COMMENTARY
Microbiology in Europe
DOI: 10.1111/1574-6968.12606
MICROBIOLOGY LETTERS
Introduction from FEMS Vice President Bauke Oudega It is a pleasure for me as Vice President of FEMS to introduce to you this third FEMS 40th birthday Virtual Issue. The Guest Editors of this issue are Eliora Ron from Israel and Gianfranco Donelli from Italy, both of whom play important roles in the FEMS organisation. They have selected 10 papers highlighting contributions from various FEMS societies and regions. FEMS is a Federation of European Microbiological Societies. Almost all microbiological societies in all European countries from North to South and East to West have joined FEMS. In addition, some societies from adjacent countries and affiliated members from all over the world are part of FEMS. Forty years ago, FEMS was formed, not to copy the activities of associated member societies but to represent and to further microbiology at a European level. FEMS has grown enormously: today, over 50 societies are members. At the moment, the FEMS organisation is working on a new strategy document. The FEMS strategy document will describe how we as an organisation want to help our member societies in microbiological research, teaching, internationalisation and business development. Furthermore, we would like to raise the public awareness on microbiology in general and on important topics such as antibiotic resistance, biofuels. Especially, the role that microbiologists can play will be highlighted. More than in the past, we like to influence European politicians and captains of industry on microbiological topics. After 40 years, FEMS is a healthy organisation, financially sound and full of plans. I hope you enjoy this selection of FEMS publications.
Articles selected by Eliora Ron and Gianfranco Donelli Selecting the papers was a difficult task, as there were many excellent ones. Our decision was based on novelty, contribution to our microbiological knowledge base and impact on microbiological concepts. Clearly, the selection of papers is therefore quite subjective and depends on what excites us, as selectors. We hope you find our
FEMS Microbiol Lett 359 (2014) 131–133
selection of interest and enjoy reading a broad spectrum of high level papers. Hydrophobins: the protein-amphiphiles of filamentous fungi (Linder et al., 2005)
This is a very interesting and well-written review on the relatively small proteins of about 10 kDa secreted by filamentous fungi, firstly described and named hydrophobins by Linder et al. (2005). These surface-active proteins are amphiphilic molecules having hydrophilic and hydrophobic parts, as demonstrated by the three-dimensional structure at 1 angstrom resolution obtained for the hydrophobin HFB11 from Trichoderma reesei. In this comprehensive review, authors also report on the role of hydrophobins in the diverse phases of fungal life, including surface adhesion, aerial growth and sporulation. Apart from the described ability of hydrophobins to act as surfactants, emulsifiers, surface modifiers and stabilisers, is also of interest the exhaustive discussion on the range of applications at the industrial level, including their strong separation behaviour in aqueous two-phase systems and their possible use for enzyme immobilisation and surface coating of biomaterials. Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria (Maeda et al., 2003)
Real-time PCR was proposed by the authors of this paper as a valid alternative to the time-consuming culture-based assays for the identification and quantification of periodontal bacteria. The GeneAmp Sequence Detection System, using TaqMan probe and SYBR Green dye as fluorescence sources, was successfully experimented. Probes and primers were specifically designed for Actinobacillus actinomycetemcomitans (recently renamed Aggregatibacter actinomycetemcomitans), Porphyromonas gingivalis, Prevotella intermedia and for total bacteria. Moreover, in the light of the increasing spread of antibiotic resistance, quantitative detection of tetQ gene, which confers resistance to tetracycline, was also included in this investigation. Any
ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
132
significant difference in the specificity, sensitivity and quantitativity between TaqMan and SYBR Green was observed. Thus, the easier to manipulate SYBR Green was used to analyse plaque samples obtained from the periodontal pockets of patients before and 1 week after local administration of minocycline. As expected, a significant decrease in the number of periodontal bacteria after antibiotic treatment was revealed while higher numbers of tetQ gene were detectable. On the basis of their results, authors conclude that real-time PCR can be considered as a powerful tool for a timely laboratory diagnosis of periodontal pathogens and for the quantitative monitoring of antibiotic resistance genes. Gentamicin resistance genes in environmental bacteria: prevalence and transfer (Heuer et al., 2002)
The main target of this study was to ascertain the prevalence and transfer of genes conferring resistance to gentamicin (Gm) in a variety of environmental samples collected in different European countries (Belgium, Germany, Greece, the Netherlands and UK) including soils, rhizosphere, animal faeces, polluted and not-polluted costal sea waters as well as sewage from community and hospital wastewater treatment plants. All samples were analysed by culture-dependent and independent methods, particularly following a multiphasic approach consisting in the selective plating, the exogenous isolation of transferable elements carrying Gm resistance genes and the PCR-based detection of Gm resistance genes. According to the experiments performed, genes conferring resistance to gentamicin were revealed in almost all the analysed environmental samples and in a variety of host bacterial species (Enterobacteriaceae, Pseudomonas, Acinetobacter, Proteobacteria, etc.). Thus, also in the light of the results reported in this very comprehensive study, the common belief that hospitals, because of their essentially closed environment, are basically the only cause of the rising antibiotic resistance has been reconsidered since. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis (Von Wintzingerode et al., 1997)
This is a precious paper that summarises and discusses the main pitfalls encountered by microbiologists in a decade of molecular ecological studies using PCR-based analyses of prokaryotic small-subunit ribosomal RNAs. This critical review has been applied to all the steps of the PCR-based rRNA analyses, including sample collection, cell lysis and extraction of nucleic acids, PCR amplification and separation of amplified DNA, use of nucleic ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
Commentary
probes and analysis of 16S rRNA sequence data. However, authors even alarming on the numerous pitfalls that can lead researchers to an erroneous description of an ecological niche underline the power of this molecular approach particularly to reveal microorganisms occurring in small numbers, uncultivable, difficult to cultivate or in dormant conditions. The species concept for prokaryotes (Rossello Mora & Amann, 2001)
What is a species? Difficult question to answer at any level, but much more difficult in prokaryotes. Yet, this term has to be well defined for practical reasons, such as communication between researchers. This review describes the inherent problems of defining a species in prokaryotes and suggests the use of new concepts that may define microbial taxonomy that will be more compatible with the concepts used for eukaryotes. Classification and phylogeny of hydrogenases (Vignais et al., 2001)
The scientific world is urgently looking for new energy sources that will be efficient and environmentally friendly. In this respect, the study of bacterial hydrogen metabolism and hydrogenases is most timely. Hydrogenases – that catalyse the reversible oxidation of molecular hydrogen – are found mostly in Archaea and Bacteria and are well described in this review. Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae (C ß akar et al., 2005)
Industrially important microorganisms are undergoing improvements continuously. One of the important issues in such improvements is the optimisation of the selection method. This paper describes and compares several selection procedures – both in chemostats and batch cultures – for selection of multiple-stress-resistant mutants in the important yeast Saccharomyces cerevisiae. The paper presents successful results for selection of yeast resistant to freezing–thawing procedures and discusses general selection principles. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis (Sipos et al., 2007)
This paper is intended to solve the critical problem of differential amplification in studies using hybridisation to FEMS Microbiol Lett 359 (2014) 131–133
133
Commentary
phylogenetically highly conserved regions of 16S rRNA genes for the study of environmental bacteria communities. The results of an extensive study lead to a straight forward conclusion that reduction in the annealing temperature results in significant reduction of preferential amplification while still maintaining the required specificity. The ability of probiotic bacteria to bind to human intestinal mucus (Kirjavainen et al., 1998)
One of the most impressive recent advances in microbiology involves the studies of microbiomes. Of special interest is the human microbiome and its changes as the human body develops. The results presented in this study clearly indicate that the probiotic microbiome is affected by the age of infants and should be considered in future design of functional foods or probiotic therapy. Diversity of bacterial polyhydroxyalkanoic € chel & Valentin, 1995) acids (Steinbu
Bacterial polyhydroxyalkanoic acids are interesting storage compounds, first discovered in Bacillus megaterium. Recently, it became clear that there are a large number of hydroxyalkanoic acid derivatives and they are accumulated in many bacteria. Currently, there are about 90 known compounds, whose physiological role, biosynthesis and potential applications have not been fully studied and exploited. These finding provide an exciting potential to be exploited by the use of microbial genetic technologies. Bauke Oudega Faculty of Earth and Life Sciences, Vrije Universiteit, Amsterdam, The Netherlands Gianfranco Donelli Microbial Biofilm Laboratory (LABIM) IRCCS ‘Fondazione Santa Lucia’, Rome, Italy E-mail: [email protected]
FEMS Microbiol Lett 359 (2014) 131–133
Eliora Z. Ron Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel E-mail: [email protected]
References C ß akar ZP, Seker UOS, Tamerler C, Sonderegger M & Sauer U (2005) Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res 5: 569–578. Heuer H, Kr€ ogerrecklenfort E, Wellington EMH et al. (2002) Gentamicin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol Ecol 42: 289–302. Kirjavainen PV, Ouwehand AC, Isolauri E & Salminen SJ (1998) The ability of probiotic bacteria to bind to human intestinal mucus. FEMS Microbiol Lett 167: 185–189. Linder MB, Szilvay GR, Nakari-Set€al€a T & Penttil€a ME (2005) Hydrophobins: the protein-amphiphiles of filamentous fungi. FEMS Microbiol Rev 29: 877–896. Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, Arai H, Tanimoto I, Nishimura F & Takashiba S (2003) Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunol Med Microbiol 39: 81–86. Rossell o-Mora R & Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39–67. Sipos R, Szekely AJ, Palatinszky M, Revesz S, Marialigeti K & Nikolausz M (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol 60: 341–350. Steinb€ uchel A & Valentin HE (1995) Diversity of bacterial polyhydroxyalkanoic acids. FEMS Microbiol Lett 128: 219– 228. Vignais PM, Billoud B & Meyer J (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25: 455– 501. Von Wintzingerode F, G€ obel UB & Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213–229.
ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
Microbiology in Europe
DOI: 10.1111/1574-6968.12606
MICROBIOLOGY LETTERS
Introduction from FEMS Vice President Bauke Oudega It is a pleasure for me as Vice President of FEMS to introduce to you this third FEMS 40th birthday Virtual Issue. The Guest Editors of this issue are Eliora Ron from Israel and Gianfranco Donelli from Italy, both of whom play important roles in the FEMS organisation. They have selected 10 papers highlighting contributions from various FEMS societies and regions. FEMS is a Federation of European Microbiological Societies. Almost all microbiological societies in all European countries from North to South and East to West have joined FEMS. In addition, some societies from adjacent countries and affiliated members from all over the world are part of FEMS. Forty years ago, FEMS was formed, not to copy the activities of associated member societies but to represent and to further microbiology at a European level. FEMS has grown enormously: today, over 50 societies are members. At the moment, the FEMS organisation is working on a new strategy document. The FEMS strategy document will describe how we as an organisation want to help our member societies in microbiological research, teaching, internationalisation and business development. Furthermore, we would like to raise the public awareness on microbiology in general and on important topics such as antibiotic resistance, biofuels. Especially, the role that microbiologists can play will be highlighted. More than in the past, we like to influence European politicians and captains of industry on microbiological topics. After 40 years, FEMS is a healthy organisation, financially sound and full of plans. I hope you enjoy this selection of FEMS publications.
Articles selected by Eliora Ron and Gianfranco Donelli Selecting the papers was a difficult task, as there were many excellent ones. Our decision was based on novelty, contribution to our microbiological knowledge base and impact on microbiological concepts. Clearly, the selection of papers is therefore quite subjective and depends on what excites us, as selectors. We hope you find our
FEMS Microbiol Lett 359 (2014) 131–133
selection of interest and enjoy reading a broad spectrum of high level papers. Hydrophobins: the protein-amphiphiles of filamentous fungi (Linder et al., 2005)
This is a very interesting and well-written review on the relatively small proteins of about 10 kDa secreted by filamentous fungi, firstly described and named hydrophobins by Linder et al. (2005). These surface-active proteins are amphiphilic molecules having hydrophilic and hydrophobic parts, as demonstrated by the three-dimensional structure at 1 angstrom resolution obtained for the hydrophobin HFB11 from Trichoderma reesei. In this comprehensive review, authors also report on the role of hydrophobins in the diverse phases of fungal life, including surface adhesion, aerial growth and sporulation. Apart from the described ability of hydrophobins to act as surfactants, emulsifiers, surface modifiers and stabilisers, is also of interest the exhaustive discussion on the range of applications at the industrial level, including their strong separation behaviour in aqueous two-phase systems and their possible use for enzyme immobilisation and surface coating of biomaterials. Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria (Maeda et al., 2003)
Real-time PCR was proposed by the authors of this paper as a valid alternative to the time-consuming culture-based assays for the identification and quantification of periodontal bacteria. The GeneAmp Sequence Detection System, using TaqMan probe and SYBR Green dye as fluorescence sources, was successfully experimented. Probes and primers were specifically designed for Actinobacillus actinomycetemcomitans (recently renamed Aggregatibacter actinomycetemcomitans), Porphyromonas gingivalis, Prevotella intermedia and for total bacteria. Moreover, in the light of the increasing spread of antibiotic resistance, quantitative detection of tetQ gene, which confers resistance to tetracycline, was also included in this investigation. Any
ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
132
significant difference in the specificity, sensitivity and quantitativity between TaqMan and SYBR Green was observed. Thus, the easier to manipulate SYBR Green was used to analyse plaque samples obtained from the periodontal pockets of patients before and 1 week after local administration of minocycline. As expected, a significant decrease in the number of periodontal bacteria after antibiotic treatment was revealed while higher numbers of tetQ gene were detectable. On the basis of their results, authors conclude that real-time PCR can be considered as a powerful tool for a timely laboratory diagnosis of periodontal pathogens and for the quantitative monitoring of antibiotic resistance genes. Gentamicin resistance genes in environmental bacteria: prevalence and transfer (Heuer et al., 2002)
The main target of this study was to ascertain the prevalence and transfer of genes conferring resistance to gentamicin (Gm) in a variety of environmental samples collected in different European countries (Belgium, Germany, Greece, the Netherlands and UK) including soils, rhizosphere, animal faeces, polluted and not-polluted costal sea waters as well as sewage from community and hospital wastewater treatment plants. All samples were analysed by culture-dependent and independent methods, particularly following a multiphasic approach consisting in the selective plating, the exogenous isolation of transferable elements carrying Gm resistance genes and the PCR-based detection of Gm resistance genes. According to the experiments performed, genes conferring resistance to gentamicin were revealed in almost all the analysed environmental samples and in a variety of host bacterial species (Enterobacteriaceae, Pseudomonas, Acinetobacter, Proteobacteria, etc.). Thus, also in the light of the results reported in this very comprehensive study, the common belief that hospitals, because of their essentially closed environment, are basically the only cause of the rising antibiotic resistance has been reconsidered since. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis (Von Wintzingerode et al., 1997)
This is a precious paper that summarises and discusses the main pitfalls encountered by microbiologists in a decade of molecular ecological studies using PCR-based analyses of prokaryotic small-subunit ribosomal RNAs. This critical review has been applied to all the steps of the PCR-based rRNA analyses, including sample collection, cell lysis and extraction of nucleic acids, PCR amplification and separation of amplified DNA, use of nucleic ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
Commentary
probes and analysis of 16S rRNA sequence data. However, authors even alarming on the numerous pitfalls that can lead researchers to an erroneous description of an ecological niche underline the power of this molecular approach particularly to reveal microorganisms occurring in small numbers, uncultivable, difficult to cultivate or in dormant conditions. The species concept for prokaryotes (Rossello Mora & Amann, 2001)
What is a species? Difficult question to answer at any level, but much more difficult in prokaryotes. Yet, this term has to be well defined for practical reasons, such as communication between researchers. This review describes the inherent problems of defining a species in prokaryotes and suggests the use of new concepts that may define microbial taxonomy that will be more compatible with the concepts used for eukaryotes. Classification and phylogeny of hydrogenases (Vignais et al., 2001)
The scientific world is urgently looking for new energy sources that will be efficient and environmentally friendly. In this respect, the study of bacterial hydrogen metabolism and hydrogenases is most timely. Hydrogenases – that catalyse the reversible oxidation of molecular hydrogen – are found mostly in Archaea and Bacteria and are well described in this review. Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae (C ß akar et al., 2005)
Industrially important microorganisms are undergoing improvements continuously. One of the important issues in such improvements is the optimisation of the selection method. This paper describes and compares several selection procedures – both in chemostats and batch cultures – for selection of multiple-stress-resistant mutants in the important yeast Saccharomyces cerevisiae. The paper presents successful results for selection of yeast resistant to freezing–thawing procedures and discusses general selection principles. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis (Sipos et al., 2007)
This paper is intended to solve the critical problem of differential amplification in studies using hybridisation to FEMS Microbiol Lett 359 (2014) 131–133
133
Commentary
phylogenetically highly conserved regions of 16S rRNA genes for the study of environmental bacteria communities. The results of an extensive study lead to a straight forward conclusion that reduction in the annealing temperature results in significant reduction of preferential amplification while still maintaining the required specificity. The ability of probiotic bacteria to bind to human intestinal mucus (Kirjavainen et al., 1998)
One of the most impressive recent advances in microbiology involves the studies of microbiomes. Of special interest is the human microbiome and its changes as the human body develops. The results presented in this study clearly indicate that the probiotic microbiome is affected by the age of infants and should be considered in future design of functional foods or probiotic therapy. Diversity of bacterial polyhydroxyalkanoic € chel & Valentin, 1995) acids (Steinbu
Bacterial polyhydroxyalkanoic acids are interesting storage compounds, first discovered in Bacillus megaterium. Recently, it became clear that there are a large number of hydroxyalkanoic acid derivatives and they are accumulated in many bacteria. Currently, there are about 90 known compounds, whose physiological role, biosynthesis and potential applications have not been fully studied and exploited. These finding provide an exciting potential to be exploited by the use of microbial genetic technologies. Bauke Oudega Faculty of Earth and Life Sciences, Vrije Universiteit, Amsterdam, The Netherlands Gianfranco Donelli Microbial Biofilm Laboratory (LABIM) IRCCS ‘Fondazione Santa Lucia’, Rome, Italy E-mail: [email protected]
FEMS Microbiol Lett 359 (2014) 131–133
Eliora Z. Ron Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel E-mail: [email protected]
References C ß akar ZP, Seker UOS, Tamerler C, Sonderegger M & Sauer U (2005) Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res 5: 569–578. Heuer H, Kr€ ogerrecklenfort E, Wellington EMH et al. (2002) Gentamicin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol Ecol 42: 289–302. Kirjavainen PV, Ouwehand AC, Isolauri E & Salminen SJ (1998) The ability of probiotic bacteria to bind to human intestinal mucus. FEMS Microbiol Lett 167: 185–189. Linder MB, Szilvay GR, Nakari-Set€al€a T & Penttil€a ME (2005) Hydrophobins: the protein-amphiphiles of filamentous fungi. FEMS Microbiol Rev 29: 877–896. Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, Arai H, Tanimoto I, Nishimura F & Takashiba S (2003) Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunol Med Microbiol 39: 81–86. Rossell o-Mora R & Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39–67. Sipos R, Szekely AJ, Palatinszky M, Revesz S, Marialigeti K & Nikolausz M (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol 60: 341–350. Steinb€ uchel A & Valentin HE (1995) Diversity of bacterial polyhydroxyalkanoic acids. FEMS Microbiol Lett 128: 219– 228. Vignais PM, Billoud B & Meyer J (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25: 455– 501. Von Wintzingerode F, G€ obel UB & Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213–229.
ª 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved
