BiotecVisions 2013, June

Special Edition: Microbial biotechnology

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Editors: Judy Peng /jp; Lucie Kalvodova /lk; Adriana Kantcheva /ak


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Contributors: Danny Asling /da; Frédérique Belliard /fb; Allison Goldstein /ag; Frances Harding /fh; Meghana Hemphill /mh; Loes van de Pasch /lp; Melissa McCulloch /mmc; Prisca Henheik /ph; Erwin Ripmeester /er; Mia Ricci /mr; Andrew Moore /am; Gillian van Beest /gvb

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June 2013

World Environment Day

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“Although individual decisions may seem small in the face of global threats and trends, when billions of people join forces in common purpose, we can make a tremendous difference.”

UN Secretary-General Ban Ki-Moon

Since 1972, the United Nations Environment Program has celebrated the World Environment Day (WED), an initiative aimed at fostering environmental awareness and encouraging political attention and positive action.

The theme of this year's WED is Think Eat Save is intended to focus our attention on the food that we waste. There are compelling reasons for us to examine this – everyday, 1 in 7 of us go to bed hungry, and not by choice. According to UN Food and Agriculture Organization, we waste 1.3 billion tonnes of food per year. If this number alone is not enough to shock you, it may help you recognize the seriousness of the situation when you realize that, for example, wasting a litre of milk is not as innocent as it seems – behind every litre of milk is 1000 litres of water that went into its production.

So, some action points that we can all implement, starting now!

• Eat locally – locally produced foods reduce the amount of energy and resources needed for transportation

• Eat seasonally – similar to eating locally, eating seasonally implies that the food on your table is less likely to have been transported long distances, stored for long periods of time, all of which require energy

Eat responsibly – some food choices have less environmental impact than others, an obvious example is meat – a hamburger requires 2400 L of water whereas an apple 70 L /jp

Getting published

A review article from the reviewer's perspective...

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So you've written your review of field X, and now it's in peer review with journal Y. What will the peer reviewers be looking for/at in particular? A major focus of attention is the balance between the primary and review literature that you cite. Because this is a review, you should keep the number of citations to other review articles to a minimum. But there are definitely circumstances under which you can cite review articles, e.g. to direct the reader to a topic that is not the focus of the current review, but which might be interesting or useful to her/him in way of background or context; another permissible situation arises when you wish to build on, qualify, or criticize the novel insights of a previous review; a further justifiable case is the citation of an authoritative encyclopedic review in order to save citations for more recent primary works that are more relevant to your current thesis. Most journals set limits on the length of bibliographies, and for good reasons.

A desirable result of concentrating overwhelmingly on the primary literature is that you manage to come up with some novel, integrative, insights: a kind of secondary research. And that is another major focus of attention among reviewers of reviews. I have frequently read the comment “This review brings nothing new to the field”. Remember, you are writing the review for a readership that includes the core of the field in question. Many of these researchers will have a very good grasp of the most important primary papers in the topic area, and they won't want to read a mere condensed catalogue of these primary findings. It is these very people whom an Editor will choose to review your paper, so in return for the work that they put into assessing, give them something tasty to think about! /am

Andrew Moore is Editor-in-Chief of BioEssays

For all “Getting Published” articles, see archive at:

Cover story

Bacteriophage lysis harnessed to create broad spectrum antibiotic

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Bacteriophages have evolved to target specific weaknesses in bacterial armour. By investigating a cell wall receptor in that central to bacteriophage infection of Bacillus anthracis, a crucial enzyme involved in cell wall synthesis was uncovered. Small molecule inhibitors of this enzyme, 2-epimerase, were screened to identify a new and highly potent antibiotic, epimerox. Epimerox was demonstrated to prevent growth of a broad range of Gram-positive pathogens, including Staphylococcus aureus, and mice could be rescued from lethal doses of Bacillus anthracis. Intriguingly, the development of bacterial resistance to Epimerox appears to be retarded in comparison to other gram positive targeted antibiotics. /fh

Schuch et al., PLoS One, 2013

Sticky tails: How bacterial flagella assist biofilm formation

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The formation of bacterial biofilms on implant surfaces can cause serious infection and implant rejection. Biofilm prevention is also important to avoid contamination and malfunction of industrial processing equipment. One method proposed to prevent bacterial adhesion is to pattern surfaces with nanoscale features to produce superhydrophobic surfaces. Research recently published in PNAS reveals that while Escherichia coli adhesion is initially reduced on such surfaces, this behavior is reversed over time. Bacterial flagella are key to this process. At first, topographical features trap air bubbles at the surface, preventing the attachment of bacteria. However, the bacteria can gradually force these bubbles aside by flagella motion. Once the crevices are wet, flagella can reach inside to attach bacterium to the surface. /fh

Friedlander et al., PNAS, 2013

Glycosylation increases bioproduction

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2-Phenylethanol (2PE) is an important rose-like flavor and fragrance compound. The biotechnological process of 2PE by Saccharomyces cerevisiae often is hindered due to the growth inhibition 2PE exerts to yeast. The authors Zhang et al. “copied” the strategy of glycoconjugation which protects the plant from toxic effects. They could show that glycosylation with xylose (X-2PE) significantly reduced the inhibitory effect of 2PE on the specific growth rate of yeast. Of high interest from a biotechnological point of view is the non-linear dependence of the growth inhibition induced by X-2PE with an IC10 of 0.37 g/L for 2PE and 21.9 g/L for X-2PE. However, glycosylation will affect the aroma and a deglycosylation step has to be included in the bioproduction process. /ph

Zhang et al., J. Basic Microbiol. 2013

Cold-loving yeasts

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Glacial habitats, such as Antarctica, the Alps and the Himalayas, include some of the largest extreme biospheres on Earth. These environments are inhabited by a wide diversity of cold-loving (psychrophilic) microorganisms that have adapted to life in extremely cold environments. This MiniReview from the latest thematic issue on polar and alpine ecosystems in FEMS Microbiology Ecology presents an overview of the worldwide distribution of psychrophilic yeasts and their survival strategies. Attention is focused on their biotechnological potential, especially on their exploitation as a source of cold-active enzymes and for bioremediation purposes. /lp

Buzzini et al., FEMS Microbiology Ecology, 2012

Novel manganese starvation-inducible expression system

Researchers from the University of Hohenheim, Germany, report their new manganese starvation-inducible expression system for Lactobacillus plantarum in the May issue of FEMS Microbiology Letters. Two major advantages of this novel system are that addition of external inducing agents is not required and no regulatory genes need to be introduced. /er

Böhmer et al., FEMS Microbiology Letters, 2013

Metabolic footprinting in Chardonnay fermentations

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The metabolic footprints and fermentation profiles of commercial wine yeast strains in Chardonnay is revealed in the June issue of FEMS Yeast Research. Group of strains with related phenotypes were found and these similarities can be linked to genomic similarities, providing insight into the diversity of this unique class of industrial strains. /fb

Richter et al., FEMS Yeast Research, 2013

Paving the way for thermophilic bioethanol production

Bioethanol is a promising fuel candidate to replace fossil fuels, especially in the transportation sector. However, only when it is produced from residual biomass can it actually be considered a sustainable biofuel. Pentose sugars, which constitute a large fraction of residual and lignocellulosic biomass, are not fermented by industrial strains of ethanologenic yeasts. In the June 2013 issue of Biotechnology and Bioengineering, Tomás and coworkers have recently isolated a new extreme thermophilic microorganism, Thermoanaerobacter pentosaceus, which has shown the highest ethanol yield from pentose sugars ever reported for a wild-type strain. In this work, the authors demonstrate that T. pentosaceus can be used in combination with Saccharomyces cerevisiae to convert rapeseed straw into bioethanol in a more efficient manner than using each microorganism separately. This is an important achievement because it can be easily implemented into existing bioethanol production plants. /mr

Tomás et. al., Biotechnol. Bioeng. 2013

Real-time monitoring of influenza virus production kinetics in HEK293 cell cultures

In the March/April 2013 issue Biotechnology Progress, Pedram Fatehi reviewed the recent advancements and technical challenges associated with the production of ethanol, butanol, and isobutanol via bioconversion routes from celluloses of woody materials. Physicochemical processes, e.g. steam explosion, seem to be the most viable process for pretreating woody materials. Although enzymatic hydrolysis is selective, it is rather a slow process. Acid hydrolysis is a relatively fast process with a high yield, but it produces inhibitory compounds of fermentation, which necessitates a detoxification process before the fermentation. Presently, the major challenges in the production of ethanol, butanol, and isobutanol via biological conversions are the rather low production yield and the sensitivity of microorganisms to the presence of inhibitors and products in fermentation media. In this study, the recent advancements in the applications of Saccharomyces cerevisiae, Clostridium acetobutylicum, and Corynebacterium glutamicum, the most promising microorganisms, for ethanol, butanol, and isobutanol production are also discussed. /mr

Pedram Fatehi, Biotechnol. Prog. 2013

Understanding the metabolism of cyanobacteria with multiomics analysis

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Cyanobacteria have received considerable attention as a sustainable energy resource because of their capacity to produce organic materials using CO2 as a carbon source and energy from light. Therefore, understanding the metabolism of cyanobacteria is important for the area of cyanobacterial metabolic engineering. Multi-omics analysis is a powerful tool for understanding complex metabolisms; however, there are relatively few ‘omics studies on cyanobacteria. In this article, Yoshikawa et al. (Osaka University, Japan) performed transcriptomic and metabolomic analyses of Synechocystis sp. PCC 6803 under different trophic conditions, such as autotrophic, mixotrophic and photoheterotrophic conditions. The ‘omics dataset reported in this work provides clues to help better understand the metabolism of cyanobacteria. /ak

Yoshikawa et al., Biotechnol. J. 2013

‘Convincing’ microbes to use synthetic pathways

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Synthetic metabolic pathways enable microbes to produce new biofuels and value-added commodity chemicals. However, metabolic engineers are faced with the challenge of ensuring that the engineered microbe continue to uses these synthetic pathways and that production remains high as the engineered strain evolves. Previous approaches have used computational modeling of metabolism to identify gene knockouts and up/down gene regulatory strategies to improve microbial productivity and guide evolution. In this study, Yen et al. (Virginia Tech, USA) introduce a new modeling strategy based on ‘flux ratios’. The new approach called flux balance analysis using flux ratios (FBrAtio) enables identification of 'fine-tuned' metabolic engineering strategies that lead to optimum product formation rates. The FBrAtio approach was tested by the authors on five separate case studies with publicly available genome-scale metabolic flux models, and was shown to successfully guide the development of effective metabolic engineering strategies. /ak

Yen et al., Biotechnol. J. 2013

Continuous flux modifications provide flexibility in strain design

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Strain design algorithms are used to facilitate metabolic engineering efforts by systematically identifying genetic changes that will cause an organism to increase production of a desired chemical. Existing constraint-based methods use a variety of techniques with some strengths and limitations. In this paper, Cotten and Reed (University of Wisconsin-Madison, USA) report the development of a computational method (CosMos) that encompasses several previously reported techniques, while overcoming their limitations. CosMos considers continuous changes to fluxes rather than using pre-determined values as done previously. As a result, CosMos leads to novel strain designs that cannot be derived with current approaches. /ak

Cotten and Reed, Biotechnol. J. 2013

Hydroxy fatty acid production by Pediococcus sp.

Hydroxy fatty acids are useful as starting materials for industrial applications including chemical synthesis, functional foods, and pharmaceuticals. Researchers from Japan screened about 300 strains of lactic acid bacteria and selected Pediococcus sp. AKU 1080 for its ability to hydrate linoleic acid to three different hydroxy fatty acids. The hydration pathway is also discussed. /lk

Takeuchi et al., Eur. J. Lipid Sci. Technol. 2013

Acinetobacter baylyi mutants with an altered lipid accumulation

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Crucial amino acid residues and domains of AtfA, a structurally unknown bacterial acyltransferase that catalyzes wax ester and triacylglycerol synthesis, were identified by random mutagenesis and in silico analysis. The mutated atfA genes were then screened for variants leading to an increased or decreased accumulation of lipids. /lk

Röttig and Steinbüche, Eur. J. Lipid Sci. Technol. 2013

Clostridium difficile cytotoxicity

This is an excellent study in the February issue of Pathogens and Disease. The leading cause of infectious diarrhea in hospitalized patients, pathogenic strains of Clostridium difficile may produce two potent exotoxins – TcdA and TcdB – that induce mucosal inflammation and are largely responsible for the associated diarrhea. Paradigm-shifting in Clostridium difficile toxin-mediated pathogenesis, the authors' findings revise and refine the current model for the mode of the action and cellular trafficking of TcdB. /gvb

Shan Li et al., Pathogens and Disease, 2013

Cholera conjugate vaccines

Vibrio cholerae continues to be a major disease worldwide and requires improved vaccines. This study in the March issue of Pathogens and Disease reports the use of an experimental V. cholerae Inaba LPS-protein conjugate vaccine and shows that pmLPS is a superior immunogen and a viable potential vaccine candidate. /gvb

Grandjean et al., Pathogens and Disease, 2013

G.I.T. Laboratory Journal

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Thermo Fisher Scientific and Life Technologies have signed a definitive agreement under which Thermo Fisher will acquire Life Technologies for $76.00 in cash per fully diluted common share, or approximately $13.6 billion, plus the assumption of net debt at close ($2.2 billion as of yearend 2012). /aga

Read more on the transaction at

Forum Labo & Biotech 2013

The 10th edition of the Labo & Biotech Forum will take place on 4–7 June in Paris. 8,500 professional visitors from both public and private laboratories are expected to attend. A feature of this year's event will be an Expert Forum session focused on quality. /aga

Read more on this event at

Grand Opening of new Laboratory World

Shimadzu has created a new Laboratory World for its customers from all over Europe. The Laboratory World is located at the European headquarters in Duisburg, Germany. On an area greater than 1,500 m2, testing facilities are available for the company's entire product range – from chromatographs, spectrophotometers, TOC analyzers, mass spectrometers and balances up to material testing machines. /aga

Take a look at pictures from this new facility at


Dr. Rodney Ho wins 2013 AAPS Research Achievement Award in Biotechnology

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On May 22nd, 2013, the American Association of Pharmaceutical Scientists honored Wiley author Dr. Rodney Ho by awarding him the 2013 AAPS Research Achievement Award in Biotechnology. This award is among the highest honors conferred by the AAPS, and recognizes Dr. Ho's lifetime achievement in biotechnology. /ag

Dr. Ho coathored Biotechnology and Biopharmaceuticals: Transforming Proteins and Genes into Drugs. The second edition of this bestselling title is currently in press and will publish in September 2013. Read more and preorder the book at

Microbial Biotechnology has moved to open access!

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Microbial Biotechnology publishes original research papers reporting significant advances in any aspect of applied microbiology, and received its first IF of 2.5 in 2012. /mmc

Read the latest content now, including the 2013 Crystal Ball article, and the Special Issues on Plant-Microbe Interactions and The Corynebacterium Cell Factory.

Be part of the future of research and submit your paper now at

For more information about Microbial Biotechnology visit


Understanding Microbes: An Introduction to a Small World

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Jeremy W. Dale

This concise and engaging book provides the basics of microbiology, including sections demonstrating their applicability such as “Microbial Biotechnology – Practical Uses of Microbes.” /ag

Microbes: Concepts and Applications

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P. S. Bisen, Mousumi Debnath, G. B. Prasad

Microbes: Concepts and Applications places a major emphasis on omics technology, exploring the role of microbes in industry and agriculture, as well as in related fields such as immunology, cell biology, and molecular biology. /ag

Molecular Microbial Ecology of the Rhizosphere, 2 Volume Set

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Frans J. de Bruijn

Molecular Microbial Ecology of the Rhizosphere covers current knowledge on the molecular basis of plant-microbe interactions in the rhizosphere, and will be a valuable resource for molecular microbiologists and plant soil scientists, as well as upper level students in microbiology, ecology, and agriculture. /ag

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For detailed book reviews

BiotecCareers – continuing education with on-course®

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“The only thing that is constant is change” – Heraclitus

Staying nimble in a rapidly changing environment, be it business, industry, or academia, requires constant adaptation and having the necessary skills and qualifications to meet the needs of the employer. Similarly, in this rapidly changing environment, what you have set out to study may no longer be the most in-demand skill set by the time you graduate – how do you avoid becoming obsolete even before you get old?

In order to provide the skilled workforce required to maintain Europe's competitive edge in biomedical research, the Innovative Medicines Initiative (IMI), a public-private partnership between the European Union the European Federation of Pharmaceutical Industries and Associations (EFPIA), aims to provide the training and education necessary. To compile all the training programs available, the IMI's European Medicines Research Training Network (EMTRAIN) has developed an on-line platform to help you navigate the large amount of information available and also compare and contrast these programs, known as on-course®.

The on-course® platform provides an easy to navigate, free resource for you to choose the right course for your needs. The courses are divided into three main areas, including the “short courses”, otherwise known as continuing professional development (CPD) courses, Masters courses as well as PhD courses. There is also a convenient keyword search function that allows you to narrow your searches based on your needs, such as language, location, and duration requirements. Importantly, you can also bookmark courses and compare them to one another in one table. /jp


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WIREs featured collections are truly interdisciplinary, with articles drawn from multiple WIREs titles and including content that bridges the life, physical, and medical sciences. /mh

Bacteria: An Interdisciplinary View

RNA decay: a novel therapeutic target in bacteria

This article discusses the factors that govern bacterial RNA degradation, highlight members of this machinery that represent attractive antimicrobial drug development targets and describe the use of high-throughput screening as a means of developing antimicrobials that target these enzymes.

Eidem, et al., WIREs RNA 2012. doi: 10.1002/wrna.1110

Engineered viral nanoparticles for flow cytometry and fluorescence microscopy applications

Fluorescence microscopy allows the direct observation of viral nanoparticles (VNPs) on the cell surface or inside the cell, while flow cytometry allows the statistical quantification of nanoparticle uptake and targeting specificity. These techniques are essential when characterizing the properties of VNPs and provide information toward the use of VNPs for targeting, imaging, and/or cargo delivery.

Robertson and Liu, WIREs Nanomed Nanobiotechnol 2012. doi: 10.1002/wnan.1177

Influenza A virus infection kinetics: quantitative data and models

This article discusses how recent viral kinetic models for influenza have been used to provide insight into pathogenesis and treatment. The authors highlight the challenges of viral kinetic analysis, including accurate model formulation, estimation of important parameters, and the collection of detailed data sets that measure multiple variables simultaneously.

Smith and Perelson, WIREs Syst Biol Med 2011. doi: 10.1002/wsbm.129