Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

The sponge holobiont in a changing ocean: from microbes to ecosystems

(2018) L. Pita et al.   Microbiome

Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges

(2018) Marta Turon et al.   Scientific Reports

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

(2017) Beate M Slaby et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Predicting the HMA-LMA Status in Marine Sponges by Machine Learning

(2017) Lucas Moitinho-Silva et al.   Frontiers in Microbiology

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

(2017) Qi Yang et al.   Scientific Reports

Weakly supervised learning of biomedical information extraction from curated data

(2016) Suvir Jain et al.   BMC BIOINFORMATICS

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples

(2016) Jennifer J. Barb et al.   PLoS One

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies

(2016) Bram Beckers et al.   Frontiers in Microbiology

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Microbiology

The HMA-LMA Dichotomy Revisited: an Electron Microscopical Survey of 56 Sponge Species

(2016) Volker Gloeckner et al.   BIOLOGICAL BULLETIN

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

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pyrosequencing Reveals the Microbial Communities in the Red Sea Sponge Carteriospongia foliascens and Their Impressive Shifts in Abnormal Tissues

(2014) Zhao-Ming Gao et al.   MICROBIAL ECOLOGY

Integration of Culture-Based and Molecular Analysis of a Complex Sponge-Associated Bacterial Community

(2014) Naomi F. Montalvo et al.   PLoS One

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

(2014) Shunsuke Takahashi et al.   PLoS One

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

First insights into the microbiome of a carnivorous sponge

(2013) Samuel Dupont et al.   FEMS MICROBIOLOGY ECOLOGY

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

Archaea Appear to Dominate the Microbiome of Inflatella pellicula Deep Sea Sponges

(2013) Stephen A. Jackson et al.   PLoS One

A single betaproteobacterium dominates the microbial community of the crambescidine-containing sponge Crambe crambe

(2013) Julie Croué et al.   Scientific Reports

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

(2012) J Gregory Caporaso et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing

(2011) Purnima S. Kumar et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Evaluating methods for the preservation and extraction of DNA and RNA for analysis of microbial communities in marine sponges

(2010) Rachel L. Simister et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS