Special Issue "Advances and New Perspectives in Microbial Research"

Quicklinks

A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (30 September 2013)

Special Issue Editor

Guest Editor
Prof. Pabulo H. Rampelotto

Center of Biotechnology and PPGBCM, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
Interests: biotechnology; next generation sequencing; metagenomics; molecular biology and biochemistry of microorganisms; extremophiles; grand challenges

Special Issue Information

Dear Colleagues,

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
Guest Editor

Submission

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. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). 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.

Keywords

  • epidemiology and prevention
  • human immunodeficiency virus (HIV)
  • human papilloma virus(HPV)
  • hepatitis virus
  • emerging/Re-emerging viruses
  • bacteria
  • fungi
  • parasite
  • mycoplasma, rickettsia and chlamydia
  • antimicrobial research
  • therapies
  • drug and vaccine

Published Papers (9 papers)

View options order results:
result details:
Displaying articles 1-9
Export citation of selected articles as:

Research

Jump to: Review, Other

Open AccessArticle Effect of Electrical Stimulation on Fruit Body Formation in Cultivating Mushrooms
Microorganisms 2014, 2(1), 58-72; doi:10.3390/microorganisms2010058
Received: 9 December 2013 / Revised: 25 December 2013 / Accepted: 23 January 2014 / Published: 12 February 2014
Cited by 2 | PDF Full-text (1402 KB) | HTML Full-text | XML Full-text
Abstract
The effect of high-voltage electrical stimulation on fruit body formation in cultivating mushrooms was evaluated using a compact pulsed power generator designed and based on an inductive energy storage system. An output voltage from 50 to 130 kV with a 100 ns [...] Read more.
The effect of high-voltage electrical stimulation on fruit body formation in cultivating mushrooms was evaluated using a compact pulsed power generator designed and based on an inductive energy storage system. An output voltage from 50 to 130 kV with a 100 ns pulse width was used as the electrical stimulation to determine the optimum amplitude. The pulsed high 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 of mushrooms increased 1.3–2.0 times in terms of the 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 upon increasing the applied voltage from 100 to 130 kV. The yield of the other types of mushrooms showed tendencies similar to those of Lentinula edodes when voltage was applied. An optimal voltage was confirmed for efficient fruit body induction. The hypha activity was evaluated by the amount of hydrophobin release, which was mainly observed before the fruit body formation. The hydrophobin release decreased for three hours after stimulation. However, the hydrophobin release from the vegetative hyphae increased 2.3 times one day after the stimulation. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Figure 1

Open AccessArticle Macroalgal Endophytes from the Atlantic Coast of Canada: A Potential Source of Antibiotic Natural Products?
Microorganisms 2013, 1(1), 175-187; doi:10.3390/microorganisms1010175
Received: 9 October 2013 / Revised: 8 November 2013 / Accepted: 5 December 2013 / Published: 13 December 2013
PDF Full-text (160 KB) | HTML Full-text | XML Full-text
Abstract
As the need for new and more effective antibiotics increases, untapped sources of biodiversity are being explored in an effort to provide lead structures for drug discovery. Endophytic fungi from marine macroalgae have been identified as a potential source of biologically active [...] Read more.
As the need for new and more effective antibiotics increases, untapped sources of biodiversity are being explored in an effort to provide lead structures for drug discovery. Endophytic fungi from marine macroalgae have been identified as a potential source of biologically active natural products, although data to support this is limited. To assess the antibiotic potential of temperate macroalgal endophytes we isolated endophytic fungi from algae collected in the Bay of Fundy, Canada and screened fungal extracts for the presence of antimicrobial compounds. A total of 79 endophytes were isolated from 7 species of red, 4 species of brown, and 3 species of green algae. Twenty of the endophytes were identified to the genus or species level, with the remaining isolates designated codes according to their morphology. Bioactivity screening assays performed on extracts of the fermentation broths and mycelia of the isolates revealed that 43 endophytes exhibited antibacterial activity, with 32 displaying antifungal activity. Endophytic fungi from Bay of Fundy macroalgae therefore represent a significant source of antibiotic natural products and warrant further detailed investigation. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Open AccessCommunication 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 / Revised: 13 November 2013 / Accepted: 22 November 2013 / Published: 2 December 2013
PDF Full-text (111 KB) | HTML Full-text | XML Full-text
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 [...] Read more.
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, 29 patients were infected, significantly raising their hospitalization periods and treatment costs. Interestingly, the outbreak was put under control after the department’s previously programmed relocation. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Figure 1

Review

Jump to: Research, Other

Open AccessReview The Science behind the Probiotic Strain Bifidobacterium animalis subsp. lactis BB-12®
Microorganisms 2014, 2(2), 92-110; doi:10.3390/microorganisms2020092
Received: 9 December 2013 / Revised: 8 January 2014 / Accepted: 7 February 2014 / Published: 28 March 2014
Cited by 6 | PDF Full-text (896 KB) | HTML Full-text | XML Full-text
Abstract
This review presents selected data on the probiotic strain Bifidobacterium animalis subsp. lactis BB-12® (BB-12®), which is the world’s most documented probiotic Bifidobacterium. It is described in more than 300 scientific publications out of which more than 130 [...] Read more.
This review presents selected data on the probiotic strain Bifidobacterium animalis subsp. lactis BB-12® (BB-12®), which is the world’s most documented probiotic Bifidobacterium. It is described in more than 300 scientific publications out of which more than 130 are publications of human clinical studies. The complete genome sequence of BB-12® has been determined and published. BB-12® originates from Chr. Hansen’s collection of dairy cultures and has high stability in foods and as freeze dried powders. Strain characteristics and mechanisms of BB-12® have been established through extensive in vitro testing. BB-12® exhibits excellent gastric acid and bile tolerance; it contains bile salt hydrolase, and has strong mucus adherence properties, all valuable probiotic characteristics. Pathogen inhibition, barrier function enhancement, and immune interactions are mechanisms that all have been demonstrated for BB-12®. BB-12® has proven its beneficial health effect in numerous clinical studies within gastrointestinal health and immune function. Clinical studies have demonstrated survival of BB-12® through the gastrointestinal tract and BB-12® has been shown to support a healthy gastrointestinal microbiota. Furthermore, BB-12® has been shown to improve bowel function, to have a protective effect against diarrhea, and to reduce side effects of antibiotic treatment, such as antibiotic-associated diarrhea. In terms of immune function, clinical studies have shown that BB-12® increases the body’s resistance to common respiratory infections as well as reduces the incidence of acute respiratory tract infections. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Open AccessReview Temporal Variation of Mycotoxin Producing Fungi in Norwegian Cereals
Microorganisms 2013, 1(1), 188-198; doi:10.3390/microorganisms1010188
Received: 1 October 2013 / Revised: 19 November 2013 / Accepted: 10 December 2013 / Published: 17 December 2013
PDF Full-text (211 KB) | HTML Full-text | XML Full-text
Abstract
Spring barley is grown on about half of the Norwegian cereal area. The rest of the area 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 [...] Read more.
Spring barley is grown on about half of the Norwegian cereal area. The rest of the area 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 have led to increased mycotoxin contamination of cereals. During that period, precipitation was above normal during anthesis and grain maturation. The most important mycotoxin producers have been F. avenaceum, F. culmorum, F. graminearum and F. langsethiae. Increased deoxynivalenol contamination of Norwegian cereals during recent years is due to severe F. graminearum epidemics. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Open AccessReview 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 / Revised: 5 November 2013 / Accepted: 25 November 2013 / Published: 3 December 2013
Cited by 5 | PDF Full-text (500 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Fusarium species produce important mycotoxins, such as deoxynivalenol (DON), nivalenol (NIV) and T-2/HT-2-toxins 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 >1.75 mg·kg−1 [...] Read more.
Fusarium species produce important mycotoxins, such as deoxynivalenol (DON), nivalenol (NIV) and T-2/HT-2-toxins 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 >1.75 mg·kg−1 of DON, which belongs to type B trichothecenes. Fusarium graminearum is the most important DON producer in northern Europe and Asia and it has been displacing the closely related F. culmorum in northern Europe. The 3ADON chemotype of F. graminearum is dominant in most northern areas, while the 15ADON chemotype of F. graminearum is predominating in Central and southern Europe. We suggest that the northern population of F. graminearum may be more specialized to oats than the southern population. 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 gas chromatography-mass spectrometry (GC-MS). When the RIDA® QUICK SCAN kit results (DON) were compared to DNA levels of F. graminearum, the variation was much higher. The homogenization of the oats flour by grinding oats with 1 mm sieve seems to be connected to this variation. 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 2010–2012. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Figure 1

Open AccessReview 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 / Revised: 5 November 2013 / Accepted: 8 November 2013 / Published: 20 November 2013
Cited by 2 | PDF Full-text (2506 KB) | HTML Full-text | XML Full-text
Abstract
With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on [...] Read more.
With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Figure 1

Open AccessReview Elements in the Development of a Production Process for Modified Vaccinia Virus Ankara
Microorganisms 2013, 1(1), 100-121; doi:10.3390/microorganisms1010100
Received: 27 September 2013 / Revised: 18 October 2013 / Accepted: 24 October 2013 / Published: 1 November 2013
Cited by 3 | PDF Full-text (5310 KB) | HTML Full-text | XML Full-text
Abstract
The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.pIX), developed chemically-defined media, and established production processes for different vaccine viruses. [...] Read more.
The production of several viral vaccines depends on chicken embryo fibroblasts or embryonated chicken eggs. To replace this logistically demanding substrate, we created continuous anatine suspension cell lines (CR and CR.pIX), developed chemically-defined media, and established production processes for different vaccine viruses. One of the processes investigated in greater detail was developed for modified vaccinia virus Ankara (MVA). MVA is highly attenuated for human recipients and an efficient vector for reactogenic expression of foreign genes. Because direct cell-to-cell spread is one important mechanism for vaccinia virus replication, cultivation of MVA in bioreactors is facilitated if cell aggregates are induced after infection. This dependency may be the mechanism behind our observation that a novel viral genotype (MVA-CR) accumulates with serial passage in suspension cultures. Sequencing of a major part of the genomic DNA of the new strain revealed point mutations in three genes. We hypothesize that these changes confer an advantage because they may allow a greater fraction of MVA-CR viruses to escape the host cells for infection of distant targets. Production and purification of MVA-based vaccines may be simplified by this combination of designed avian cell line, chemically defined media and the novel virus strain. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Figure 1

Other

Jump to: Research, Review

Open AccessOpinion Sad State of Phage Electron Microscopy. Please Shoot the Messenger
Microorganisms 2014, 2(1), 1-10; doi:10.3390/microorganisms2010001
Received: 23 October 2013 / Revised: 29 November 2013 / Accepted: 9 December 2013 / Published: 24 December 2013
Cited by 1 | PDF Full-text (1242 KB) | HTML Full-text | XML Full-text
Abstract
Two hundred and sixty publications from 2007 to 2012 were classified according to the quality of electron micrographs; namely as good (71); mediocre (21); or poor (168). Publications were from 37 countries; appeared in 77 journals; and included micrographs produced with about [...] Read more.
Two hundred and sixty publications from 2007 to 2012 were classified according to the quality of electron micrographs; namely as good (71); mediocre (21); or poor (168). Publications were from 37 countries; appeared in 77 journals; and included micrographs produced with about 60 models of electron microscopes. The quality of the micrographs was not linked to any country; journal; or electron microscope. Main problems were poor contrast; positive staining; low magnification; and small image size. Unsharp images were frequent. Many phage descriptions were silent on virus purification; magnification control; even the type of electron microscope and stain used. The deterioration in phage electron microscopy can be attributed to the absence of working instructions and electron microscopy courses; incompetent authors and reviewers; and lenient journals. All these factors are able to cause a gradual lowering of standards. Full article
(This article belongs to the Special Issue Advances and New Perspectives in Microbial Research)
Figures

Figure 1

Journal Contact

MDPI AG
Microorganisms Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
microorganisms@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Microorganisms
Back to Top