Herwig Bachmann


  • Experimental evolution
  • Molecular Microbiology
  • Molecular biology of lactic acid bacteria
  • Resource distribution and metabolic efficiency
  • Microbial growth in emulsions
  • Mixed culture fermentation processes
  • Heterogeneity of clonal bacterial populations

Selected Publications

Availability of public goods shapes the evolution of competing metabolic strategies

H. Bachmann et al.; Proceedings of the National Academy of Sciences of the United States of America, Published online before print August 12, 2013, doi: 10.1073/pnas.1308523110 PNAS August 12, 2013

In this article we show that microbial growth in isolation leads to the selection of strains with increased metabolic efficiency but slower growth rates. To our knowledge we show here for the first time the selection of cells with increased yield at the cost of growth rate. Such yield-selection is not possible in a suspension culture where faster growing cells will out-compete slower, but more efficient ones. We solved this problem through culturing single cells in emulsion droplets which leads to an increase of mutants that have a higher number of offspring. Serial propagation in such a system allowed eventually the identification of strains with increased efficiency. The results are relevant to numerous fundamental questions in evolutionary biology but also to biotechnological applications like the increase of biomass yield.

Principle of yield selection in emulsion (panel b) as compared to selection in suspension culture (panel a)

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

H. Bachmann et al.; 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.


Transcriptome analysis of evolved strains

High local substrate availability stabilizes a cooperative trait

H. Bachmann et al.; 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

Time-resolved genetic responses of Lactococcus lactis to a dairy environment

H. Bachmann et al.; 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)

Brief CV

  • 2011-current Project leader Functional Fermentation, NIZO Food Research and TIFN, Ede, NL
  • 2013-current Guest Scientist VU-University, Amsterdam, NL
  • 2009-2013 PostDoc, Systems Bioinformatics, VU-University, Amsterdam, NL
  • 2004-2009 PhD student NIZO Food Research, (Wageningen University), NL
  • 2002-2004 Junior scientist - Galapagos Genomics, Leiden, NL
  • 2002 Master thesis Center for Applied Genetics, University of Agricultural sciences, Vienna, AT

My publications

Contact details
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T: +31 20 59 87xxx
F: +31 20 59 87229

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