Starter Culture Microorganisms
An inventory of microorganisms used in food fermentations covering a wide range of food matrices (dairy, meat, fish, vegetables, legumes, cereals, beverages and vinegar) was published by Bourdichon et al. in 2012. This work was the result of a review and update of the list published in 2002 by the joint project between the International Dairy Federation (IDF) and the European Food and Feed Cultures Association (EFFCA). In 2002, the IDF inventory became a de facto reference for food cultures in practical use. However, as the focus was mainly on commercially available dairy cultures, there was an unmet need for a list with a wider scope. Bourdichon et al. (2012) also reviewed the literature for each species in order to maintain in the new inventory only microbial species that make desirable contributions to the food fermentations.
Currently, this list of microbial species with a documented presence in fermented foods is the better grouping of information that can be visualized as supplementary data in the article of Bourdichon et al. (2012) using the Digital Object Identifier System (DOI) 10.1016/j.ijfoodmicro.201U2.030.
Not all of these microorganisms cited in the Bourdichon et al. (2012) list, however, are produced as commercial SC. Some of the products do not lend themselves to industrial applications, and for others, the potential market is simply too small or too specialized. For example, sauerkraut fermentation is mediated by the natural microbiota. Manufacturers can produce these products without a commercial SC and may prefer to maintain and propagate their own cultures. Many dairies and breweries also have personal and laboratory facilities to support internal culture spread. The production of fungal-derived fermented foods also frequently relies on house strains.
MFC have directly or indirectly come under various regulatory frameworks in the last years. These frameworks place emphasis on “the history of use in traditional food” or “general recognition of safety”. Generally Recognized as Safe (GRAS) from the US and Qualified Presumption of Safety (QPS) from the European regulatory environmental status are applicable to MFC adequately shown to be safe under the conditions of its intended conditions of usage. When microorganisms with a safe history in food are employed for a different use, a new GRAS determination is needed. The QPS system was proposed to harmonize approaches to the safety assessment of microorganisms. The list of QPS is updated annually by the European Food Safety Authority (EFSA) (Herody et al. 2010).
Taxonomy and systematics constitute the basis for the regulatory framework for MFCs. Bourdichon et al. (2012) have also reviewed and updated the taxonomy of the microorganisms used in food fermentations in order to bring the taxonomy in agreement with the current standing in nomenclature. The detailed list of microorganisms (bacteria, fungi, filamentous fungi and yeasts) that include 62 genera and 264 species with demonstration in food usage can be found in this publication.
There is no simple definition of the species as a taxonomical unit. Generally, a polyphasic approach is required to quantify the degree of phenotypic and/or genotypic similarity between strains belonging to the same species. A special issue of the Journal Systematic and Applied Microbiology introduced by Schleifer et al. (2015) offered in its manuscripts an overview of some of the future perspectives that challenges both taxonomy and the characterization of the cultures diversity. As pointed out by Rossello-Mora and Amann (2015), the history of species classification has been linked to the technological developments to retrieve information on the organisms. Molecular methods that produce genetic and genomic data can be used to establish taxa boundaries. The retrieval of genomic information by using Next Generation Sequencing methods (NGS) has started a revolution in the study of species diversity. Almost complete genome sequences may take supremacy in circumscribing species and even higher taxa.
The wide variety of fermented food products consumed around the world requires a diverse array of microorganisms. Although lactic acid-producing bacteria and ethanol-producing yeasts are certainly the most frequently used microorganisms in fermented foods, there are many other bacteria, yeast and fungi that contribute to essential flavour, texture, appearance and other functional properties to the finished products. In most cases, more than one organism or group of organisms is involved in the fermentation.