Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

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

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

(2013) Danilo Ercolini   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Surface Microbes in the Neonatal Intensive Care Unit: Changes with Routine Cleaning and over Time

(2013) N. A. Bokulich et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Monitoring Seasonal Changes in Winery-Resident Microbiota

(2013) Nicholas A. Bokulich et al.   PLoS One

“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

Next-generation approaches to the microbial ecology of food fermentations

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

Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

(2012) Tina S Lusk et al.   BMC MICROBIOLOGY

Diversity, distribution and sources of bacteria in residential kitchens

(2012) Gilberto E. Flores et al.   ENVIRONMENTAL MICROBIOLOGY

Characteristics of microbial biofilm on wooden vats (‘gerles’) in PDO Salers cheese

(2012) Robert Didienne et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Architectural design influences the diversity and structure of the built environment microbiome

(2012) Steven W Kembel et al.   ISME Journal

Identification of Microbiota Present on the Surface of Taleggio Cheese Using PCR-DGGE and RAPD-PCR

(2012) Maria Feligini et al.   JOURNAL OF FOOD SCIENCE

Isolation and Identification of the Microbiota of Danish Farmhouse and Industrially Produced Surface-Ripened Cheeses

(2012) Klaus Gori et al.   MICROBIAL ECOLOGY

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Office Space Bacterial Abundance and Diversity in Three Metropolitan Areas

(2012) Krissi M. Hewitt et al.   PLoS One

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

SitePainter: a tool for exploring biogeographical patterns

(2011) A. Gonzalez et al.   BIOINFORMATICS

Diversity and assessment of potential risk factors of Gram-negative isolates associated with French cheeses

(2011) Monika Coton et al.   FOOD MICROBIOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

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

Microbial Biogeography of Public Restroom Surfaces

(2011) Gilberto E. Flores et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Microbial interactions in cheese: implications for cheese quality and safety

(2009) Françoise Irlinger et al.   CURRENT OPINION IN BIOTECHNOLOGY

Influence of pasteurization, brining conditions and production environment on the microbiota of artisan Gouda-type cheeses

(2009) Koenraad Van Hoorde et al.   FOOD MICROBIOLOGY

Pecorino Crotonese cheese: Study of bacterial population and flavour compounds

(2009) C.L. Randazzo et al.   FOOD MICROBIOLOGY

Tina wooden vat biofilm: A safe and highly efficient lactic acid bacteria delivering system in PDO Ragusano cheese making

(2009) Sylvie Lortal et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses

(2009) A. Bleicher et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Human gut microbiome adopts an alternative state following small bowel transplantation

(2009) A. L. Hartman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Commercial Ripening Starter Microorganisms Inoculated into Cheese Milk Do Not Successfully Establish Themselves in the Resident Microbial Ripening Consortia of a South German Red Smear Cheese

(2008) S. Goerges et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiological characterisation of Robiola di Roccaverano cheese using PCR–DGGE

(2008) S BONETTA et al.   FOOD MICROBIOLOGY

Maturing dynamics of surface microflora in Fontina PDO cheese studied by culture-dependent and -independent methods

(2008) P. Dolci et al.   JOURNAL OF APPLIED MICROBIOLOGY