Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus

Patterns, causes and consequences of defensive microbiome dynamics across multiple scales

(2015) Andrew H. Smith et al.   MOLECULAR ECOLOGY

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider

(2015) Bram Vanthournout et al.   PLoS One

Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA

(2015) Jean-Pierre Gauthier et al.   PLoS One

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

Endosymbiotic microorganisms of aphids (Hemiptera: Sternorrhyncha: Aphidoidea): Ultrastructure, distribution and transovarial transmission

(2014) Anna MICHALIK et al.   EUROPEAN JOURNAL OF ENTOMOLOGY

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life

(2014) Alejandro Manzano-Marín et al.   Genome Biology and Evolution

Identifying the core microbial community in the gut of fungus-growing termites

(2014) Saria Otani et al.   MOLECULAR ECOLOGY

Anterior Foregut Microbiota of the Glassy-Winged Sharpshooter Explored Using Deep 16S rRNA Gene Sequencing from Individual Insects

(2014) Elizabeth E. Rogers et al.   PLoS One

Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects

(2014) Frank O. Aylward et al.   mBio

DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

(2014) Benjamin E. R. Rubin et al.   MicrobiologyOpen

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

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

How Conserved Are the Bacterial Communities Associated With Aphids? A Detailed Assessment of the Brevicoryne brassicae (Hemiptera: Aphididae) Using 16S rDNA

(2013) E. L. Clark et al.   ENVIRONMENTAL ENTOMOLOGY

Is ecological speciation a major trend in aphids? Insights from a molecular phylogeny of the conifer-feeding genus Cinara

(2013) Emmanuelle Jousselin et al.   Frontiers in Zoology

Defensive symbiosis in the real world - advancing ecological studies of heritable, protective bacteria in aphids and beyond

(2013) Kerry M. Oliver et al.   FUNCTIONAL ECOLOGY

The bacterial communities in plant phloem-sap-feeding insects

(2013) Xiangfeng Jing et al.   MOLECULAR 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

Microbiome diversity ofAphis glycineswith extensive superinfection in native and invasive populations

(2013) Raman Bansal et al.   Environmental Microbiology Reports

Phylogenetic divergence between the obligate luminous symbionts of flashlight fishes demonstrates specificity of bacteria to host genera

(2013) Tory A. Hendry et al.   Environmental Microbiology Reports

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Insect symbionts as hidden players in insect–plant interactions

(2012) Enric Frago et al.   TRENDS IN ECOLOGY & EVOLUTION

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Bacterial Communities of Two Parthenogenetic Aphid Species Cocolonizing Two Host Plants across the Hawaiian Islands

(2011) Ryan T. Jones et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

The phylogeny of Sodalis-like symbionts as reconstructed using surface-encoding loci

(2011) Anna K. Snyder et al.   FEMS MICROBIOLOGY LETTERS

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Population genetics of beneficial heritable symbionts

(2011) John Jaenike   TRENDS IN ECOLOGY & EVOLUTION

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont

(2011) Araceli Lamelas et al.   PLoS Genetics

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Evolution and Diversity of Facultative Symbionts from the Aphid Subfamily Lachninae

(2009) G. R. Burke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the Secondary Symbiont "Candidatus Serratia symbiotica" in Aphid Species of the Subfamily Lachninae

(2008) A. Lamelas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids

(2008) E. Jousselin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES