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Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models. It is therefore unclear for potential users which tool best fits the purpose of their research. In this work, we performed a systematic assessment of the current genome-scale reconstruction software platforms. To meet our goal, we first defined a list of features for assessing software quality related to genome-scale reconstruction, which we expect to be useful for the potential users of these tools. Subsequently, we used the feature list to evaluate the performance of each tool. In order to assess the similarity of the draft reconstructions to high-quality models, we compared each tool’s output networks with that of the high-quality, manually curated, models of Lactobacillus plantarum and Bordetella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We showed that none of the tools outperforms the others in all the defined features and that model builders should carefully choose a tool (or combinations of tools) depending on the intended use of the metabolic model.Author SummaryMetabolic networks that comprise biochemical reactions at genome-scale have become very useful to study and predict the phenotype of important microorganisms. Several software platforms exist to build these metabolic networks. Based on different approaches and utilizing a variety of databases it is, unfortunately, unclear what are the best scenarios to use each of these tools. Hence, to understand the potential uses of these tools, we created a list of relevant features for metabolic reconstruction and we evaluated the tools in all these categories. Here, we show that none of the tools is better than the other in all the evaluated categories; instead, each tool is more suitable for particular purposes. Therefore, users should carefully select the tool(s) that best fit the purpose of their research. This is the first time these tools are systematically evaluated and this overview can be used as a guide for selecting the correct tool(s) for each case.

The 11th International Symposium on Lactic Acid BacteriaLactic Acid Bacteria play important roles in the pro- duction of food and feed and are increasingly used as health-promoting probiotics. The incessant scientific interest in these microorganisms by academic research groups as well as by industry has resulted in many sig- nificant scientific breakthroughs and has led to new applications. A series of tri-annual symposia on Lactic Acid Bacteria was started in 1983 in order to communi- cate and stimulate research on Lactic Acid Bacteria and their application. These symposia have allowed research- ers from academia and industry to meet, present their work and be informed in an international, open and pleasant atmosphere. Thus, the LAB symposia have, over the years, always presented the state-of-the-art in the field. We have over the past decades witnessed a tre- mendous increase in our understanding of the basic physiology and genetic make-up of these microorgan- isms and, from the turn of the millennium onwards, have been able to apply all ‘omics’ techniques in order to get in-depth understanding of the molecular biology and application potential of lactic acid bacteria.Now, in 2014, we are looking forward to embarking on the next phase and to set the stage for another 30 years of research on this industrially highly relevant group of bacteria. Focus will be on their eminent impor- tance in health and nutrition of humans all over the world. The breadth and richness of LAB research is exemplified by the six selected scientific areas that will be covered at the LAB11 Symposium: Diversity and Evo- lution; Genetics and Physiology; Ecosystems and Sus- tainability; Fermentation and Industrial Application; Host-Microbe Interactions; and Emerging Technologies.Leading, as well as upcoming LAB scientists have been selected to cover the latest developments in these research areas, while renowned scientists from outside the LAB-community have been invited to cover impor- tant emerging fields.For all 11 LAB lectures presented at the LAB11 sym- posium the authors have prepared review-type manu- scripts. These have gone through a standard peer review process, for which we were invited to act as Guest Edi- tors for Microbial Cell Factories. These papers are pre- sented here, online and in a printed version as the “Symposium Proceedings” for all who attend the meet- ing in Egmond aan Zee. We are obliged to the MCF Editor-in-Chief, dr. Antonio Villaverde, to Isobel Peters at BioMed Central and to all our authors and reviewers for the smooth editorial process. We wish you good reading.

Background The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists. Results The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/. Conclusions With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike.

Background Thioredoxin (TRX) is a powerful disulfide oxido-reductase that catalyzes a wide spectrum of redox reactions in the cell. The aim of this study is to elucidate the role of the TRX system in the oxidative stress response in Lactobacillus plantarum WCFS1. Results We have identified the trxB1-encoded thioredoxin reductase (TR) as a key enzyme in the oxidative stress response of Lactobacillus plantarum WCFS1. Overexpression of the trxB1 gene resulted in a 3-fold higher TR activity in comparison to the wild-type strain. Subsequently, higher TR activity was associated with an increased resistance towards oxidative stress. We further determined the global transcriptional response to hydrogen peroxide stress in the trxB1-overexpression and wild-type strains grown in continuous cultures. Hydrogen peroxide stress and overproduction of TR collectively resulted in the up-regulation of 267 genes. Additionally, gene expression profiling showed significant differential expression of 27 genes in the trxB1-overexpression strain. Over expression of trxB1 was found to activate genes associated with DNA repair and stress mechanisms as well as genes associated with the activity of biosynthetic pathways for purine and sulfur-containing amino acids. A total of 16 genes showed a response to both TR overproduction and hydrogen peroxide stress. These genes are involved in the purine metabolism, energy metabolism (gapB) as well as in stress-response (groEL, npr2), and manganese transport (mntH2). Conclusion Based on our findings we propose that overproduction of the trxB1-encoded TR in L. plantarum improves tolerance towards oxidative stress. This response coincides with simultaneous induction of a group of 16 transcripts of genes. Within this group of genes, most are associated with oxidative stress response. The obtained crossover between datasets may explain the phenotype of the trxB1-overexpression strain, which appears to be prepared for encountering oxidative stress. This latter property can be used for engineering robustness towards oxidative stress in industrial strains of L. plantarum.