Genomics of dairy fermentations

Microbes are used in the process of making industrial and artisanal fermented dairy products, such as cheese, yogurt, sour cream and fermented milks (Fig. 1). These microbes are predominately lactic acid bacteria (LAB), such as lactococci, lactobacilli and streptococci. For quality and consistency, industrial production requires the use of starter cultures, which are very carefully created, cultivated and maintained (Fig. 2). What happens in the fermentation process? Milk sugars (mainly lactose) are fermented with the major final product being lactic acid. Lactic acid not only inhibits the out-growth of other organisms but also lowers the pH of the food product. Taste and texture, the feeling of food in your mouth, is also important. Lactic acid bacteria make the specific end-products that impart flavour and modify the texture of the final product. Cheese production makes use of predominantly Lactococcus lactis. It is the major component of cheese starter cultures and, as the worldwide cheese market is huge, it is one of the most important microbes for the food industry. Several of the important functions for fermentation are encoded on conjugative plasmids in these bacteria, among them lactose metabolism and the breakdown of milk proteins during cheese production (Siezen et al., 2005; Shearman et al., 2008). The lactobacilli are also important players in dairy fermentations with Lactobacillus bulgaricus mainly used in yoghurt manufacture, together with Streptococcus thermophilus. This use of microbial consortia adds yet another degree of complexity to an already complex production process. There are now over 20 genomes of LAB published and annotated, providing insight into their metabolic capabilities, as reviewed in (Pfeiler and Klaenhammer, 2007; Mayo et al., 2008). Comparing these genomes for shared or unique genotypes is a start, but the world of dairy fermentation is not content just with comparison. The real questions that are being asked are: what makes my yogurt or cheese different, and how can I develop new flavours, textures and products? This is increasingly being investigated by natural diversity analysis of microbes, and in situ omics measurements in dairy products. These and many other studies were reported at the 9th Symposium on LAB: Health, Evolution and Systems Biology, held in September 2008 (http://www.lab9.nl). Here we highlight some of the latest developments in genomics in these areas.