Lactic acid bacteria: life after genomics

As powerhouses for the food industry, lactic acid bacteria continue to be the focus of considerable interest. While traditionally applied in industrial dairy and other food fermentations, lactic acid bacteria are now used in a great variety of drinks, yoghurts or other products that are marketed with specific health benefits. This has been the largest growth segment in the functional foods market with an annual sales value of over a billion Euro. The lactic acid bacteria in these products include notably species of Lactobacillus and Bifidobacterium that are marketed as probiotics (Saxelin et al., 2005). Hence it is no surprise that these species are actively studied and often considered together as will be detailed below. The attention for these groups of lactic acid bacteria represents a marked shift in the attention from the traditional focus on strains of notably Lactococcus and Streptococcus spp. that are used as starters in important milk fermentations, resulting in commodity products, such as cheese and yoghurt. However, Lactococcus lactis can still be seen as a model for lactic acid bacteria as will be discussed below. All these genera belong to the Gram-positive bacteria and produce lactic acid from sugars. Bifidobacteria belong to the Actinobacteria and contain genomic DNA with a high G+C content, while the other lactic acid bacteria are phylogenetically closely related and belong to the Firmicutes that are characterized by genomes with a low G + C content. It is of more than anecdotal importance to note here that the bacteria belonging to the Actinobacteria and Firmicutes make up the vast majority of microbial taxa present in our intestinal tract (Zoetendal et al., 2008). Both Lactobacillus and Bifidobacterium spp. are early colonizers and belong to our microbes inside where – in adult life – they are notably present in the upper and lower intestinal tract respectively (Kleerebezem and Vaughan, 2009). This explains why the growing interest in these different groups of lactic acid bacteria and their application in health-promoting products is paralleled by attention for their activity and diversity in the human body. The impact of consumed lactobacilli has recently been established in pioneering studies addressing the human response in the upper intestinal tract (van Baarlen et al., 2009; 2011). The results show specific and straindependent transcriptional host responses that are dependent on the physiological state of the consumed cells. In this way, the provide support for the functionality of probiotics, which are often defined as microbial cultures providing when consumed in adequate amounts a health benefit to the host (Saxelin et al., 2005). In line with the industrial importance and scientific interest, this issue of Microbial Biotechnology addresses various aspects of Lactobacillus and Bifidobacterium spp. and the genetic model L. lactis. All contributions capitalize in different forms on the post-genomic progress that set off a revolution in the understanding of the lactic acid bacteria (De Vos, 2001). A decade ago, the 2 Mb genome was characterized of a plasmid-free L. lactis strain (Bolotin et al., 2001) and the first complete genome sequence of a Lactobacillus strain was reported with the 3.3-Mb-large genome of Lactobacillus plantarum (Kleerebezem et al., 2003). Subsequently, a great number of industrial and model strains have been characterized at the genome level. These include representatives of the over 100 Lactobacillus spp., as well as different strains belonging to the same species. However, many genomes have only been partially sequenced and have some gaps as the genomes are notably highly repetitive because of the presence of IS elements, repeated domains or other unusual sequences. These include several intestinal isolates that recently have been reported as part of the Human Microbiome Jumpstart Initiative (Nelson et al., 2010). In a review article, Ravi Kant and colleagues focus on the 20 completely genomes of Lactobacillus spp. and describe their comparative bioinformatic analysis (Kant et al., 2011). These genomes varied in size between 1.8 and 3.3 Mb, reflecting the large variation of niches occupied by these lactic acid bacteria. The deduced Lactobacillus pangenome of over 14 000 proteinencoding genes was predicted together with the Lactobacillus Core Genome that includes several hundreds of orthologous genes. This detailed analysis provides a platform for functional and comparative genomics of presently known lactobacilli as well as future analysis of new Lactobacillus genomes. Knowledge of a genome sequence does not directly provide insight in the activity or behaviour of an organism. The relations between the genomic blueprint and the apparent functional properties can be unravelled using functional genomic approaches that target different molecular levels, i.e. transcriptomics, proteomics and Microbial Biotechnology (2011) 4(3), 318–322 doi:10.1111/j.1751-7915.2011.00262.x