A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology

Rare Plankton Subcommunities Are Far More Affected by DNA Extraction Kits Than Abundant Plankton

(2019) Min Liu et al.   Frontiers in Microbiology

Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: A full-scale study

(2018) Joonyeob Lee et al.   BIORESOURCE TECHNOLOGY

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

(2018) Yuanyuan Mo et al.   ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

(2018) Yuanyuan Xue et al.   ISME Journal

Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom

(2018) Jin Zhou et al.   Frontiers in Microbiology

Distribution of extracellular flavins in a coastal marine basin and their relationship to redox gradients and microbial community members

(2018) Danielle Monteverde et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by “Candidatus Phytoplasma prunorum”

(2018) Ales Eichmeier et al.   MICROBIAL ECOLOGY

Eigenvector centrality for characterization of protein allosteric pathways

(2018) Christian F. A. Negre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of a Commercial Microbial Agent on the Bacterial Communities in Shrimp Culture System

(2018) Zidan Liu et al.   Frontiers in Microbiology

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter

(2017) Marc Garcia-Garcera et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2017) Alexandre Jousset et al.   ISME Journal

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils

(2017) Shuo Jiao et al.   MOLECULAR ECOLOGY

DNA metabarcoding reveals that 200-μ m-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

(2017) Lemian Liu et al.   Molecular Ecology Resources

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments

(2017) Arghya Mukherjee et al.   Scientific Reports

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

(2017) Min Liu et al.   Frontiers in Microbiology

Patterns and Processes in Marine Microeukaryotic Community Biogeography from Xiamen Coastal Waters and Intertidal Sediments, Southeast China

(2017) Weidong Chen et al.   Frontiers in Microbiology

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

(2017) Yanying Zhang et al.   Frontiers in Microbiology

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Pyrosequencing reveals microbial community profile in anaerobic bio-entrapped membrane reactor for pharmaceutical wastewater treatment

(2016) Kok Kwang Ng et al.   BIORESOURCE TECHNOLOGY

Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France

(2016) A. Volant et al.   MICROBIAL ECOLOGY

Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China

(2015) Yan Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Microbial "social networks"

(2015) Mitch Fernandez et al.   BMC GENOMICS

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

(2015) Lemian Liu et al.   ISME Journal

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims 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

Integrated metagenomics and network analysis of soil microbial community of the forest timberline

(2015) Junjun Ding et al.   Scientific Reports

Biogeography of the Sediment Bacterial Community Responds to a Nitrogen Pollution Gradient in the East China Sea

(2014) Jinbo Xiong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of wastewater disposal on the bacterial and archaeal community of sea sediment in an industrial area in China

(2014) Yan Zhang et al.   FEMS MICROBIOLOGY ECOLOGY

Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea

(2014) Manhua Hou et al.   MARINE POLLUTION BULLETIN

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

(2014) David Berry et al.   Frontiers in Microbiology

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity, Abundance, and Spatial Distribution of Ammonia-Oxidizing β-Proteobacteria in Sediments from Changjiang Estuary and Its Adjacent Area in East China Sea

(2013) Yangyang Chen et al.   MICROBIAL ECOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) Albert Barberán et al.   ISME Journal

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea

(2009) Bi-Wei Feng et al.   FEMS MICROBIOLOGY ECOLOGY

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

What is principal component analysis?

(2008) Markus Ringnér   NATURE BIOTECHNOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH