes all: inhibitory priority effects dominate competition between co-infecting Borrelia burgdorferi strains

(2015) Godefroy Devevey et al.   BMC MICROBIOLOGY

Antifungal isolates database of amphibian skin-associated bacteria and function against emerging fungal pathogens

(2015) Douglas C. Woodhams et al.   ECOLOGY

Resilience vs. historical contingency in microbial responses to environmental change

(2015) Christine V. Hawkes et al.   ECOLOGY LETTERS

Low multifunctional redundancy of soil fungal diversity at multiple scales

(2015) Akira S. Mori et al.   ECOLOGY LETTERS

Urban stress is associated with variation in microbial species composition—but not richness—in Manhattan

(2015) Aspen T Reese et al.   ISME Journal

Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogenBatrachochytrium dendrobatidis

(2015) Matthew H. Becker et al.   MOLECULAR ECOLOGY

Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

(2015) David J. Krause et al.   SYSTEMATIC BIOLOGY

Panamanian frog species host unique skin bacterial communities

(2015) Lisa K. Belden et al.   Frontiers in Microbiology

Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

(2015) Ana V. Longo et al.   Royal Society Open Science

Accelerated modern human-induced species losses: Entering the sixth mass extinction

(2015) G. Ceballos et al.   Science Advances

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus

(2015) Jenifer B. Walke et al.   PLoS One

Natural Competence and the Evolution of DNA Uptake Specificity

(2014) J. C. Mell et al.   JOURNAL OF BACTERIOLOGY

Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities

(2014) Fabiana S. Paula et al.   MOLECULAR ECOLOGY

Fungal Infection Intensity and Zoospore Output of Atelopus zeteki, a Potential Acute Chytrid Supershedder

(2014) Graziella V. DiRenzo et al.   PLoS One

Interacting Symbionts and Immunity in the Amphibian Skin Mucosome Predict Disease Risk and Probiotic Effectiveness

(2014) Douglas C. Woodhams et al.   PLoS One

Cool Temperatures Reduce Antifungal Activity of Symbiotic Bacteria of Threatened Amphibians – Implications for Disease Management and Patterns of Decline

(2014) Joshua H. Daskin et al.   PLoS One

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Does urbanization shape bacterial community composition in urban park soils? A case study in 16 representative Chinese cities based on the pyrosequencing method

(2013) Hui-Juan Xu et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2013) Zhigang Zhang et al.   ISME Journal

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome

(2013) Matthew G. Bakker et al.   MOLECULAR ECOLOGY

The amphibian skin-associated microbiome across species, space and life history stages

(2013) Jordan G. Kueneman et al.   MOLECULAR ECOLOGY

Shifts in soil bacterial community after eight years of land-use change

(2013) Afnan Khalil Ahmad Suleiman et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Screening bacterial metabolites for inhibitory effects against Batrachochytrium dendrobatidis using a spectrophotometric assay

(2012) SC Bell et al.   DISEASES OF AQUATIC ORGANISMS

Microbes inside—from diversity to function: the case of Akkermansia

(2012) Clara Belzer et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Examining the Fish Microbiome: Vertebrate-Derived Bacteria as an Environmental Niche for the Discovery of Unique Marine Natural Products

(2012) Laura M. Sanchez et al.   PLoS One

Urban biodiversity: patterns and mechanisms

(2011) Stanley H. Faeth et al.   Annals of the New York Academy of Sciences

Long-term land use effects on soil microbial community structure and function

(2011) Andrew Bissett et al.   APPLIED SOIL ECOLOGY

Disease dynamics vary spatially and temporally in a North American amphibian

(2011) Anna E. Savage et al.   BIOLOGICAL CONSERVATION

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Tropical amphibian populations experience higher disease risk in natural habitats

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

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

(2011) R. A. Farrer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Amphibian pathogen Batrachochytrium dendrobatidis prevalence is correlated with season and not urbanization in central Virginia

(2010) K Duncan Pullen et al.   DISEASES OF AQUATIC ORGANISMS

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

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

From Structure to Function: the Ecology of Host-Associated Microbial Communities

(2010) C. J. Robinson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

(2010) A. BISSETT et al.   MOLECULAR ECOLOGY

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Cutaneous Bacteria of the Redback Salamander Prevent Morbidity Associated with a Lethal Disease

(2010) Matthew H. Becker et al.   PLoS One

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Characterization of the Fecal Microbiome from Non-Human Wild Primates Reveals Species Specific Microbial Communities

(2010) Suleyman Yildirim et al.   PLoS One

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

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Magnitude of the US trade in amphibians and presence of Batrachochytrium dendrobatidis and ranavirus infection in imported North American bullfrogs (Rana catesbeiana)

(2009) Lisa M. Schloegel et al.   BIOLOGICAL CONSERVATION

Gut Commensal Bacteria Direct a Protective Immune Response against Toxoplasma gondii

(2009) Alicia Benson et al.   Cell Host & Microbe

Urbanization Alters Soil Microbial Functioning in the Sonoran Desert

(2009) S. J. Hall et al.   ECOSYSTEMS

Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus

(2009) Reid N Harris et al.   ISME Journal

What are the consequences of the disappearing human microbiota?

(2009) Martin J. Blaser et al.   NATURE REVIEWS MICROBIOLOGY

The versatility and adaptation of bacteria from the genus Stenotrophomonas

(2009) Robert P. Ryan et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Addition of antifungal skin bacteria to salamanders ameliorates the effects of chytridiomycosis

(2008) RN Harris et al.   DISEASES OF AQUATIC ORGANISMS

Amphibian Chemical Defense: Antifungal Metabolites of the Microsymbiont Janthinobacterium lividum on the Salamander Plethodon cinereus

(2008) Robert M. Brucker et al.   JOURNAL OF CHEMICAL ECOLOGY

Are we in the midst of the sixth mass extinction? A view from the world of amphibians

(2008) D. B. Wake et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA