Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

Integrating gut microbiota immaturity and disease-discriminatory taxa to diagnose the initiation and severity of shrimp disease

(2017) Jinbo Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

(2017) Ellen M. Black et al.   PeerJ

Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages

(2017) Shenzheng Zeng et al.   PeerJ

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change

(2017) Cheng-Yu Chen et al.   PLoS One

Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease

(2017) Wei-Yu Chen et al.   Scientific Reports

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions

(2017) Fernanda Cornejo-Granados et al.   Scientific Reports

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system

(2016) Emilie Cardona et al.   BMC MICROBIOLOGY

Bacterial dynamics in intestines of the black tiger shrimp and the Pacific white shrimp during Vibrio harveyi exposure

(2016) Wanilada Rungrassamee et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp

(2016) Jinyong Zhu et al.   MICROBIAL ECOLOGY

Isolation of TDA-producing Phaeobacter strains from sea bass larval rearing units and their probiotic effect against pathogenic Vibrio spp. in Artemia cultures

(2016) Torben Grotkjær et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Individuality, Stability, and Variability of the Plaque Microbiome

(2016) Daniel R. Utter et al.   Frontiers in Microbiology

Monitoring and managing microbes in aquaculture - Towards a sustainable industry

(2016) Mikkel Bentzon-Tilia et al.   Microbial Biotechnology

A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China

(2015) LianTai Li et al.   ANNALS OF MICROBIOLOGY

Changes in intestinal bacterial communities are closely associated with shrimp disease severity

(2015) Jinbo Xiong et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Photorhabdus insect-related (Pir) toxin-like genes in a plasmid of Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (AHPND) of shrimp

(2015) JE Han et al.   DISEASES OF AQUATIC ORGANISMS

Prevalence ofVibriospp. in raw shrimps (Parapenaeus longirostris) and performance of a chromogenic medium for the isolation ofVibriostrains

(2015) M.R. Kriem et al.   LETTERS IN APPLIED MICROBIOLOGY

The opportunistic marine pathogenVibrio parahaemolyticusbecomes virulent by acquiring a plasmid that expresses a deadly toxin

(2015) Chung-Te Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing

(2015) Shuai Liu et al.   Frontiers in Microbiology

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources

(2014) Meiling Zhang et al.   AQUACULTURE

Changes in the intestinal bacterial community during the growth of white shrimp,Litopenaeus vannamei

(2014) Zhaobin Huang et al.   AQUACULTURE RESEARCH

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Identification of Bacterial Community Composition in Freshwater Aquaculture System Farming of Litopenaeus vannamei Reveals Distinct Temperature-Driven Patterns

(2014) Yuyi Tang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Sensor data as a measure of native freshwater mussel impact on nitrate formation and food digestion in continuous-flow mesocosms

(2014) Jeremy S. Bril et al.   Freshwater Science

Early Mortality Syndrome Outbreaks: A Microbial Management Issue in Shrimp Farming?

(2014) Peter De Schryver et al.   PLoS Pathogens

Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp

(2013) L Tran et al.   DISEASES OF AQUATIC ORGANISMS

Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section

(2013) Hedvig E Jakobsson et al.   GUT

Diversity ofVibriospp. isolated at ambient environmental temperature in the Eastern English Channel as determined bypyrHsequencing

(2013) A. Tall et al.   JOURNAL OF APPLIED MICROBIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Evaluation of Pacific White Shrimp (Litopenaeus vannamei) Health during a Superintensive Aquaculture Growout Using NMR-Based Metabolomics

(2013) Tracey B. Schock 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

The Gut Bacterial Community of Mammals from Marine and Terrestrial Habitats

(2013) Tiffanie M. Nelson et al.   PLoS One

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores

(2012) Kevin D. Kohl et al.   ECOLOGY LETTERS

More rapid and severe disease outbreaks for aquaculture at the tropics: implications for food security

(2012) Tommy L. F. Leung et al.   JOURNAL OF APPLIED ECOLOGY

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Thermal tolerance of Litopenaeus vannamei (Crustacea: Penaeidae) acclimated to four temperatures

(2010) Metin Kumlu et al.   JOURNAL OF THERMAL BIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH