Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity

Interesting Starter Culture Strains for Controlled Cocoa Bean Fermentation Revealed by Simulated Cocoa Pulp Fermentations of Cocoa-Specific Lactic Acid Bacteria

(2011) Timothy Lefeber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Species Diversity, Community Dynamics, and Metabolite Kinetics of the Microbiota Associated with Traditional Ecuadorian Spontaneous Cocoa Bean Fermentations

(2011) Zoi Papalexandratou 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

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

(2011) Ozkan U Nalbantoglu et al.   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Theobroma cacaoL., “The Food of the Gods”: Quality Determinants of Commercial Cocoa Beans, with Particular Reference to the Impact of Fermentation

(2011) Lídia J. R. Lima et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

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

(2011) Alleson Dobson et al.   FEMS MICROBIOLOGY LETTERS

Assessment of the yeast species composition of cocoa bean fermentations in different cocoa-producing regions using denaturing gradient gel electrophoresis

(2011) Zoi Papalexandratou et al.   FEMS YEAST RESEARCH

Comparison of the bacterial species diversity of spontaneous cocoa bean fermentations carried out at selected farms in Ivory Coast and Brazil

(2011) Zoi Papalexandratou et al.   FOOD MICROBIOLOGY

Spontaneous organic cocoa bean box fermentations in Brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria

(2011) Zoi Papalexandratou et al.   FOOD MICROBIOLOGY

On-farm implementation of a starter culture for improved cocoa bean fermentation and its influence on the flavour of chocolates produced thereof

(2011) Timothy Lefeber et al.   FOOD MICROBIOLOGY

Bacteriophages of lactic acid bacteria and their impact on milk fermentations

(2011) Josiane E Garneau et al.   Microbial Cell Factories

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

(2011) Sebastian Jaenicke et al.   PLoS One

Metagenomic Analysis of the Viral Communities in Fermented Foods

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

Diversity of the total bacterial community associated with Ghanaian and Brazilian cocoa bean fermentation samples as revealed by a 16 S rRNA gene clone library

(2010) Tamara Garcia-Armisen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

Clustering metagenomic sequences with interpolated Markov models

(2010) David R Kelley et al.   BMC BIOINFORMATICS

Dynamics and species diversity of communities of lactic acid bacteria and acetic acid bacteria during spontaneous cocoa bean fermentation in vessels

(2010) Timothy Lefeber et al.   FOOD MICROBIOLOGY

An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

(2010) R. Henrik Nilsson et al.   Fungal Ecology

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

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Achievements and new knowledge unraveled by metagenomic approaches

(2009) Carola Simon et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

Methods for comparative metagenomics

(2009) Daniel H Huson et al.   BMC BIOINFORMATICS

Yeast diversity of Ghanaian cocoa bean heap fermentations

(2009) Heide-Marie Daniel et al.   FEMS YEAST RESEARCH

Bacteriophages of Lactobacillus

(2009) Manuela Villion   Frontiers in Bioscience-Landmark

Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater

(2009) Orr H Shapiro et al.   ISME Journal

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

New dimensions of the virus world discovered through metagenomics

(2009) David M. Kristensen et al.   TRENDS IN MICROBIOLOGY

Flavor Formation and Character in Cocoa and Chocolate: A Critical Review

(2008) Emmanuel Ohene Afoakwa et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

Diversity of Predominant Lactic Acid Bacteria Associated with Cocoa Fermentation in Nigeria

(2008) Melanie Kostinek et al.   CURRENT MICROBIOLOGY

New tools for discovering and characterizing microbial diversity

(2008) Erick Cardenas et al.   CURRENT OPINION IN BIOTECHNOLOGY

The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

(2008) Andreas Schlüter et al.   JOURNAL OF BIOTECHNOLOGY

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH