for Journals by Title or ISSN
for Articles by Keywords
Followed Journals
Journal you Follow: 0
Sign Up to follow journals, search in your chosen journals and, optionally, receive Email Alerts when new issues of your Followed Journals are published.
Already have an account? Sign In to see the journals you follow.
Journal Cover Microorganisms
  [2 followers]  Follow
  This is an Open Access Journal Open Access journal
   ISSN (Online) 2076-2607
   Published by MDPI Homepage  [154 journals]
  • Microorganisms, Vol. 5, Pages 64: Markers of Microbial Translocation and
           Immune Activation Predict Cognitive Processing Speed in Heavy-Drinking Men
           Living with HIV

    • Authors: Mollie Monnig, Christopher Kahler, Patricia Cioe, Peter Monti, Kenneth Mayer, David Pantalone, Ronald Cohen, Bharat Ramratnam
      First page: 64
      Abstract: HIV infection and alcohol use disorder are associated with deficits in neurocognitive function. Emerging evidence points to pro-inflammatory perturbations of the gut-brain axis as potentially contributing to neurocognitive impairment in the context of HIV and chronic heavy alcohol use. This study examined whether plasma markers of microbial translocation (LPS) from the gastrointestinal tract and related immune activation (sCD14, EndoCAb) were associated with neurocognition in 21 men living with HIV who were virally suppressed on antiretroviral therapy. All participants met federal criteria for heavy drinking and were enrolled in a randomized controlled trial (RCT) of a brief alcohol intervention. This secondary analysis utilized blood samples and cognitive scores (learning, memory, executive function, verbal fluency, and processing speed) obtained at baseline and three-month follow-up of the RCT. In generalized estimating equation models, LPS, sCD14, and EndoCAb individually were significant predictors of processing speed. In a model with all biomarkers, higher LPS and sCD14 both remained significant predictors of lower processing speed. These preliminary findings suggest that inflammation stemming from HIV and/or alcohol could have negative effects on the gut-brain axis, manifested as diminished processing speed. Associations of microbial translocation and immune activation with processing speed in heavy-drinking PLWH warrant further investigation in larger-scale studies.
      Citation: Microorganisms
      PubDate: 2017-09-21
      DOI: 10.3390/microorganisms5040064
      Issue No: Vol. 5, No. 4 (2017)
  • Microorganisms, Vol. 5, Pages 35: Free and Nanoencapsulated Tobramycin:
           Effects on Planktonic and Biofilm Forms of Pseudomonas

    • Authors: Eulalia Sans-Serramitjana, Marta Jorba, Ester Fusté, José Pedraz, Teresa Vinuesa, Miguel Viñas
      First page: 35
      Abstract: Cystic fibrosis (CF) is a genetic disorder in which frequent pulmonary infections develop secondarily. One of the major pulmonary pathogens colonizing the respiratory tract of CF patients and causing chronic airway infections is Pseudomonas aeruginosa. Although tobramycin was initially effective against P. aeruginosa, tobramycin-resistant strains have emerged. Among the strategies for overcoming resistance to tobramycin and other antibiotics is encapsulation of the drugs in nanoparticles. In this study, we explored the antimicrobial activity of nanoencapsulated tobramycin, both in solid lipid nanoparticles (SLN) and in nanostructured lipid carriers (NLC), against clinical isolates of P. aeruginosa obtained from CF patients. We also investigated the efficacy of these formulations in biofilm eradication. In both experiments, the activities of SLN and NLC were compared with that of free tobramycin. The susceptibility of planktonic bacteria was determined using the broth microdilution method and by plotting bacterial growth. The minimal biofilm eradication concentration (MBEC) was determined to assess the efficacy of the different tobramycin formulations against biofilms. The activity of tobramycin-loaded SLN was less than that of either tobramycin-loaded NLC or free tobramycin. The minimum inhibitory concentration (MIC) and MBEC of nanoencapsulated tobramycin were slightly lower (1–2 logs) than the corresponding values of the free drug when determined in tobramycin-susceptible isolates. However, in tobramycin-resistant strains, the MIC and MBEC did not differ between either encapsulated form and free tobramycin. Our results demonstrate the efficacy of nanoencapsulated formulations in killing susceptible P. aeruginosa from CF and from other patients.
      PubDate: 2017-06-26
      DOI: 10.3390/microorganisms5030035
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 36: Reply to the Comment on “Melanisation
           of Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of
           Both DOPA and DHN Types of Pigments in Submerged Culture'
           Microorganisms 2017, 5, 22”

    • Authors: Elina Palonen, Sheetal Raina, Annika Brandt, Jussi Meriluoto, Tajalli Keshavarz, Juhani Soini
      First page: 36
      Abstract: n/a
      PubDate: 2017-07-04
      DOI: 10.3390/microorganisms5030036
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 37: Antifungal Microbial Agents for Food
           Biopreservation—A Review

    • Authors: Marcia Leyva Salas, Jérôme Mounier, Florence Valence, Monika Coton, Anne Thierry, Emmanuel Coton
      First page: 37
      Abstract: Food spoilage is a major issue for the food industry, leading to food waste, substantial economic losses for manufacturers and consumers, and a negative impact on brand names. Among causes, fungal contamination can be encountered at various stages of the food chain (e.g., post-harvest, during processing or storage). Fungal development leads to food sensory defects varying from visual deterioration to noticeable odor, flavor, or texture changes but can also have negative health impacts via mycotoxin production by some molds. In order to avoid microbial spoilage and thus extend product shelf life, different treatments—including fungicides and chemical preservatives—are used. In parallel, public authorities encourage the food industry to limit the use of these chemical compounds and develop natural methods for food preservation. This is accompanied by a strong societal demand for ‘clean label’ food products, as consumers are looking for more natural, less severely processed and safer products. In this context, microbial agents corresponding to bioprotective cultures, fermentates, culture-free supernatant or purified molecules, exhibiting antifungal activities represent a growing interest as an alternative to chemical preservation. This review presents the main fungal spoilers encountered in food products, the antifungal microorganisms tested for food bioprotection, and their mechanisms of action. A focus is made in particular on the recent in situ studies and the constraints associated with the use of antifungal microbial agents for food biopreservation.
      PubDate: 2017-07-08
      DOI: 10.3390/microorganisms5030037
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 38: Strategies for Pathogen Biocontrol Using
           Lactic Acid Bacteria and Their Metabolites: A Focus on Meat Ecosystems and
           Industrial Environments

    • Authors: Patricia Castellano, Mariana Pérez Ibarreche, Mariana Blanco Massani, Cecilia Fontana, Graciela Vignolo
      First page: 38
      Abstract: The globalization of trade and lifestyle ensure that the factors responsible for the emergence of diseases are more present than ever. Despite biotechnology advancements, meat-based foods are still under scrutiny because of the presence of pathogens, which causes a loss of consumer confidence and consequently a fall in demand. In this context, Lactic Acid Bacteria (LAB) as GRAS organisms offer an alternative for developing pathogen-free foods, particularly avoiding Listeria monocytogenes, with minimal processing and fewer additives while maintaining the foods’ sensorial characteristics. The use of LAB strains, enabling us to produce antimicrobial peptides (bacteriocins) in addition to lactic acid, with an impact on quality and safety during fermentation, processing, and/or storage of meat and ready-to-eat (RTE) meat products, constitutes a promising tool. A number of bacteriocin-based strategies including the use of bioprotective cultures, purified and/or semi-purified bacteriocins as well as their inclusion in varied packaging materials under different storage conditions, have been investigated. The application of bacteriocins as part of hurdle technology using non-thermal technologies was explored for the preservation of RTE meat products. Likewise, considering that food contamination with L. monocytogenes is a consequence of the post-processing manipulation of RTE foods, the role of bacteriocinogenic LAB in the control of biofilms formed on industrial surfaces is also discussed.
      Citation: Microorganisms
      PubDate: 2017-07-11
      DOI: 10.3390/microorganisms5030038
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 39: Microorganisms in Fermented Apple
           Beverages: Current Knowledge and Future Directions

    • Authors: Fabien Cousin, Rozenn Le Guellec, Margot Schlusselhuber, Marion Dalmasso, Jean-Marie Laplace, Marina Cretenet
      First page: 39
      Abstract: Production of fermented apple beverages is spread all around the world with specificities in each country. ‘French ciders’ refer to fermented apple juice mainly produced in the northwest of France and often associated with short periods of consumption. Research articles on this kind of product are scarce compared to wine, especially on phenomena associated with microbial activities. The wine fermentation microbiome and its dynamics, organoleptic improvement for healthy and pleasant products and development of starters are now widely studied. Even if both beverages seem close in terms of microbiome and process (with both alcoholic and malolactic fermentations), the inherent properties of the raw materials and different production and environmental parameters make research on the specificities of apple fermentation beverages worthwhile. This review summarizes current knowledge on the cider microbial ecosystem, associated activities and the influence of process parameters. In addition, available data on cider quality and safety is reviewed. Finally, we focus on the future role of lactic acid bacteria and yeasts in the development of even better or new beverages made from apples.
      Citation: Microorganisms
      PubDate: 2017-07-25
      DOI: 10.3390/microorganisms5030039
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 40: Should Research on the Nutritional
           Potential and Health Benefits of Fermented Cereals Focus More on the
           General Health Status of Populations in Developing Countries'

    • Authors: Caroline Laurent-Babot, Jean-Pierre Guyot
      First page: 40
      Abstract: Cereal foods fermented by lactic acid bacteria are staples in many countries around the world particularly in developing countries, but some aspects of the nutritional and health benefits of traditional fermented foods in developing countries have not been sufficiently investigated compared to fermented foods in high-income countries. Today, malnutrition worldwide is characterized by a double burden, excess leading to non-communicable diseases like obesity or diabetes alongside micronutrient deficiencies. In addition, populations in developing countries suffer from infectious and parasitic diseases that can jeopardize the health benefits provided by their traditional fermented foods. Using examples, we argue that research on traditional fermented cereals in developing countries should focus more on their effect on inflammation and oxidative stress under conditions including infectious or non-infectious gut inflammation.
      Citation: Microorganisms
      PubDate: 2017-07-25
      DOI: 10.3390/microorganisms5030040
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 41: Inoculation with Azospirillum sp. and
           Herbaspirillum sp. Bacteria Increases the Tolerance of Maize to Drought

    • Authors: José Curá, Diego Franz, Julián Filosofía, Karina Balestrasse, Lautaro Burgueño
      First page: 41
      Abstract: Stress drought is an important abiotic factor that leads to immense losses in crop yields around the world. Strategies are urgently needed to help plants adapt to drought in order to mitigate crop losses. Here we investigated the bioprotective effects of inoculating corn grown under drought conditions with two types of plant growth-promoting rhizobacteria (PGPR), A. brasilense, strain SP-7, and H. seropedicae, strain Z-152. Plants inoculated with the bacteria were grown in a greenhouse with perlite as a substrate. Two hydric conditions were tested: normal well-watered conditions and drought conditions. Compared to control non-inoculated plants, those that were inoculated with PGPR bacteria showed a higher tolerance to the negative effects of water stress in drought conditions, with higher biomass production; higher carbon, nitrogen, and chlorophyll levels; and lower levels of abscisic acid and ethylene, which are plant hormones that affect the stress response. The oxidative stress levels of these plants were similar to those of non-inoculated plants grown in well-watered conditions, showing fewer injuries to the cell membrane. We also noted higher relative water content in the vegetal tissue and better osmoregulation in drought conditions in inoculated plants, as reflected by significantly lower proline content. Finally, we observed lower gene expression of ZmVP14 in the inoculated plants; notably, ZmVP14 is involved in the biosynthesis of abscisic acid. Taken together, these results demonstrate that these bacteria could be used to help plants cope with the negative effects of drought stress conditions.
      Citation: Microorganisms
      PubDate: 2017-07-26
      DOI: 10.3390/microorganisms5030041
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 42: Diversity and Control of Spoilage Fungi
           in Dairy Products: An Update

    • Authors: Lucille Garnier, Florence Valence, Jérôme Mounier
      First page: 42
      Abstract: Fungi are common contaminants of dairy products, which provide a favorable niche for their growth. They are responsible for visible or non-visible defects, such as off-odor and -flavor, and lead to significant food waste and losses as well as important economic losses. Control of fungal spoilage is a major concern for industrials and scientists that are looking for efficient solutions to prevent and/or limit fungal spoilage in dairy products. Several traditional methods also called traditional hurdle technologies are implemented and combined to prevent and control such contaminations. Prevention methods include good manufacturing and hygiene practices, air filtration, and decontamination systems, while control methods include inactivation treatments, temperature control, and modified atmosphere packaging. However, despite technology advances in existing preservation methods, fungal spoilage is still an issue for dairy manufacturers and in recent years, new (bio) preservation technologies are being developed such as the use of bioprotective cultures. This review summarizes our current knowledge on the diversity of spoilage fungi in dairy products and the traditional and (potentially) new hurdle technologies to control their occurrence in dairy foods.
      Citation: Microorganisms
      PubDate: 2017-07-28
      DOI: 10.3390/microorganisms5030042
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 43: Effect of Non-Dairy Food Matrices on the
           Survival of Probiotic Bacteria during Storage

    • Authors: Min Min, Craig Bunt, Susan Mason, Grant Bennett, Malik Hussain
      First page: 43
      Abstract: The viability of probiotics in non-dairy food products during storage is required to meet content criteria for probiotic products. This study investigated whether non-dairy foods could be matrices for probiotics. Selected probiotic bacteria were coated on non-dairy foods under two storage conditions, and viabilities were assessed. The non-dairy foods were coated with 5–7 log cfu g−1 of Lactobacillus acidophilus ATCC4356T, Lactobacillus plantarum RC30, and Bifidobacterium longum ATCC15707T. The coated non-dairy foods were stored at 20 °C and 20% relative humidity (RH) or 30 °C and 50% RH. Viability of probiotic bacteria was determined after 0, 2, and 4 weeks of storage. B. longum showed the highest survival at week 4 of 6.5–6.7 log cfu g−1 on wheat bran and oat, compared with 3.7–3.9 log cfu g−1 of L. acidophilus and 4.2–4.8 log cfu g−1 of L. plantarum at 20 °C 20% RH. Under the storage conditions of 30 °C 50% RH, survival of 4.5 log cfu g−1 of B. longum was also found on oat and peanut. This was two and four times higher than the population of L. acidophilus and L. plantarum, respectively. The results suggest that probiotics can survive on non-dairy foods under ambient storage conditions. However, the storage conditions, food matrices, and probiotic strains should be carefully chosen to maximize probiotic bacteria survival.
      Citation: Microorganisms
      PubDate: 2017-08-01
      DOI: 10.3390/microorganisms5030043
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 44: Filamentous Fungal Human Pathogens from
           Food Emphasising Aspergillus, Fusarium and Mucor

    • Authors: R. Paterson, Nelson Lima
      First page: 44
      Abstract: Disease caused by filamentous fungal human pathogens (FFHP) is increasing. These organisms cause severe mycoses in immunosuppressed individuals, such as those: (a) with AIDS; (b) having undergone transplantation; and/or (c) undergoing chemotherapy. Immunocompetent people can become infected. Some FFHP are isolated from foods which may be fomites. However, the information concerning particular species on specific food is large, dispersed and difficult to obtain. Reports of filamentous fungi from food/crops and causing human disease are frequently only available in the literature of food mycology/plant pathology and medical mycology, respectively: it is seldom cross-referenced. Aspergillus contains some species with strains that are the most dangerous FFHP, with Aspergillus fumigatus causing the most serious diseases. Fusarium and Mucor also contain species of high importance and approximately 15 other genera are involved. A checklist and database of FFHP species isolated from food is presented herein with emphasis on Aspergillus, Fusarium and Mucor in summary tables to increase awareness of the connection between food and FFHP. Metadata on all FFHP is provided in a large supplementary table for updating and revision when necessary. Previous names of fungi have been revised to reflect current valid usage whenever appropriate. The information will form a foundation for future research and taxonomic revisions in the field. The paper will be highly useful for medical practitioners, food mycologists, fungal taxonomists, patients, regulators and food producers interested in reducing infectious diseases and producing high quality food.
      Citation: Microorganisms
      PubDate: 2017-08-02
      DOI: 10.3390/microorganisms5030044
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 45: Growth and Photosynthetic
           Characteristics of Toxic and Non-Toxic Strains of the Cyanobacteria
           Microcystis aeruginosa and Anabaena circinalis in Relation to Light

    • Authors: M. Islam, John Beardall
      First page: 45
      Abstract: Cyanobacteria are major bloom-forming organisms in freshwater ecosystems and many strains are known to produce toxins. Toxin production requires an investment in energy and resources. As light is one of the most important factors for cyanobacterial growth, any changes in light climate might affect cyanobacterial toxin production as well as their growth and physiology. To evaluate the effects of light on the growth and physiological parameters of both toxic and non-toxic strains of Microcystis aeruginosa and Anabaena circinalis, cultures were grown at a range of light intensities (10, 25, 50, 100, 150 and 200 µmol m−2 s−1). The study revealed that the toxic strains of both species (CS558 for M. aeruginosa and CS537 and CS541 for A. circinalis) showed growth (µ) saturation at a higher light intensity compared to the non-toxic strains (CS338 for M. aeruginosa and CS534 for A. circinalis). Both species showed differences in chlorophyll a, carotenoid, allophycocyanin (APC) and phycoerythrin (PE) content between strains. There were also differences in dark respiration (Rd), light saturated oxygen evolution rates (Pmax) and efficiency of light harvesting (α) between strains. All other physiological parameters showed no statistically significant differences between strains. This study suggest that the different strains respond differently to different light habitats. Thus, changes in light availability may affect bloom intensity of toxic and nontoxic strains of cyanobacteria by changing the dominance and succession patterns.
      Citation: Microorganisms
      PubDate: 2017-08-04
      DOI: 10.3390/microorganisms5030045
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 46: Culturing Toxic Benthic Blooms: The Fate
           of Natural Biofilms in a Microcosm System

    • Authors: Francesca Di Pippo, Roberta Congestri
      First page: 46
      Abstract: A microcosm designed for culturing aquatic phototrophic biofilms on artificial substrata was used to perform experiments with microphytobenthos sampled during summer toxic outbreaks of Ostreopsis cf. ovata along the Middle Tyrrhenian coast. This dynamic approach aimed at exploring the unique and complex nature of O. cf. ovata bloom development in the benthic system. Epibenthic assemblages were used as inocula for co-cultures of bloom organisms on polycarbonate slides at controlled environmental conditions. Biofilm surface adhesion, growth, and spatial structure were evaluated along with shifts in composition and matrix production in a low disturbance regime, simulating source habitat. Initial adhesion and substratum colonisation appeared as stochastic processes, then community structure and physiognomy markedly changed with time. Dominance of filamentous cyanobacteria and diatoms, and dense clusters of Amphidinium cf. carterae at the mature biofilm phases, were recorded by light and confocal microscopy, whilst O. cf. ovata growth was visibly limited in the late culture phases. Life-form strategies, competitiveness for resources, and possibly allelopathic interactions shaped biofilm structure during culture growth. HPLC (High Performance Liquid Chromatography) analysis of exopolysaccharidic matrix revealed variations in sugar total amounts and composition. No toxic compounds were detected in the final communities tested by LC-MS (Liquid Chromatography- Mass Spectrometry) and MALDI-TOF MS (Matrix Assisted Laser Desorption Ionization Time OF Flight Mass Spectroscopy) techniques.
      Citation: Microorganisms
      PubDate: 2017-08-06
      DOI: 10.3390/microorganisms5030046
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 47: MALDI-TOF MS for the Identification of
           Cultivable Organic-Degrading Bacteria in Contaminated Groundwater near
           Unconventional Natural Gas Extraction Sites

    • Authors: Inês Santos, Misty Martin, Doug Carlton, Catarina Amorim, Paula Castro, Zacariah Hildenbrand, Kevin Schug
      First page: 47
      Abstract: Groundwater quality and quantity is of extreme importance as it is a source of drinking water in the United States. One major concern has emerged due to the possible contamination of groundwater from unconventional oil and natural gas extraction activities. Recent studies have been performed to understand if these activities are causing groundwater contamination, particularly with respect to exogenous hydrocarbons and volatile organic compounds. The impact of contaminants on microbial ecology is an area to be explored as alternatives for water treatment are necessary. In this work, we identified cultivable organic-degrading bacteria in groundwater in close proximity to unconventional natural gas extraction. Pseudomonas stutzeri and Acinetobacter haemolyticus were identified using matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF MS), which proved to be a simple, fast, and reliable method. Additionally, the potential use of the identified bacteria in water and/or wastewater bioremediation was studied by determining the ability of these microorganisms to degrade toluene and chloroform. In fact, these bacteria can be potentially applied for in situ bioremediation of contaminated water and wastewater treatment, as they were able to degrade both compounds.
      Citation: Microorganisms
      PubDate: 2017-08-10
      DOI: 10.3390/microorganisms5030047
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 48: Phosphate Acquisition and Virulence in
           Human Fungal Pathogens

    • Authors: Mélanie Ikeh, Yasmin Ahmed, Janet Quinn
      First page: 48
      Abstract: The ability of pathogenic fungi to acquire essential macro and micronutrients during infection is a well-established virulence trait. Recent studies in the major human fungal pathogens Candida albicans and Cryptococcus neoformans have revealed that acquisition of the essential macronutrient, phosphate, is essential for virulence. The phosphate sensing and acquisition pathway in fungi, known as the PHO pathway, has been extensively characterized in the model yeast Saccharomyces cerevisiae. In this review, we highlight recent advances in phosphate sensing and signaling mechanisms, and use the S. cerevisiae PHO pathway as a platform from which to compare the phosphate acquisition and storage strategies employed by several human pathogenic fungi. We also explore the multi-layered roles of phosphate acquisition in promoting fungal stress resistance to pH, cationic, and oxidative stresses, and describe emerging roles for the phosphate storage molecule polyphosphate (polyP). Finally, we summarize the recent studies supporting the necessity of phosphate acquisition in mediating the virulence of human fungal pathogens, highlighting the concept that this requirement is intimately linked to promoting resistance to host-imposed stresses.
      Citation: Microorganisms
      PubDate: 2017-08-22
      DOI: 10.3390/microorganisms5030048
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 49: Transcriptional Analysis Allows Genome
           Reannotation and Reveals that Cryptococcus gattii VGII Undergoes Nutrient
           Restriction during Infection

    • Authors: Patrícia Aline Gröhs Ferrareze, Rodrigo Silva Araujo Streit, Patricia Ribeiro dos Santos, Francine Melise dos Santos, Rita Maria Cunha de Almeida, Augusto Schrank, Livia Kmetzsch, Marilene Henning Vainstein, Charley Christian Staats
      First page: 49
      Abstract: Cryptococcus gattii is a human and animal pathogen that infects healthy hosts and caused the Pacific Northwest outbreak of cryptococcosis. The inhalation of infectious propagules can lead to internalization of cryptococcal cells by alveolar macrophages, a niche in which C. gattii cells can survive and proliferate. Although the nutrient composition of macrophages is relatively unknown, the high induction of amino acid transporter genes inside the phagosome indicates a preference for amino acid uptake instead of synthesis. However, the presence of countable errors in the R265 genome annotation indicates significant inhibition of transcriptomic analysis in this hypervirulent strain. Thus, we analyzed RNA-Seq data from in vivo and in vitro cultures of C. gattii R265 to perform the reannotation of the genome. In addition, based on in vivo transcriptomic data, we identified highly expressed genes and pathways of amino acid metabolism that would enable C. gattii to survive and proliferate in vivo. Importantly, we identified high expression in three APC amino acid transporters as well as the GABA permease. The use of amino acids as carbon and nitrogen sources, releasing ammonium and generating carbohydrate metabolism intermediaries, also explains the high expression of components of several degradative pathways, since glucose starvation is an important host defense mechanism.
      Citation: Microorganisms
      PubDate: 2017-08-23
      DOI: 10.3390/microorganisms5030049
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 50: Bacterial Contaminants of Poultry Meat:
           Sources, Species, and Dynamics

    • Authors: Amélie Rouger, Odile Tresse, Monique Zagorec
      First page: 50
      Abstract: With the constant increase in poultry meat consumption worldwide and the large variety of poultry meat products and consumer demand, ensuring the microbial safety of poultry carcasses and cuts is essential. In the present review, we address the bacterial contamination of poultry meat from the slaughtering steps to the use-by-date of the products. The different contamination sources are identified. The contaminants occurring in poultry meat cuts and their behavior toward sanitizing treatments or various storage conditions are discussed. A list of the main pathogenic bacteria of concern for the consumer and those responsible for spoilage and waste of poultry meat is established.
      Citation: Microorganisms
      PubDate: 2017-08-25
      DOI: 10.3390/microorganisms5030050
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 51: The Sea as a Rich Source of Structurally
           Unique Glycosaminoglycans and Mimetics

    • Authors: Ariana Vasconcelos, Vitor Pomin
      First page: 51
      Abstract: Glycosaminoglycans (GAGs) are sulfated glycans capable of regulating various biological and medical functions. Heparin, heparan sulfate, chondroitin sulfate, dermatan sulfate, keratan sulfate and hyaluronan are the principal classes of GAGs found in animals. Although GAGs are all composed of disaccharide repeating building blocks, the sulfation patterns and the composing alternating monosaccharides vary among classes. Interestingly, GAGs from marine organisms can present structures clearly distinct from terrestrial animals even considering the same class of GAG. The holothurian fucosylated chondroitin sulfate, the dermatan sulfates with distinct sulfation patterns extracted from ascidian species, the sulfated glucuronic acid-containing heparan sulfate isolated from the gastropode Nodipecten nodosum, and the hybrid heparin/heparan sulfate molecule obtained from the shrimp Litopenaeus vannamei are some typical examples. Besides being a rich source of structurally unique GAGs, the sea is also a wealthy environment of GAG-resembling sulfated glycans. Examples of these mimetics are the sulfated fucans and sulfated galactans found in brown, red and green algae, sea urchins and sea cucumbers. For adequate visualization, representations of all discussed molecules are given in both Haworth projections and 3D models.
      Citation: Microorganisms
      PubDate: 2017-08-28
      DOI: 10.3390/microorganisms5030051
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 52: Insight into the Genome of
           Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products

    • Authors: Sabine Leroy, Aurore Vermassen, Geoffrey Ras, Régine Talon
      First page: 52
      Abstract: Staphylococcus xylosus belongs to the vast group of coagulase-negative staphylococci. It is frequently isolated from meat products, either fermented or salted and dried, and is commonly used as starter cultures in sausage manufacturing. Analysis of the S. xylosus genome together with expression in situ in a meat model revealed that this bacterium is well adapted to meat substrates, being able to use diverse substrates as sources of carbon and energy and different sources of nitrogen. It is well-equipped with genes involved in osmotic, oxidative/nitrosative, and acidic stress responses. It is responsible for the development of the typical colour of cured meat products via its nitrate reductase activity. It contributes to sensorial properties, mainly by the the catabolism of pyruvate and amino acids resulting in odorous compounds and by the limiting of the oxidation of fatty acids, thereby avoiding rancidity.
      Citation: Microorganisms
      PubDate: 2017-08-29
      DOI: 10.3390/microorganisms5030052
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 53: Multiple Antibiotic-Resistant, Extended
           Spectrum-β-Lactamase (ESBL)-Producing Enterobacteria in Fresh Seafood

