RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Mosquitoes rely on their gut microbiota for development

(2014) Kerri L. Coon et al.   MOLECULAR ECOLOGY

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data

(2014) Peter Skewes-Cox et al.   PLoS One

Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes

(2014) G. L. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic shotgun sequencing of a Bunyavirus in wild-caught Aedes aegypti from Thailand informs the evolutionary and genomic history of the Phleboviruses

(2014) James Angus Chandler et al.   VIROLOGY

Bacteriophages: an underestimated role in human and animal health?

(2014) Marianne De Paepe et al.   Frontiers in Cellular and Infection Microbiology

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Genetic characterization of novel putative rhabdovirus and dsRNA virus from Japanese persimmon

(2013) T. Ito et al.   JOURNAL OF GENERAL VIROLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversity and function of bacterial microbiota in the mosquito holobiont

(2013) Guillaume Minard et al.   Parasites & Vectors

Detection of Arboviruses and Other Micro-Organisms in Experimentally Infected Mosquitoes Using Massively Parallel Sequencing

(2013) Sonja Hall-Mendelin 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

Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

(2013) Shelley Cook et al.   PLoS One

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The emerging world of the fungal microbiome

(2013) Gary B. Huffnagle et al.   TRENDS IN MICROBIOLOGY

Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes

(2013) Lark L. Coffey et al.   VIROLOGY

Occurrence, sequence polymorphism and population structure of Circulifer tenellus virus 1 in a field population of the beet leafhopper

(2013) Allyn Spear et al.   VIRUS RESEARCH

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

Mosquito Vector Diversity across Habitats in Central Thailand Endemic for Dengue and Other Arthropod-Borne Diseases

(2013) Panpim Thongsripong et al.   PLoS Neglected Tropical Diseases

Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq

(2013) Phanidhar Kukutla et al.   Jove-Journal of Visualized Experiments

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

(2012) J. A. Foster et al.   BRIEFINGS IN BIOINFORMATICS

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

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

(2012) Andrew Tritt et al.   PLoS One

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

(2012) Ramy K. Aziz et al.   PLoS One

Fighting malaria with engineered symbiotic bacteria from vector mosquitoes

(2012) S. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional diversity within the simple gut microbiota of the honey bee

(2012) P. Engel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A new virus from the plant pathogenic oomycete Phytophthora infestans with an 8 kb dsRNA genome: The sixth member of a proposed new virus genus

(2012) Guohong Cai et al.   VIROLOGY

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

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

Malaria and other vector-borne infection surveillance in the U.S. Department of Defense Armed Forces Health Surveillance Center-Global Emerging Infections Surveillance program: review of 2009 accomplishments

(2011) Mark M Fukuda et al.   BMC PUBLIC HEALTH

Native Microbiota Shape Insect Vector Competence for Human Pathogens

(2011) Chris M. Cirimotich et al.   Cell Host & Microbe

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

“Bird biting” mosquitoes and human disease: A review of the role of Culex pipiens complex mosquitoes in epidemiology

(2011) Ary Farajollahi et al.   INFECTION GENETICS AND EVOLUTION

Gouleako Virus Isolated from West African Mosquitoes Constitutes a Proposed Novel Genus in the Family Bunyaviridae

(2011) M. Marklewitz et al.   JOURNAL OF VIROLOGY

RNA Splicing in a New Rhabdovirus from Culex Mosquitoes

(2011) R. Kuwata et al.   JOURNAL OF VIROLOGY

The wMel Wolbachia strain blocks dengue and invades caged Aedes aegypti populations

(2011) T. Walker et al.   NATURE

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

(2011) K. Megy et al.   NUCLEIC ACIDS RESEARCH

Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

(2011) Charles Runckel et al.   PLoS One

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes

(2011) Terry Fei Fan Ng et al.   PLoS One

Discovery of DNA Viruses in Wild-Caught Mosquitoes Using Small RNA High throughput Sequencing

(2011) Maijuan Ma et al.   PLoS One

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Mosquito Vectors of Dog Heartworm in the United States: Vector Status and Factors Influencing Transmission Efficiency

(2011) Nicholas Ledesma et al.   Topics in Companion Animal Medicine

Microbiome influences on insect host vector competence

(2011) Brian Weiss et al.   TRENDS IN PARASITOLOGY

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

(2011) James Angus Chandler et al.   PLoS Genetics

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The Native Wolbachia Endosymbionts of Drosophila melanogaster and Culex quinquefasciatus Increase Host Resistance to West Nile Virus Infection

(2010) Robert L. Glaser et al.   PLoS One

Plant-feeding insects harbor double-stranded RNA viruses encoding a novel proline-alanine rich protein and a polymerase distantly related to that of fungal viruses

(2010) Allyn Spear et al.   VIROLOGY

Arbovirus Detection in Insect Vectors by Rapid, High-Throughput Pyrosequencing

(2010) Kimberly A. Bishop-Lilly et al.   PLoS Neglected Tropical Diseases

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

The rhabdoviruses: Biodiversity, phylogenetics, and evolution☆

(2009) I.V. Kuzmin et al.   INFECTION GENETICS AND EVOLUTION

Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin

(2009) M. Rastgou et al.   JOURNAL OF GENERAL VIROLOGY

Sigma viruses from three species of Drosophila form a major new clade in the rhabdovirus phylogeny

(2009) B. Longdon et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Moussa virus: A new member of the Rhabdoviridae family isolated from Culex decens mosquitoes in Côte d’Ivoire

(2009) Phenix-Lan Quan et al.   VIRUS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

How many species are infected with Wolbachia? – a statistical analysis of current data

(2008) Kirsten Hilgenboecker et al.   FEMS MICROBIOLOGY LETTERS