Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems

Unique Rhizosphere Micro-characteristics Facilitate Phytoextraction of Multiple Metals in Soil by the Hyperaccumulating Plant Sedum alfredii

(2017) Dandi Hou et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation

(2017) Susana Fuentes et al.   ISME Journal

Annual community patterns are driven by seasonal switching between closely related marine bacteria

(2017) Christopher S Ward et al.   ISME Journal

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet

(2017) Hyunmin Koo et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Biological Aging and the Human Gut Microbiota

(2017) Vincent J Maffei et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function

(2017) Carolina Ramírez et al.   Frontiers in Microbiology

Human Catestatin Alters Gut Microbiota Composition in Mice

(2017) Mohammad F. Rabbi et al.   Frontiers in Microbiology

Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention

(2017) Chunlong Mu et al.   Frontiers in Microbiology

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept

(2017) Christina Pavloudi 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

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

(2017) Wei Yan et al.   Scientific Reports

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis

(2016) C. Acharya et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Metagenomic analysis shows diverse, distinct bacterial communities in biofilters among different marine recirculating aquaculture systems

(2016) Zhitao Huang et al.   AQUACULTURE INTERNATIONAL

Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation

(2016) Francis Cheng-Hsuan Weng et al.   BMC GENOMICS

From microbes to fish the next revolution in food production

(2016) Luis Rafael Martínez-Córdova et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow troutOncorhynchus mykissfrom both farm and aquarium settings

(2016) P.P. Lyons et al.   JOURNAL OF APPLIED MICROBIOLOGY

Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil

(2016) Jian-Kang Zhao et al.   JOURNAL OF HAZARDOUS MATERIALS

Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

(2016) Sunil Nagpal et al.   PLoS One

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels

(2016) Han Liu et al.   Scientific Reports

Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon

(2016) Jep Lokesh et al.   Scientific Reports

Honey Bee Gut Microbiome Is Altered by In-Hive Pesticide Exposures

(2016) Madhavi L. Kakumanu et al.   Frontiers in Microbiology

Environment shapes the fecal microbiome of invasive carp species

(2016) Jessica J. Eichmiller et al.   Microbiome

Monitoring and managing microbes in aquaculture - Towards a sustainable industry

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

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research

(2016) Karina Gajardo et al.   Scientific Reports

Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes

(2015) Daniel F. R. Cleary et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

(2015) Mamoon Rashid et al.   BIOTECHNOLOGY ADVANCES

Metaproteomic analysis of bacterial communities in marine mudflat aquaculture sediment

(2015) Rui Lin et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Microbial metagenomics in aquaculture: a potential tool for a deeper insight into the activity

(2015) Marcel Martínez-Porchas et al.   Reviews in Aquaculture

Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

(2015) Perla Munguia-Fragozo et al.   Biomed Research International

The Tara Oceans Project: New Opportunities and Greater Challenges Ahead

(2015) Houjin Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Ecological theory as a foundation to control pathogenic invasion in aquaculture

(2014) Peter De Schryver et al.   ISME Journal

Which is more important for classifying microbial communities: who’s there or what they can do?

(2014) Zhenjiang Xu et al.   ISME Journal

Microbial-based systems for aquaculture of fish and shrimp: an updated review

(2014) Luis R. Martínez-Córdova et al.   Reviews in Aquaculture

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Protein signature-based estimation of metagenomic abundances including all domains of life and viruses

(2013) Heiner Klingenberg et al.   BIOINFORMATICS

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

(2013) Blaire Steven et al.   PLoS One

Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis

(2013) Patrícia Martins et al.   PLoS One

Rickettsia-like organisms from cultured aquatic organisms, with emphasis on necrotizing hepatopancreatitis bacterium affecting penaeid shrimp: an overview on an emergent concern

(2013) Teresa Gollas-Galván et al.   Reviews in Aquaculture

Impact of water quality on the bacterial populations and off-flavours in recirculating aquaculture systems

(2012) Marc Auffret et al.   FEMS MICROBIOLOGY ECOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

GenBank

(2012) Dennis A. Benson 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

Simultaneous Detection of Multiple Fish Pathogens Using a Naked-Eye Readable DNA Microarray

(2012) Chin-I Chang et al.   SENSORS

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

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

Microbial diversity of biological filters in recirculating aquaculture systems

(2010) Harold J Schreier et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bioremediation of aquaculture wastewater using macroalgae and Artemia

(2010) E. Marinho-Soriano et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Characterization of Prochlorococcus clades from iron-depleted oceanic regions

(2010) D. B. Rusch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

The biofloc technology (BFT) in indoor tanks: Water quality, biofloc composition, and growth and welfare of Nile tilapia (Oreochromis niloticus)

(2008) M.E. Azim et al.   AQUACULTURE

A review on the interactions between gut microbiota and innate immunity of fish: Table 1

(2008) Geovanny D. Gómez et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways

(2008) C. E. Martinez-Guerrero et al.   NUCLEIC ACIDS RESEARCH