Parasite microbiome project: Grand challenges

Programmed knockout mutation of liver fluke granulin attenuates virulence of infection-induced hepatobiliary morbidity

(2019) Patpicha Arunsan et al.   eLife

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology

(2019) Christopher A. Gaulke et al.   Microbiome

Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity

(2018) Ching-Wen Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host species, and not environment, predicts variation in blood parasite prevalence, distribution, and diversity along a humidity gradient in northern South America

(2018) Paulo C. Pulgarín-R et al.   Ecology and Evolution

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Parasites and their (endo)symbiotic microbes

(2018) Vyacheslav Yurchenko et al.   PARASITOLOGY

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Parasitoid gene expression changes after adaptation to symbiont-protected hosts

(2017) Alice B. Dennis et al.   EVOLUTION

Genomic exploration of individual giant ocean viruses

(2017) William H Wilson et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Global change, parasite transmission and disease control: lessons from ecology

(2017) Joanne Cable et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

(2017) Francisco Martinez-Hernandez et al.   Nature Communications

Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers

(2017) Samantha N. McNulty et al.   PLoS Genetics

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions

(2017) Nolwenn M. Dheilly et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Elevated prevalence of Helicobacter species and virulence factors in opisthorchiasis and associated hepatobiliary disease

(2017) Raksawan Deenonpoe et al.   Scientific Reports

Independent origins of parasitism in Animalia

(2016) Sara B. Weinstein et al.   Biology Letters

The Human Microbiome during Bacterial Vaginosis

(2016) Andrew B. Onderdonk et al.   CLINICAL MICROBIOLOGY REVIEWS

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Helminth infection promotes colonization resistance via type 2 immunity

(2016) Deepshika Ramanan et al.   SCIENCE

Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control

(2016) Suzanne A. Ford et al.   PLoS Pathogens

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

A Coxiella-Like Endosymbiont Is a Potential Vitamin Source for the Lone Star Tick

(2015) Todd A Smith et al.   Genome Biology and Evolution

Distinctive Genome Reduction Rates Revealed by Genomic Analyses of TwoCoxiella-Like Endosymbionts in Ticks

(2015) Yuval Gottlieb et al.   Genome Biology and Evolution

Biological warfare: Microorganisms as drivers of host–parasite interactions

(2015) Nolwenn M. Dheilly et al.   INFECTION GENETICS AND EVOLUTION

Association of the Endobiont Double-Stranded RNA Virus LRV1 With Treatment Failure for Human Leishmaniasis Caused byLeishmania braziliensisin Peru and Bolivia

(2015) Vanessa Adaui et al.   JOURNAL OF INFECTIOUS DISEASES

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Interactions between multiple helminths and the gut microbiota in wild rodents

(2015) Jakub Kreisinger et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation

(2015) N. M. Dheilly et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Are Human Intestinal Eukaryotes Beneficial or Commensals?

(2015) Julius Lukeš et al.   PLoS Pathogens

Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

(2015) Jacob Bak Holm et al.   PLoS One

Identifying the Molecular Basis of Host-Parasite Coevolution: Merging Models and Mechanisms

(2014) Mark F. Dybdahl et al.   AMERICAN NATURALIST

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut

(2014) Matthew Jemielita et al.   mBio

Holobiont–Holobiont Interactions: Redefining Host–Parasite Interactions

(2014) Nolwenn Marie Dheilly   PLoS Pathogens

The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission

(2013) Dieter Ebert   Annual Review of Ecology Evolution and Systematics

The Villain Team-Up or howTrichomonas vaginalisand bacterial vaginosis alter innate immunity in concert

(2013) Raina N Fichorova et al.   SEXUALLY TRANSMITTED INFECTIONS

Alterations in the Porcine Colon Microbiota Induced by the Gastrointestinal Nematode Trichuris suis

(2012) Robert W. Li et al.   INFECTION AND IMMUNITY

Endobiont Viruses Sensed by the Human Host – Beyond Conventional Antiparasitic Therapy

(2012) Raina N. Fichorova et al.   PLoS One

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

Community genetics: what have we accomplished and where should we be going?

(2011) E. I. Hersch-Green et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Leishmania RNA Virus Controls the Severity of Mucocutaneous Leishmaniasis

(2011) A. Ives et al.   SCIENCE

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Anti-filarial Activity of Antibiotic Therapy Is Due to Extensive Apoptosis after Wolbachia Depletion from Filarial Nematodes

(2011) Frederic Landmann et al.   PLoS Pathogens

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Exploitation of the Intestinal Microflora by the Parasitic Nematode Trichuris muris

(2010) K. S. Hayes et al.   SCIENCE

The Wolbachia endosymbiont as an anti-filarial nematode target

(2010) Barton E. Slatko et al.   SYMBIOSIS

The evolution of parasitism in plants

(2010) James H. Westwood et al.   TRENDS IN PLANT SCIENCE

Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies

(2008) F. Pleijel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION