Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

Fermentation of African nightshade leaves with lactic acid bacterial starter cultures

(2021) Dominic A. Stoll et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Assessment of pear juice and puree as a fermentation matrix for water kefir

(2021) Jessica Hampton et al.   JOURNAL OF FOOD PROCESSING AND PRESERVATION

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods

(2021) Maria L. Marco et al.   Nature Reviews Gastroenterology & Hepatology

Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies

(2020) Raf Winand et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

(2020) Jasmine Chong et al.   Nature Protocols

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

Clostridium species as probiotics: potentials and challenges

(2020) Pingting Guo et al.   Journal of Animal Science and Biotechnology

Design of PCR assays to specifically detect and identify 37 Lactobacillus species in a single 96 well plate

(2020) Eiseul Kim et al.   BMC MICROBIOLOGY

Metagenomic analysis of bacterial community structure and functions during the fermentation of da-jiang, a Chinese traditional fermented food

(2020) Mengxi Xie et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues

(2020) Chrysa Voidarou et al.   Foods

Impact of DNA extraction and sampling methods on bacterial communities monitored by 16S rDNA metabarcoding in cold-smoked salmon and processing plant surfaces

(2020) Aurélien Maillet et al.   FOOD MICROBIOLOGY

Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults

(2019) Jonathan N. V. Martinson et al.   ISME Journal

Fishing in the Soup – Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing

(2019) Josephine Grützke et al.   Frontiers in Microbiology

Characterization and comparison of metaproteomes in traditional and commercial dajiang, a fermented soybean paste in northeast China

(2019) Mengxi Xie et al.   FOOD CHEMISTRY

Analysis of bacterial diversity and biogenic amines content during fermentation of farmhouse sauce from Northeast China

(2019) Yu Hao et al.   FOOD CONTROL

Genomic and metatranscriptomic analyses of Weissella koreensis reveal its metabolic and fermentative features during kimchi fermentation

(2018) Sang Eun Jeong et al.   FOOD MICROBIOLOGY

The dynamic changes of chemical components and microbiota during the natural fermentation process in Da-Jiang , a Chinese popular traditional fermented condiment

(2018) Junrui Wu et al.   FOOD RESEARCH INTERNATIONAL

Microbial diversity in two traditional bacterial douchi from Gansu province in northwest China using Illumina sequencing

(2018) Weibing Zhang et al.   PLoS One

Editorial: Game Changer - Next Generation Sequencing and Its Impact on Food Microbiology

(2018) Jennifer Ronholm   Frontiers in Microbiology

Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing

(2018) Hongxing Qiao et al.   AMB Express

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Molecular techniques reveal more secrets of fermented foods

(2018) Aly Farag El Sheikha et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

The use of next generation sequencing for improving food safety: Translation into practice

(2018) Balamurugan Jagadeesan et al.   FOOD MICROBIOLOGY

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Occurrence of Toxigenic Bacillus cereus and Bacillus thuringiensis in Doenjang, a Korean Fermented Soybean Paste

(2016) KYUNG MIN PARK et al.   JOURNAL OF FOOD PROTECTION

Characterization of microbiota in Plaisentif cheese by high-throughput sequencing

(2016) Alessandra Dalmasso et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

Produce from Africa’s Gardens: Potential for Leafy Vegetable and Fruit Fermentations

(2016) Folarin A. Oguntoyinbo et al.   Frontiers in Microbiology

Functional Properties of Microorganisms in Fermented Foods

(2016) Jyoti P. Tamang et al.   Frontiers in Microbiology

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis

(2016) Yongjie Zhang et al.   PLoS One

Quantification of persistence of the food-borne pathogens Listeria monocytogenes and Salmonella enterica during manufacture of Italian fermented sausages

(2015) M. Mataragas et al.   FOOD CONTROL

An accurate and efficient experimental approach for characterization of the complex oral microbiota

(2015) Wei Zheng et al.   Microbiome

Occurrence of an Environmental Acinetobacter baumannii Strain Similar to a Clinical Isolate in Paleosol from Croatia

(2014) J. Hrenovic et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

General patterns of background microbiota and selected bacterial pathogens during production of fermented sausages in Serbia

(2014) Miroslav Ducic et al.   FOOD CONTROL

A specific polymerase chain reaction method to identify Stenotrophomonas maltophilia

(2014) Stephanie Wagner Gallo et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land cover

(2014) Christopher Staley et al.   Frontiers in Microbiology

Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation

(2013) Luca Cocolin et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Evaluation of Multiplex PCR with Enhanced Spore Germination for Detection ofClostridium difficilefrom Stool Samples of the Hospitalized Patients

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Identification and virulence ofChryseobacterium indologenesisolated from diseased yellow perch (Perca flavescens)

(2012) J.W. Pridgeon et al.   JOURNAL OF APPLIED MICROBIOLOGY

Microbial dynamics and biodiversity in table olive fermentation: culture-dependent and -independent approaches

(2012) Cristian Botta et al.   Frontiers in Microbiology

We Are What We Eat: Food Safety and Proteomics

(2011) Angelo D’Alessandro et al.   JOURNAL OF PROTEOME RESEARCH

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

Fermentation, biodegradation and tensile strength of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) synthesized by Delftia acidovorans

(2009) Wen-Chuan Hsieh et al.   Journal of the Taiwan Institute of Chemical Engineers

Specific detection and differentiation of Ochrobactrum anthropi, Ochrobactrum intermedium and Brucella spp. by a multi-primer PCR that targets the recA gene

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