Special Issue "Advances and New Perspectives in Microbial Research"
A special issue of Microorganisms (ISSN 2076-2607).
Deadline for manuscript submissions: closed (30 September 2013)
Mr. Pabulo Henrique Rampelotto
Interdisciplinary Center for Biotechnology Research, Federal University of Pampa, Antônio Trilha Avenue, P.O.Box 1847, 97300-000, São Gabriel – RS, Brazil
Microorganisms, or microbes, are the most diverse and abundant forms of life on Earth. Nevertheless, despite our current advances, we are just beginning to explore and characterize the microbial world. For the coming decade, exciting discoveries in microbiology have the potential to make a great impact on the development of different fields of life science, including basic and applied research. This special issue offers the latest scientific research in microbiology presented at the 3rd Annual World Congress of Microbes-2013 (WCM -2013), an influential Conference consisting of 8 parallel symposia. WCM aims to strengthen the academic research and application ties in microbiology, to bring together experts and industry leaders to share the latest research and technological advancements. This congress provides an ideal platform for industrial practitioners and academia to keep up to date with current research trends, interact with microbiologist and industry experts with peers. The wide-ranging set of topics makes this special issue interesting not only for microbiologists, but also for those interested in expanding or updating their knowledge on the recent cutting-edge research involving the fascinating world of microbes.
Professor Pabulo Henrique Rampelotto
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed Open Access quarterly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.
- epidemiology and prevention
- human immunodeficiency virus (HIV)
- human papilloma virus(HPV)
- hepatitis virus
- emerging/Re-emerging viruses
- mycoplasma, rickettsia and chlamydia
- antimicrobial research
- drug and vaccine
Microorganisms 2013, 1(1), 100-121; doi:10.3390/microorganisms1010100
Received: 27 September 2013; in revised form: 18 October 2013 / Accepted: 24 October 2013 / Published: 1 November 2013| Download PDF Full-text (5310 KB) | Download XML Full-text
Review: A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)
Microorganisms 2013, 1(1), 137-157; doi:10.3390/microorganisms1010137
Received: 26 September 2013; in revised form: 5 November 2013 / Accepted: 8 November 2013 / Published: 20 November 2013| Download PDF Full-text (2506 KB) | Download XML Full-text
Communication: Control of a Multi-Drug-Resistant Acinetobacter baumannii Outbreak after Orthopedics Department Relocation
Microorganisms 2013, 1(1), 158-161; doi:10.3390/microorganisms1010158
Received: 6 September 2013; in revised form: 13 November 2013 / Accepted: 22 November 2013 / Published: 2 December 2013| Download PDF Full-text (111 KB) | Download XML Full-text
Review: Molecular Quantification and Genetic Diversity of Toxigenic Fusarium Species in Northern Europe as Compared to Those in Southern Europe
Microorganisms 2013, 1(1), 162-174; doi:10.3390/microorganisms1010162
Received: 27 September 2013; in revised form: 5 November 2013 / Accepted: 25 November 2013 / Published: 3 December 2013| Download PDF Full-text (500 KB) | Download XML Full-text | Supplementary Files
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Type of Paper: Review
Title: Bioinformatics Method to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self Organizing Map (BLSOM)
Authors: Yuki Iwasaki 1,2, Toshimichi Ikemura 1, Kennosuke Wada 1, Yoshiko Wada 1,3 and Takashi Abe 1,4,*
Affiliations: 1 Nagahama Institute of Bio-Science and Technology, Japan
2 Research Fellow of the Japan Society for the Promotion of Science, Japan
3 Shiga University of Medical Science, Japan
4 Niigata University, Japan; * E-mail: firstname.lastname@example.org
Abstract: With remarkable increase of microbial genome sequences obtained from high-throughput DNA sequencers, novel tools are needed for comprehensive analyses of big sequences data. A clustering algorithm, Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional data (e.g. oligonucleotide composition) on one map. By modifying the conventional SOM, we have developed Batch-Learning SOM (BLSOM) for oligonucleotide composition, which allowed classification (self-organization) of sequence fragments (e.g. 1 kb) according to phylogenetic groups, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in medical and environmental science. Traditional methods of phylogenetic assignment of metagenomic sequences have been based on sequence homology searches and therefore inevitably focused on well-characterized genes, for which orthologous sequences required for constructing a reliable phylogenetic tree are available. However, the well-characterized genes often are not industrially attractive. The BLSOM is most suitable for phylogenetic assignment of all kinds of sequences including novel gene sequences, because sequence fragments can be clustered according to phylotypes, solely depending on oligonucleotide composition. When we conduct phylogenetic classification of species-unknown metagenomic sequences, BLSOMs have to be constructed in advance with all available sequences from species-known prokaryotes and eukaryotes, as well as from viruses and organelles. By mapping all metagenomic sequences on this BLSOM, we can predict phylotypes of individual metagenomic sequences and thus reveal a microbial community of uncultured microorganisms including viruses. BLSOM has been used in many metagenome analyses conducted in Japan.
Type of Paper: Article
Title: Electrical Stimulation for Improvement of Mushroom Growth
Authors: Koichi Takaki 1,*, Tatsuya Saito 1, Kyusuke Takahashi 2 and Yuichi Sakamoto 3
Affiliations: 1 Department of Electrical Eng., Iwate University, Morioka, Japan
2 Sotoyama Forest Park, Morioka Forest Union, Morioka, Japan
3 Iwate Biotechnology Research Center, Kitakami, Japan; * E-mail: email@example.com
Abstract: A compact pulsed power generator was developed as an electrical stimulation system for improving fruiting body yields and the effect was evaluated using wood-decay fungi(1)-(4). The pulsed power generator was designed based on an inductive energy storage system that minimizes size and weight. The output voltage of the pulsed power generator was varied from 50 to 130 kV with a 100 ns pulse width to determine the optimum amplitude. The output voltage was applied to a sawdust-based substrate of Lyophyllum decastes, and natural logs hosting Lentinula edodes, Pholiota nameko, and Naematoloma sublateritium. The experimental results showed that the fruit body formation for some kinds of mushrooms increased 1.3-2.0 times as measured by total weight. The accumulated yield of Lentinula edodes for four cultivation seasons was improved from 160 to 320 g by applying voltages of 50 or 100 kV. However, the yield was decreased from 320 to 240 g with increasing applied voltage from 100 to 130 kV. The yield of the other kinds of mushrooms showed similar tendencies to the yield of Lentinula edodes with applied voltage. These results show that an optimal voltage is needed for efficient fruit body induction. The laccase Lcc1, which was predicted to contribute to the fruit body formations, was confirmed to be activated from the vegetative hyphae when applying the pulse voltage.
Type of Paper: Article
Title: Temporal Variation in Mycotoxin-Producing Fungi in Norway
Author: Leif Sundheim 1,2
Affiliations: 1 Norwegian Institute for Agricultural and Environmental Research, Norway
2 Norwegian Scientific Committee for Food Safety, Norway; E-Mail: firstname.lastname@example.org
Abstract: Spring barley is grown on half of the Norwegian cereal areas. The rest is equally divided between wheat and oats. Most years the domestic production provides 70- 80% of the domestic market for bread wheat. Barley and oats are mainly grown for animal feed.During the years 2008-2012 severe epidemics of Fusarium head blight haveled to increased mycotoxin contamination of cereals. In that period the precipitation has been above average during anthesis and grain maturation. The most important mycotoxin producers are F. avenaceum,F. culmorum, F. graminearumand F. langsethiae.Enniatins are mainly produced by F. avenaceum. Increased DON contaminationof Norwegian cereals during recent years is related to severeF. graminearum infection. The levels of F. langsethiae and the mycotoxins T-2 and HT-2 have not increased during the same period.
Type of Paper: Review
Title: The Sad State of Phage Electron Microscopy
Author: Hans-W. Ackermann
Affiliation: Department of Microbiology, Medical School, Laval University, Quebec, QC, G1K 7P4, Canada; E-Mails: email@example.com or firstname.lastname@example.org
Abstract: About 6,300 bacterial viruses were examined in the electron microscope until 2012. Each year, 100 novel phages are described. A total of 261 publications from the years 1966 to 2012 were sorted according to the quality of micrographs. They were subjectively classified as good (71), mediocre (22), and poor (168). This is in agreement with a downward trend already noticed 10 years ago. The publications are from 36 countries and appeared in 77 journals. Two journals featured 60 articles with phage descriptions. Micrographs were obtained by means of an astonishing selection of about 70 electron microscopes or models, all produced by 4 manufacturers (Philips/FEI, 24; JEOL, 22; Hitachi 12; Zeiss, 10). The benchmark for quality is the atlas of viral electron microscopy by Dalton and Haguenau (1973). Poor papers typically feature low-magnification, unsharp, contrastless, grey to dark micrographs with pint-size viruses without details such as tail striations and tail fibers. Some show no micrographs at all and many are silent on virus purification, calibration, dimensions, and even the types of EMs and stains used. Micrographs are often wildly inferior to the very first pictures of negatively stained phages published in 1959 (Brenner et al.). The most common problem is lack of contrast (all is grey in grey). Due to frequent absence of magnification control (calibration), dimensions are often unlikely. Such kind of research is useless for virology. This situation is not related to a particular country, journal, electron microscope, or camera. Indeed, any countries or electron microscopes may produce good or poor pictures. However, manual EMs (with films and darkrooms) offers the possibility of improving contrast with graded filters and paper, whereas digital EMs (in particular certain JEM models) seem to have intractable contrast problems. The deterioration of phage electron microscopy (this applies to all viruses) is attributed to lowered standards, disappearance of important electron microscopists, absence of instructions and EM courses, incompetent authors or reviewers, and over-emphasis on genomics to the detriment of electron microscopy.
Type of Paper: Communication
Title: Control of a Multi-Drug-Resistant Acinetobacterbaumannii Outbreak after Orthopedics Department Translocation
Authors: Vasiliki Gogou 1, Georgios Meletis 1,* and Dimosthenis Tsitouras 2
Affiliations: 1 Department of Clinical Microbiology, Veroia General Hospital, Veroia, Greece; E-Mails: email@example.com (V.G.), firstname.lastname@example.org (G.M)
2 Orthopedics Department, Veroia General Hospital, Veroia, Greece; E-Mail: email@example.com (D.T.)
Abstract: Acinetobacter baumannii clinical isolates have the ability to survive in the hospital niche for prolonged time periods and to develop resistance against multiple antimicrobial agents. Therefore, A. baumannii has emerged as an important cause of nosocomial outbreaks worldwide, especially in critical-care environments such as intensive care units. In the present communication we report a multi-drug-resistant A. baumannii outbreak that occurred in an orthopedics department in Greece after the admission of a patient previously hospitalized in the intensive care unit of a Greek tertiary care hospital. Despite the implementation of infection control measures, twenty-nine patients were infected, raising significantly their hospitalization periods and treatment costs. Interestingly, the outbreak was put under control after the department’s previously programmed translocation.
Type of Paper: Article
Title: Molecular Identification, Quantification and Genetic Diversity of Toxigenic Fusarium Species in Northern Europe as Compared to those in Southern Europe and Asia.
Authors: Tapani Yli-Mattila 1,*, Sari Rämö 2, Veli Hietaniemi 2, Taha Hussien 1,3, Ana Liza Carlobos-Lopez 1,4, Christian Joseph R. Cumagun 4 and Tatiana Gagkaeva 5
1Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland. *E-mail:firstname.lastname@example.org
2MTT Agrifood Research Finland, Jokioinen, Finland.
3Mycotoxins Lab, Department of Food Toxicology and Contaminant, National Research Center, Cairo, Egypt.
4Crop Protection Cluster, College of Agriculture, University of the Philippines Los Baños, Laguna, Philippines.
5Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection (VIZR), Pushkin, Russia.
Abstract: Fusarium species are important mycotoxin, such as deoxynivelenol (DON), nivalenol (NIV) and T-2/HT-2-toxins, producers in cereals. The highest DON and T-2/HT-2 toxin levels in northern Europe have been found in oats. About 12-24% of Finnish oat samples in 2012 contained >1750 ppb of DON, which belongs to type B trichothecenes. F. graminearum is the most important DON producer in northern Europe and Asia and it has been replacing the closely related F. culmorum in northern Europe. The 3ADON chemotype of F. graminearum dominates in most northern areas, while the 15ADON chemotype of F. graminearum is dominating in Central and southern Europe. F. asiaticum together with F. ussurianum, F. vorosii and F. nepalense form the Asian subclade, which is endemic in Asia and is a common cause of Fusarium head blight of cereals in China, Japan, Korea, Nepal and Russian Far East. Only low levels of F. culmorum DNA were found in a few oat samples and no correlation was found between F. culmorum DNA and DON levels. DNA levels of F. graminearum were in all cases in agreement with DON levels in 2011 and 2012, when DON was measured by GC-MS. When the RIDA®QUICK SCAN kit results (DON) were compared to DNA levels of F. graminearum, the variation was much higher. F. langsethiae, F. sporotrichioides, F. sibiricum and F. armeniacum produce T-2 and HT-2 toxins, of the type A trichothecene. F. langsethiae found recently in Europe can be divided into two lineages (subgroups). There was a significant correlation between the combined T-2 and HT-2 and the combined DNA levels of F. langsethiae and F. sporotrichioides in Finland in 2011 and 2012. Type A and B trichothecene producing F. poae is the main NIV-producer in northern Europe and northern Japan, while the NIV chemotype of F. graminearum species complex is also a NIV producer in Central Europe. On the other hand, F. sibiricum is mainly found in Siberia and Russian Far East. In the present paper, the identification of a F. sibiricum isolate from Iran is confirmed by molecular methods and new findings on the correlation between mycotoxins and DNA levels of Fusarium species in Finland are presented. A single isolate of F. sibiricum is also found in Norway. In conclusion, the actual distribution of F. sibiricum may be much larger than what is presently known.
Last update: 11 September 2013