The time lapse movie above shows 96 individual MicroCheeses that were made simultaneously and where the emission of light was monitored over a period of roughly one day. What you see here is literally switching on and off light. The light is produced by a bacterial enzyme (luciferase) which we placed in the cheese bacterium L. lactis. We are able to control this switch in a way that the word "NIZO" can be read in cheese and it is underlined from left to right. The technologies allowing us to produce such a movie are extremely useful for the parallel production of cheeses and in situ screening procedures as well as for fundamental understanding of microbial behavior in cheese (for more details see publications below).
Next to understanding complex microbial consortia in situ I am also very interested in using experimental evolution and strain selection procedures for strain improvement.
Apart from my research activities, I am attached to the NIZO Speakers Academy. This speakers academy offers presentations by NIZO experts on a wide variety of topics. I can give you insight in the latest trends and developments on food fermentation and developing / optimizing starter cultures. Should you wish to learn more about my presentations, feel free to contact me!
Genome Res. 2012 Jan;22(1):115-24
L. lactis is mainly isolated from plants and the dairy environment. Literature suggests that dairy isolates have evolved from plant isolates. In this paper we mimicked the transition from the plant to the dairy environment by propagating a L. lactis plant isolate in milk for 1000 generations. Evolved strains showed faster growth rates and increased fitness in milk. The transcriptome of evolved strains converged towards that of a dairy isolate. We showed that changes in nitrogen metabolism and the down-regulation of genes which are dispensable in the dairy environment are the main adaptations.
The ISME Journal (2011) 5, 929–932
Cooperative behavior is widely spread in microbial populations. An example is the expression of an extracellular protease by the lactic acid bacterium Lactococcus lactis, which degrades milk proteins into free utilizable peptides that are essential to allow growth to high cell densities in milk. Cheating, protease-negative strains can invade the population and drive the protease-positive strain to extinction. By using multiple experimental approaches, as well as modeling population dynamics, we demonstrate that the persistence of the proteolytic trait is determined by the fraction of the generated peptides that can be captured by the cell before diffusing away from it. The mechanism described is likely to be relevant for the evolutionary stability of many extracellular substrate degrading enzymes.
Schematic representation of the system and results of modelling population dynamics
Environmental Microbiology, Vol 12(5), p1260–1270, May 2010
Lactococcus lactis is one of main bacterial species found in mixed dairy starter cultures for the production of semi-hard cheese. Despite the appreciation that mixed cultures are essential for the eventual properties of the manufactured cheese the vast majority of studies on L. lactis were carried out in laboratory media with a pure culture. In this study we applied an advanced recombinant in vivo expression technology (R-IVET) assay in combination with a high-throughput cheese-manufacturing protocol for the identification and subsequent validation of promoter sequences specifically induced during the manufacturing and ripening of cheese. The system allowed gene expression measurements in an undisturbed product environment without the use of antibiotics and in combination with a mixed strain starter culture. The utilization of bacterial luciferase as reporter enabled the real-time monitoring of gene expression in cheese for up to 200 h after the cheesemanufacturing process was initiated. The results revealed a number of genes that were clearly induced in cheese such as cysD, bcaP, dppA, hisC, gltA, rpsE, purL, amtB as well as a number of hypothetical genes, pseudogenes and notably genetic elements located on the non-coding strand of annotated open reading frames. Furthermore genes that are likely to be involved in interactions with bacteria used in the mixed strain starter culture were identified.
Gene expression of 96 lactococcal promotors in cheese (measured through luciferase expression)
H. Bachmann, M. J. C. Starrenburg, D. Molenaar, M. Kleerebezem, J. E. T. van Hylckama Vlieg (2012) Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution. Genome Res. 22:115-124
H. Bachmann, D. Molenaar, M. Kleerebezem, J. E. T. van Hylckama Vlieg (2011) High local substrate availability stabilizes a cooperative trait. ISME J. 5:929-932
B. Teusink, H. Bachmann, D. Molenaar (2011) Systems biology of lactic acid bacteria: a critical review. Microb. Cell. Fact. 10 Suppl 1:S11
H. Bachmann, L. de Wilt, M. Kleerebezem, J. E. T. van Hylckama Vlieg (2010) Time-resolved genetic responses of Lactococcus lactis to a dairy environment. Environ. Microbiol. 12:1260-1270
H. Bachmann, Z. Kruijswijk, D. Molenaar, M. Kleerebezem, J. E. T. van Hylckama Vlieg (2009) A high-throughput cheese manufacturing model for effective cheese starter culture screening. J. Dairy Sci. 92:5868-5882
H. Bachmann, M. J. C. Starrenburg, A. Dijkstra, D. Molenaar, M. Kleerebezem, J. L. W. Rademaker, J. E. T. van Hylckama Vlieg (2009) Regulatory phenotyping reveals important diversity within the species Lactococcus lactis. Appl. Environ. Microbiol. 75:5687-5694
H. Bachmann, M. Kleerebezem, J. E. T. van Hylckama Vlieg (2008) High-throughput identification and validation of in situ-expressed genes of Lactococcus lactis. Appl. Environ. Microbiol. 74:4727-4736
R. Siezen, H. Bachmann (2008) Genomics of dairy fermentations. Microb. Biotechnol. 1:435-442
H. Bachmann, F. Santos, M. Kleerebezem, J. E. T. van Hylckama Vlieg (2007) Luciferase detection during stationary phase in Lactococcus lactis. Appl. Environ. Microbiol. 73:4704-4706
J. E. T. van Hylckama Vlieg, J. L. W. Rademaker, H. Bachmann, D. Molenaar, W. J. Kelly, R. J. Siezen (2006) Natural diversity and adaptive responses of Lactococcus lactis. Curr. Opin. Biotechnol. 17:183-190
B. Poppenberger, F. Berthiller, H. Bachmann, D. Lucyshyn, C. Peterbauer, R. Mitterbauer, R. Schuhmacher, R. Krska, J. Glössl, G. Adam (2006)Heterologous expression of Arabidopsis UDP-glucosyltransferases in Saccharomyces cerevisiae for production of zearalenone-4-O-glucoside. Appl. Environ. Microbiol. 72:4404-4410