Created September 2015, updated September 2016. Also see my page on Beer, Wine and Other fermented drinks.

Bread

Drivers for the establishment and composition of the sourdough lactic acid bacteria biota – Marco Gobbetti – International Journal of Food Microbiology

Review: Enzymatic and bacterial conversions during sourdough fermentation – Michael G. Gänzle – Food Microbiology – February 2014

Review: Sourdough lactic acid bacteria: Exploration of non-wheat cereal-based fermentation – Rossana Coda – Food Microbiology – February 2014

Review: Ecological parameters influencing microbial diversity and stability of traditional sourdough – Fabio Minervini et al. – International Journal of Food Microbiology – February 2014

Review: Sourdough in gluten-free bread-making: An ancient technology to solve a novel issue? – Alice V. Moroni – Food Microbiology – October 2009

Review: Microorganisms of the San Francisco Sour Dough Bread Process: II. Isolation and Characterization of Undescribed Bacterial Species Responsible for the Souring Activity – Leo Kline and T. F. Sugihara – Applied and Environmental Microbiology – March 1971

Cheese

Highlighting the microbial diversity of 12 French cheese varieties – Eric Dugat-Bony – International Journal of Food Microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology – January 2016

Metabolomics and microbiological profile of Italian mozzarella cheese produced with buffalo and cow milk – Maria Barbara Pisano – Food Chemistry – July 2015

Review: Growth and adaptation of microorganisms on the cheese surface – Christophe Monnet – FEMS Microbiology Letters – December 2014

Review: Cheese rind microbial communities: diversity, composition and origin – Françoise Irlinger – FEMS Microbiology Letters – December 2014

Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity – Benjamin E. Wolfe – Cell – July 2014

Review: Traditional cheeses: Rich and diverse microbiota with associated benefits –
Marie-Christine Montel – International Journal of Food Microbiology – May 2014

Review: The Microfloras of Traditional Greek Cheeses – Evanthia Litopoulou-Tzanetaki – Microbiology Spectrum – February 2014

Review: The Microfloras and Sensory Profiles of Selected Protected Designation of Origin Italian Cheeses – Giuseppe Licitra – Microbiology Spectrum – January 2014

Review: Cheese Classification, Characterization, and Categorization: A Global Perspective –  Montserrat Almena-Aliste – Microbiology Spectrum – January 2014

Review: Wooden Tools: Reservoirs of Microbial Biodiversity in Traditional Cheesemaking – Sylvie Lortal – Microbiology Spectrum – January 2014

Yogurt and Kefir

Review: The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir – Benjamin C. T. Bourrie – Frontiers in Microbiology – May 2016

Review: Yogurt, living cultures, and gut health – Lorenzo Morelli – The American Journal of Clinical Nutrition – April 2014

Review: Fermented Milks and Milk Products as Functional Foods—A Review – V.K. Shiby – Critical Reviews in Food Science and Nutrition – August 2012

Review: Selective and differential enumerations of Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus casei and Bifidobacterium spp. in yoghurt — A review – Rabia Ashraf – International Journal of Food Microbiology – October 2011

Olives

New process for production of fermented black table olives using selected autochthonous microbial resources – Maria Tufariello – Frontiers in Microbiology – September 2015

Biotechnological innovations for table olives – Antonio Bevilacqua – International Journal of Food Sciences and Nutrition – January 2015

Review: Yeasts in table olive processing: Desirable or spoilage microorganisms? –
F.N. Arroyo-López – International Journal of Food Microbiology – November 2012

Lactic acid bacteria from fermented table olives – Albert Hurtado – Food Microbiology – August 2012

Kimchi, Sauerkraut, and other fermented vegetables

Screening and Characterization of Purine Nucleoside Degrading Lactic Acid Bacteria Isolated from Chinese Sauerkraut and Evaluation of the Serum Uric Acid Lowering Effect in Hyperuricemic Rats – Ming Li – PLOS ONE – September 2014

Traditionally produced sauerkraut as source of autochthonous functional starter cultures – Jasna Beganović – Microbiological Research – July 2014

Effect of ripening stage on the development of the microbial community during spontaneous fermentation of green tomatoes – Spiros Paramithiotis – Journal of the Science of Food and Agriculture – June 2014

Review: Fermented Fruits and Vegetables of Asia: A Potential Source of Probiotics – Manas Ranjan Swain – Biotechnology Research International – May 2014

Review: Kimchi microflora: history, current status, and perspectives for industrial kimchi production – Ji Young Jung – Applied Microbiology and Biotechnology – March 2014

Review: Health Benefits of Kimchi (Korean Fermented Vegetables) as a Probiotic Food – Park Kun-Young – Journal of Medicinal Food – January 2014

Review: Controlled fermentation of kimchi using naturally occurring antimicrobial agents – Jinsol Kim – Food Microbiology – October 2012

Chocolate

The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate – Nádia Nara Batista – Journal of Food Science and Technology – December 2015

Review: Fungi and mycotoxins in cocoa: From farm to chocolate – Marina V. Copetti – International Journal of Food Microbiology – May 2014

The Microbiology of Cocoa Fermentation and its Role in Chocolate Quality – Rosane F. Schwan – Critical Reviews in Food Science and Nutrition – August 2010

Review: The Microbiology of Cocoa Fermentation and its Role in Chocolate Quality – Rosane F. Schwan – Critical Reviews in Food Science and Nutrition – 2004

Influence of food production microbes on aromas

Also see the Oral Microbiome paper collection, where I included a section about how oral microbes can release flavors from wine.

Unraveling the Enzymatic Basis of Wine “Flavorome”: A Phylo-Functional Study of Wine Related Yeast Species – Ignacio Belda – Frontiers in Microbiology – January 2016

Tuning chocolate flavor through development of thermotolerant Saccharomyces cerevisiae starter cultures with increased acetate ester production – Esther Meersman – Applied and Environmental Microbiology – November 2015

Yeast strains as potential aroma enhancers in dry fermented sausages –
Mónica Flores – International Journal of Food Microbiology – November 2015

Metagenomics of Ancient Fermentation Pits Used for the Production of Chinese Strong-Aroma Liquor – Ming-Yi Guo – Genome Announcements – September 2014

Microbial origin of non proteolytic aminoacyl derivatives in long ripened cheeses –
Elisa Sgarbi – Food Microbiology – September 2013

Comparison of different IlvE aminotransferases in Lactobacillus sakei and investigation of their contribution to aroma formation from branched chain amino acids – Simone Freiding – Food Microbiology – April 2012

Flavor network and the principles of food pairing – Yong-Yeol Ahn – Scientific Reports, December 2011

General reviews

Review: Diversity of Microorganisms in Global Fermented Foods and Beverages – Jyoti P. Tamang – Frontiers in Microbiology

Review: Taming Wild Yeast: Potential of Conventional and Nonconventional Yeasts in Industrial Fermentations – Annual Review of Microbiology – Jan Steensels – April 2014

Review: Microbe–microbe interactions in mixed culture food fermentations – Eddy J Smid – Current Opinion in Biotechnology – April 2013

Popular press and other resources

How bread, beer, and soy sauce changed the human microbiome – Francie Depp – Popular Science – January 2015

Introduction to the Microbiology of Food – Texas Aggie Horticulture

Producers – Microbiology Online

Fungi In Manufacturing of Food – Botany Hawaii

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