Optimization of DNA extraction for advancing coral microbiota investigations

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

(2017) Matthew J. Neave et al.   Scientific Reports

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

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

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

(2016) Matthew J. Neave et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales

(2016) Matthew J Neave et al.   ISME Journal

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea

(2016) Maren Ziegler et al.   MARINE POLLUTION BULLETIN

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes

(2016) Amy Apprill et al.   mSystems

Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification

(2015) Qi Yang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

(2015) Tracy D Ainsworth et al.   ISME Journal

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

(2015) Janelle R. Thompson et al.   Frontiers in Cellular and Infection Microbiology

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

(2015) Brett Wagner Mackenzie et al.   Frontiers in Microbiology

Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment

(2014) Joseph Nesme et al.   CURRENT BIOLOGY

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean

(2014) Christina A. Kellogg et al.   PLoS One

The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals

(2014) J. M. Sneed et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum

(2014) Chuya Shinzato et al.   Frontiers in Microbiology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

(2013) H. Mori et al.   DNA RESEARCH

Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals

(2013) Amy Apprill et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals

(2013) Gizele D. Garcia et al.   MICROBIAL ECOLOGY

Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites

(2013) Shaomei He et al.   PLoS One

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

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

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

(2013) George R. Feehery et al.   PLoS One

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

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

Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability

(2012) Kathleen M. Morrow et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Comparison of different protocols for the extraction of microbial DNA from reef corals

(2012) H.F. Santos et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Changes in coral microbial communities in response to a natural pH gradient

(2012) Dalit Meron et al.   ISME Journal

Members of native coral microbiota inhibit glycosidases and thwart colonization of coral mucus by an opportunistic pathogen

(2012) Cory J Krediet et al.   ISME Journal

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Coral-Bacterial Communities before and after a Coral Mass Spawning Event on Ningaloo Reef

(2012) Janja Ceh et al.   PLoS One

Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

(2012) Rebecca Vega Thurber et al.   PLoS One

Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa

(2012) N. S. Webster et al.   Environmental Microbiology Reports

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

(2011) Daniel Aguirre de Cárcer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef

(2011) Raechel Littman et al.   Environmental Microbiology Reports

Coral-Associated Bacterial Assemblages: Current Knowledge and the Potential for Climate-Driven Impacts

(2010) Morgan E. Mouchka et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Extraction of Total Nucleic Acids From Ticks for the Detection of Bacterial and Viral Pathogens

(2010) Chris D. Crowder et al.   JOURNAL OF MEDICAL ENTOMOLOGY

Threatened Corals Provide Underexplored Microbial Habitats

(2010) Shinichi Sunagawa et al.   PLoS One

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

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

Metagenomic analysis of stressed coral holobionts

(2009) Rebecca Vega Thurber et al.   ENVIRONMENTAL MICROBIOLOGY

The onset of microbial associations in the coral Pocillopora meandrina

(2009) Amy Apprill et al.   ISME Journal

Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata

(2009) Shinichi Sunagawa et al.   ISME Journal

Microbial disease and the coral holobiont

(2009) David G. Bourne et al.   TRENDS IN MICROBIOLOGY

Cross-Kingdom Amplification Using Bacteria-Specific Primers: Complications for Studies of Coral Microbial Ecology

(2008) J. P. Galkiewicz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenetic diversity of bacteria associated with the mucus of Red Sea corals

(2008) Yael Lampert et al.   FEMS MICROBIOLOGY ECOLOGY

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH