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Department of Food Science and Southeast Dairy Foods Research Center, and Functional Genomics Program, North Carolina State University, Raleigh, NC 27695-7624
* To whom correspondence should be addressed. E-mail: klaenhammer{at}ncsu.edu.
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ABSTRACT |
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 TOP ABSTRACT LITERATURE CITED |
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30 LAB genomes reported, the following genomes have now been completed: Lactococcus lactis (3), Bifidobacterium longum (4), Lactobacillus plantarum (5), L. johnsonii (6), L. acidophilus (7), 2 strains of Streptococcus thermophilus (8), and 11 genomes have been sequenced by the Department of Energy Joint Genome Institute (JGI, http://www.jgi.doe.gov) in collaboration with the LAB Genome Consortium and placed in the National Center for Biotechnology Information (9). Comparative genomic analysis of members of the LAB, using both published genomes (Lactobacillus plantarum and Lactococcus lactis) and whole-genome transcriptional arrays is quickly elucidating critical gene sets involved in key metabolic and functional activities. Moreover, whole genome transcriptional arrays are providing in-depth views of environmental influences on gene expression and culture behavior, similarities and differences by comparative genomics, and elucidation of the metabolic and functional roles of these organisms. Hence, this article summarizes recent advances in comparative genomics and transcriptional arrays that are identifying critical gene sets within probiotic cultures and how environmental conditions encountered in biomanufacturing and dairy products may impact expression and regulation of important properties. There are numerous genome projects currently ongoing with LAB. Six LAB genomes have been completed (Lactococcus lactis, L. plantarum, L. johnsonii, L. acidophilus, L. gasseri, and S. thermophilus), and >20 more are in progress (9). There are cases where genome sequences for multiple strains of the same species will become available. In the immediate future, such examples are L. lactis (3 strains), L. casei (2 strains), L. delbrueckii (3 strains), S. thermophilus (3 strains), Oenococcus oeni (2 strains), and B. longum (2 strains). Comparative data from these studies should reveal a great deal about genetic stability and diversity among species and within different strains of a single species. This article makes a comparative genome analysis of Lactobacillus gasseri and Lactobacillus acidophilus against all the other LAB that are present as draft genomes in the LAB Genome Consortium package as well as against other probiotic lactobacilli, specifically L. plantarum and L. johnsonii.
Although they are phylogenetically closely related by their small genomes (2–4 Mb) and common metabolic pathways for sugar fermentation and lactic acid production, the LAB occupy a diverse set of ecological niches (e.g., fermenting plants, milk, wine, GI tract). This suggests that considerable genetic adaptation has occurred during their evolution. Comparison of the genome sequences of multiple LAB species and strains is providing an important view of their metabolic pathways and the genetic events responsible for their adaptation to specialized environments. Comparative genomics among the microbes sequenced thus far has illustrated that essential housekeeping gene functions are widely conserved among the LAB. In contrast, the probability of horizontal gene transfer of unique genetic regions has also been reported, revealing functions that appear critical to the organism's evolution (5,10). Examples discussed include discovery of unique regions in probiotic LAB that encode bacteriocin production, polysaccharide biosynthesis, mucin-binding proteins, and sugar catabolism. It is now apparent that comparative genomics will quickly reveal both the conserved and unique components of LAB that occupy different environmental niches. This information will be invaluable in our understanding of their roles in foods and the human GI tract. Knowledge of key gene sets that promote functionality for starter cultures or probiotics will also be critically important in guiding strain selection for multiple roles, either as probiotic or bioprocessing/fermentation cultures.
Some of the key genes and gene networks of interest that are suspected to direct important functional properties of probiotic LAB, and are presumed to be important for colonization, survival, and functionality, include the following [summarized from McAuliffe and Klaenhammer (11) and Reid et al. (12)]: Acid tolerance, Bile tolerance, Stress tolerance, Surface proteins, Lipoteichoic acid, Extracellular proteins, Exopolysaccharides, Adherence factors, Aggregation, Biofilm formation, Immunomodulation, Putative autoimmunity-promoting factors, Bacteriocin production, Carbohydrate (prebiotic) utilization and metabolism, Gene transfer potential, Antibiotic resistance, Putative virulence factor homologs, Siderophores, scavengers of Fe2+, Quorum sensors and response regulators, Prophages, prophage remnants, lysogenic conversion characters, and Mobile genetic elements involved in lateral gene transfer.
Functional and comparative genomic analyses are quickly revealing key gene systems that direct these functions and, further, correlating them to important phenotypic behavior. Examples include prebiotic utilization (13), adherence factors (14), and acid tolerance and adaptation (15).
Analysis of the products of gene expression will also be critically important to unraveling the functional properties and behavior of these organisms, particularly within specialized environments. Key elements in this aspect of functional genomics are the transcriptome—the complement of mRNAs transcribed from all the genes in the genome and their relative levels of expression under a defined set of conditions; the proteome—the complete complement of proteins encoded by the genome; and the metabolome—the quantitative complement of all the molecules present in cells in various physiological or developmental states. By using approaches that include gene chips, microarrays, and proteomic analyses, it has become possible to view a dynamic picture of the genome and begin the process of identifying gene networks that direct behavior and responses to varying environmental conditions. A whole-genome microarray has been developed for Lactobacillus acidophilus, and transcription profiling has been carried out under varying conditions. A comparison of alternative carbohydrate sources (lactose vs. fruto-oligosaccharides) (13) and varying conditions of acid exposure that reflect those encountered in fermented dairy products (15).
For centuries, probiotic LAB have naturally been delivered to the human GI tract via milk, dairy, and fermented milk systems. In fact, milk and acidified milk and dairy products are a primary environment for dairy LAB. Initial studies using the whole genome array for L. acidophilus NCFM will be conducted to address whether or not growth in, or exposure to, milk influences the genes expressed and their regulatory networks in a manner that promotes probiotic survival and/or functionality. Within the year, whole genome arrays will be available for most of the LAB undergoing genomic sequencing, and soon the entire field will have the means to openly investigate the role of milk and dairy on gene expression and phenotypic outcomes for probiotic and bioprocessing dairy LAB.
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FOOTNOTES |
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2 Author disclosure: no relationships to disclose.
3 Support for the dairy fermentation and probiotic research activities at NC State University has been provided by the North Carolina Dairy Foundation, Danisco USA, Inc. (Madison, WI), Southeast Dairy Foods Research Center, Dairy Management, Inc., and the U.S. Department of Agriculture National Research Initiative Competitive Grants Program, # 2005-35503-16167
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LITERATURE CITED |
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TOPABSTRACTLITERATURE CITED |
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1. Tannock GW. A fresh look at the intestinal microflora. In: Tannock GW, editor. Probiotics: a critical review. Wymondham, UK: Horizon Scientific Press; 1999. p. 5–14.
2. Ouwehand AC, Salminen S, Isolauri E. Probiotics: an overview of beneficial effects. Antonie Van Leeuwenhoek. 2002;82:279–89.[Medline]
3. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A. The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 2001;11:731–53.
4. Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, et al. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci USA. 2002;99:14422–7.
5. Kleerebezem M, Boekhorst J, Van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, et al. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA. 2003;100:1990–5.
6. Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, et al. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci USA. 2004;101:2512–7.
7. Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobsn A, Duong T, et al. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci USA. 2005;102:3906–12.
8. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, et al. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 2004;22:1554–8.[Medline]
9. Klaenhammer TR, Alterman E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, et al. Discovering lactic acid bacteria by genomics. Antonie Van Leeuwenhoek. 2002;82:29–58.[Medline]
10. Barrangou R, Altermann E, Hutkins R, Cano R, Klaenhammer TR. Functional and comparative genomic analyses of an operaon involved in fructo-oligosaccharide utilization by Lactobacillus acidophilus. Proc Natl Acad Sci USA. 2003;100:8957–62.
11. McAuliffe OE, Klaenhammer TR. Genomic perspectives on probiotics and the intestinal microflora. In: Tannock G, editor. Probiotics and prebiotics: where are we going? Norfolk, UK: Caister Academic Press; 2002. p. 263–310
12. Reid G, Sanders ME, Gaskins HR, Gibson GR, Mercenier A, Rastall R, Roberfroid M, Rowland I, Cherbut C, Klaenhammer TR. New scientific paradigms for probiotics and prebiotics. J Clin Gastroenterol. 2003;37:105–18.[Medline]
13. Barrangou R, Azcarate-Peril MA, Duong T, Conners SB, Kelly RM, Klaenhammer TR. Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proc Natl Acad Sci USA. 2006;103:3816–21.
14. Buck BL, Altermann E, Svingerud T, Klaenhammer TR. Functional analysis of putative adhesion factors in Lactobacillus acidophilus NCFM. Appl Environ Microbiol. 2005;71:8344–51.
15. Azcarate-Peril MA, McAuliffe O, Altermann E, Lick S, Russell WM, Klaenhammer TR. Microarray analysis of a two-component regulatory system involved with acid resistance and proteolytic activity in Lactobacillus acidophilus. Appl Environ Microbiol. 2005;71:5794–804.
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