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MICROBIOLOGY COMMENT |
1 Centre for Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands
2 Friesland Foods Corporate Research, Deventer, The Netherlands
3 NIZO food research, Ede, The Netherlands
4 Wageningen Centre for Food Sciences, Wageningen, The Netherlands
Correspondence
Roland J. Siezen
(siezen{at}cmbi.ru.nl)
The 8th Symposium on Lactic Acid Bacteria (LAB) held in August 2005 in Egmond aan Zee, The Netherlands (www.lab8.nl), was again the largest meeting of its kind, bringing together 700 scientists from academia and industry around the world to discuss genetics, metabolism and applications in bioprocessing and health of these industrially important bacteria. One of the most striking advances demonstrated at this event was the explosion in the characterization of the genomes of LAB and their genetic elements.
Lactic acid bacteria (LAB) are a heterogeneous family of mainly low G+C Gram-positive, anaerobic, non-sporulating and acid-tolerant bacteria. They can ferment various nutrients in a homofermentative or heterofermentative fashion into primarily lactic acid, but also into by-products such as acetic acid, formic acid, ethanol and carbon dioxide. They contribute to rapid acidification of food products, but also to flavour, texture and nutrition. Lactic acid bacteria are naturally found in plant, meat, dairy and cereal fermentation environments, and have a long tradition of use in industrial and artisan food and feed fermentations, where they are used as starter cultures for fermenting raw materials of vegetable or animal origin.
More recently, it has been recognized that some LAB and high G+C Gram-positive bifidobacteria are natural inhabitants of the human and animal gastro-intestinal tract, where they contribute to and stimulate gastro-intestinal health (Vaughan et al., 2005
). This probiotic (health-promoting) activity is now being exploited by enriching functional foods and drinks with probiotic LAB, mainly lactobacilli and bifidobacteria (Saxelin et al., 2005). Emphasis in scientific research of LAB has shifted towards unravelling and understanding the mechanisms of probiotic effects, and survival and colonization of LAB in the gastro-intestinal tract as this evidence is required to substantiate health claims of commercial probiotic products.
Genome sequencing of food and health-related LAB and bifidobacteria was slow to start, as only Lactococcus lactis IL1403 (Bolotin et al., 2001) and Bifidobacterium longum NCC2705 (Schell et al., 2002) were published at the time of the 7th Symposium on Lactic Acid Bacteria in 2002, shortly followed by the largest known LAB genome to date, Lactobacillus plantarum WCFS1 (Kleerebezem et al., 2003). High hopes for rapid up-scaling were expressed at that time, since many genome projects worldwide were in the pipeline (Klaenhammer et al., 2002), including the sequencing of 11 LAB genomes by the Joint Genome Institute (http://genome.jgi-psf.org/mic_home.html), initiated by the LAB Genomics Consortium in the USA. Now, at the 8th LAB Symposium in 2005, the keynote lecturer (Klaenhammer et al., 2005) showed that the published genome sequences of Lactobacillus johnsonii (Pridmore et al., 2004), Lactobacillus acidophilus (Altermann et al., 2005) and two Streptococcus thermophilus strains (Bolotin et al., 2004) and whole LAB genome comparisons (Boekhorst et al., 2004) have been added to this list (Table 1). But the real state-of-the-art was evident from oral presentations and numerous posters (abstracts at www.lab8.nl), describing genome sequencing of about 30 LAB and bifidobacteria strains (Table 1). In fact, many of these genome sequences are now complete and in the process of annotation or being submitted for publication, as is the case for the JGI genomes (Klaenhammer et al., 2005). Sequencing of large LAB plasmids, known to encode important traits and provide competitive advantage to parent strains, was also reported (Siezen et al., 2005).
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; Klaenhammer et al., 2005), streptococci (Bolotin et al., 2004; Hols et al., 2005) and bifidobacteria (Klijn et al., 2005). Starting with this explosion in complete genome information for a wide range of food-relevant LAB and bifidobacteria, large-scale comparative genomics studies become feasible not only to identify conserved and variable genes and pathways, but also to elucidate horizontal gene transfer, evolutionary relationships and niche adaptations. With the wealth of LAB genome information forthcoming, these comparisons can be tackled at the genus, species, subspecies and even strain level. Strain diversity studies have previously been limited to comparative genome hybridization studies of Lb. plantarum strains (Molenaar et al., 2005). Table 1
now shows that multiple strains have been sequenced of the yoghurt bacteria Streptococcus thermophilus and Lb. delbrueckii subsp. bulgaricus, but also for Lactococcus lactis and several Bifidobacterium species.
It is very encouraging to see that starter culture and food companies have now adopted an open attitude by presenting details of genome sequencing (Table 1) of their in-house bioprocessing and probiotic organisms which are used in different fermented foods and health drinks. Even though these industrial LAB genomes may never be published in the scientific literature, this openness allows academia, R&D organizations and industry to learn from each others' genomics activities, paving the way for fruitful collaborations, win–win situations and novel industrial applications (Pedersen et al., 2005).
Looking to the future, the knowledge of the complete genetic potential of numerous LAB and bifidobacteria will now allow integration of genomics, transcriptomics, proteomics and metabolomics data, aimed at developing metabolic models and understanding gene regulation (Francke et al., 2005; Siezen et al., 2004; Teusink et al., 2005). Hopefully, this can soon be used to predict and optimize the molecular components and pathways leading to the production of flavours, health-promoting and other functional ingredients (Smid et al., 2005a, b).
Acknowledgements
This work was supported by grant CSI4017 from the Casimir programme of the Ministry of Economic Affairs, the Netherlands.
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