Gut interkingdom predator-prey interactions are key determinants of shrimp health

Responses of sediment resistome, virulence factors and potential pathogens to decades of antibiotics pollution in a shrimp aquafarm

(2021) Jiaqi Lu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Rhizosphere protists are key determinants of plant health

(2020) Wu Xiong et al.   Microbiome

Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing

(2020) Shenzheng Zeng et al.   Frontiers in Genetics

Understanding the role of the shrimp gut microbiome in health and disease

(2020) Corey C. Holt et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa

(2020) Jiaqi Lu et al.   MICROBIAL ECOLOGY

Variations in microbiota composition of laboratory mice influence Citrobacter rodentium infection via variable short-chain fatty acid production

(2020) Lisa Osbelt et al.   PLoS Pathogens

Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome

(2020) Zhijian Huang et al.   Microbiome

Comparable Ecological Processes Govern the Temporal Succession of Gut Bacteria and Microeukaryotes as Shrimp Aged

(2020) Jinbo Xiong et al.   MICROBIAL ECOLOGY

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

(2020) Qingqing Cao et al.   Frontiers in Microbiology

Quantifying the importance of external and internal sources to the gut microbiota in juvenile and adult shrimp

(2020) Xuechen Zhang et al.   AQUACULTURE

Host–microbiota interactions and responses to grass carp reovirus infection in Ctenopharyngodon idellus

(2020) Fanshu Xiao et al.   ENVIRONMENTAL MICROBIOLOGY

Activation of Both TLR and NOD Signaling Confers Host Innate Immunity-Mediated Protection Against Microbial Infection

(2019) Huiting Zhou et al.   Frontiers in Immunology

Gut eukaryotic disease-discriminatory taxa are indicative of Pacific white shrimp (Litopenaeus vannamei) white feces syndrome

(2019) Wenfang Dai et al.   AQUACULTURE

Bdellovibrio and Like Organisms Are Predictors of Microbiome Diversity in Distinct Host Groups

(2019) Julia Johnke et al.   MICROBIAL ECOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression

(2018) Wenfang Dai et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Progress in the gut microbiota in exploring shrimp disease pathogenesis and incidence

(2018) Jinbo Xiong   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Intestinal bacterial signatures of white feces syndrome in shrimp

(2018) Dongwei Hou et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota

(2018) Jinbo Xiong et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Toll-receptor 9 gene in the black tiger shrimp ( Penaeus monodon ) induced the activation of the TLR–NF-κB signaling pathway

(2018) Qian Liu et al.   GENE

Biological Approaches for Disease Control in Aquaculture: Advantages, Limitations and Challenges

(2018) Tania Pérez-Sánchez et al.   TRENDS IN MICROBIOLOGY

Toll-Like Receptors, Associated Biological Roles, and Signaling Networks in Non-Mammals

(2018) Li Nie et al.   Frontiers in Immunology

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

(2018) Isabelle Laforest-Lapointe et al.   mSystems

Response of host-bacterial colonization in shrimp to developmental stage, environment and disease

(2018) Jinbo Xiong et al.   MOLECULAR ECOLOGY

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

(2018) Fernanda Cornejo-Granados et al.   PeerJ

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

(2017) Jinbo Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales

(2017) Martin W. Hahn et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Soil protist communities form a dynamic hub in the soil microbiome

(2017) Wu Xiong et al.   ISME Journal

Regulation of life span by the gut microbiota in the short-lived African turquoise killifish

(2017) Patrick Smith et al.   eLife

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

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

Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil

(2016) Qinglin Chen et al.   ENVIRONMENT INTERNATIONAL

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

(2016) Jinyong Zhu et al.   MICROBIAL ECOLOGY

How colonization by microbiota in early life shapes the immune system

(2016) Thomas Gensollen et al.   SCIENCE

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Microbial Invasions: The Process, Patterns, and Mechanisms

(2015) Cyrus Alexander Mallon et al.   TRENDS IN MICROBIOLOGY

Are Human Intestinal Eukaryotes Beneficial or Commensals?

(2015) Julius Lukeš et al.   PLoS Pathogens

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia

(2014) Luisa W. Hugerth et al.   PLoS One

White Feces Syndrome of Shrimp Arises from Transformation, Sloughing and Aggregation of Hepatopancreatic Microvilli into Vermiform Bodies Superficially Resembling Gregarines

(2014) Siriporn Sriurairatana et al.   PLoS One

Evaluating the potential of marine Bacteriovorax sp. DA5 as a biocontrol agent against vibriosis in Litopenaeus vannamei larvae

(2014) Chongqing Wen et al.   VETERINARY MICROBIOLOGY

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

Recognition of bacterial infection by innate immune sensors

(2012) Sushil Kumar et al.   CRITICAL REVIEWS IN MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Pathobionts of the gastrointestinal microbiota and inflammatory disease

(2011) Janet Chow et al.   CURRENT OPINION IN IMMUNOLOGY

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

(2011) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Effects of the probiotic, Bacillus subtilis E20, on the survival, development, stress tolerance, and immune status of white shrimp, Litopenaeus vannamei larvae

(2010) Kuan-Fu Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Trade-Offs between Competition and Defense Specialists among Unicellular Planktonic Organisms: the "Killing the Winner" Hypothesis Revisited

(2010) C. Winter et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS