High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Sample Preparation: The Forgotten Beginning

(2016) BYRON BREHM-STECHER et al.   JOURNAL OF FOOD PROTECTION

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

(2013) Nicholas A. Bokulich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The effect of marination on lactic acid bacteria communities in raw broiler fillet strips

(2013) T Nieminen   Frontiers in Microbiology

“Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese

(2012) Danilo Ercolini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses

(2012) Lisa Quigley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biodiversity in Oscypek, a Traditional Polish Cheese, Determined by Culture-Dependent and -Independent Approaches

(2012) Ángel Alegría et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Changes in Microbiota Population during Fermentation ofNarezushias Revealed by Pyrosequencing Analysis

(2012) Masashi KIYOHARA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Next-generation approaches to the microbial ecology of food fermentations

(2012) Nicholas A. Bokulich et al.   BMB Reports

Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection

(2012) Brian B. Oakley et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Bacterial diversity of cheonggukjang, a traditional Korean fermented food, analyzed by barcoded pyrosequencing

(2012) Young-Do Nam et al.   FOOD CONTROL

Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis

(2012) A.M.O. Leite et al.   FOOD MICROBIOLOGY

Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

(2012) T.T. Nieminen et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Microbial community analysis of Korean soybean pastes by next-generation sequencing

(2012) Young-Do Nam et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Spoilage microbiota associated to the storage of raw meat in different conditions

(2012) Agapi I. Doulgeraki et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

A comparison of methods used to extract bacterial DNA from raw milk and raw milk cheese

(2012) L. Quigley et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Microbial Composition of the Korean Traditional Food “kochujang” Analyzed by a Massive Sequencing Technique

(2012) Young-Do Nam et al.   JOURNAL OF FOOD SCIENCE

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

(2012) Nicholas A. Bokulich et al.   PLoS One

Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine

(2012) Nicholas A. Bokulich et al.   PLoS One

The Impact of Omic Technologies on the Study of Food Microbes

(2012) Sarah O'Flaherty et al.   Annual Review of Food Science and Technology

Monitoring of Microbial Metabolites and Bacterial Diversity in Beef Stored under Different Packaging Conditions

(2011) Danilo Ercolini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

(2011) Ji Young Jung et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

High-throughput sequence-based analysis of the bacterial composition of kefir and an associated kefir grain

(2011) Alleson Dobson et al.   FEMS MICROBIOLOGY LETTERS

Recent advances in quantitative PCR (qPCR) applications in food microbiology

(2011) Florence Postollec et al.   FOOD MICROBIOLOGY

Unexpected convergence of fungal and bacterial communities during fermentation of traditional Korean alcoholic beverages inoculated with various natural starters

(2011) Mi-Ja Jung et al.   FOOD MICROBIOLOGY

Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese

(2011) Lisa Quigley et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR

(2011) Wafa Masoud et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Analyses of bacterial communities in meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods

(2011) Yi-Seul Kim et al.   JOURNAL OF MICROBIOLOGY

Pyrosequencing survey of the microbial diversity of ‘narezushi’, an archetype of modern Japanese sushi

(2011) T. Koyanagi et al.   LETTERS IN APPLIED MICROBIOLOGY

Biodiversity and dynamics of meat fermentations: The contribution of molecular methods for a better comprehension of a complex ecosystem

(2011) Luca Cocolin et al.   MEAT SCIENCE

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

(2011) Shingo Suzuki et al.   PLoS One

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

(2011) Leho Tedersoo et al.   PLoS One

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

(2011) Jesse R.R. Zaneveld et al.   TRENDS IN MICROBIOLOGY

Metagenomic Analysis of the Viral Communities in Fermented Foods

(2010) Eun-Jin Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Detection of pathogens in foods: the current state-of-the-art and future directions

(2010) Hari P. Dwivedi et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

(2010) Wafa Masoud et al.   INTERNATIONAL DAIRY JOURNAL

16S rRNA pyrosequencing-based investigation of the bacterial community in nukadoko, a pickling bed of fermented rice bran

(2010) Naoshige Sakamoto et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing of Tagged 16S rRNA Gene Amplicons for Rapid Deciphering of the Microbiomes of Fermented Foods Such as Pearl Millet Slurries

(2009) C. Humblot et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Yield and amplificability of different DNA extraction procedures for traceability in the dairy food chain

(2009) Andrea Pirondini et al.   FOOD CONTROL

Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing

(2009) Seong Woon Roh et al.   ISME Journal

The challenges of sequencing by synthesis

(2009) Carl W Fuller et al.   NATURE BIOTECHNOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

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

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