    • Authors: Asem Sanjit Singh, Manjusha Lekshmi, Sreepriya Prakasan, Binaya Nayak, Sanath Kumar
      First page: 53
      Abstract: Members of the family Enterobacteriaceae include several human pathogens that can be acquired through contaminated food and water. In this study, the incidence of extended spectrum β-lactamase (ESBL)-producing enterobacteria was investigated in fresh seafood sold in retail markets. The ESBL-positive phenotype was detected in 169 (78.60%) isolates, with Escherichia coli being the predominant species (53), followed by Klebsiella oxytoca (27), and K. pneumoniae (23). More than 90% of the isolates were resistant to third generation cephalosporins, cefotaxime, ceftazidime, and cefpodoxime. Sixty-five percent of the isolates were resistant to the monobactam drug aztreonam, 40.82% to ertapenem, and 31.36% to meropenem. Resistance to at least five antibiotics was observed in 38.46% of the isolates. Polymerase Chain Reaction (PCR) analysis of ESBL-encoding genes detected blaCTX, blaSHV, and blaTEM genes in 76.92%, 63.3%, and 44.37% of the isolates, respectively. Multiple ESBL genes were detected in majority of the isolates. The recently discovered New Delhi metallo-β-lactamase gene (blaNDM-1) was detected in two ESBL+ isolates. Our study shows that secondary contamination of fresh seafood with enteric bacteria resistant to multiple antibiotics may implicate seafood as a potential carrier of antibiotic resistant bacteria and emphasizes an urgent need to prevent environmental contamination and dissemination of such bacteria.
      Citation: Microorganisms
      PubDate: 2017-08-30
      DOI: 10.3390/microorganisms5030053
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 54: Comments to Article by Willetts A. et
           al., Microorganisms 2016, 4, 38

    • Authors: Jennifer Littlechild, Mikail Isupov
      First page: 54
      Abstract: We would like to comment on recent work published in your journal in October 2016 by Willetts A. et al. [1].[...]
      Citation: Microorganisms
      PubDate: 2017-09-06
      DOI: 10.3390/microorganisms5030054
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 55: Reply to the Comment by Littlechild and

    • Authors: Andrew Willetts, David Kelly
      First page: 55
      Abstract: I thank Drs. Littlechild and Isupov for their recent comments, which are considered below. Before addressing these specifically, their correspondence raises two more general issues which require initial clarification.[...]
      Citation: Microorganisms
      PubDate: 2017-09-06
      DOI: 10.3390/microorganisms5030055
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 56: Lactobacillus sakei: A Starter for
           Sausage Fermentation, a Protective Culture for Meat Products

    • Authors: Monique Zagorec, Marie-Christine Champomier-Vergès
      First page: 56
      Abstract: Among lactic acid bacteria of meat products, Lactobacillus sakei is certainly the most studied species due to its role in the fermentation of sausage and its prevalence during cold storage of raw meat products. Consequently, the physiology of this bacterium regarding functions involved in growth, survival, and metabolism during meat storage and processing are well known. This species exhibits a wide genomic diversity that can be observed when studying different strains and on which probably rely its multiple facets in meat products: starter, spoiler, or protective culture. The emerging exploration of the microbial ecology of meat products also revealed the multiplicity of bacterial interactions L. sakei has to face and their various consequences on microbial quality and safety at the end of storage.
      Citation: Microorganisms
      PubDate: 2017-09-06
      DOI: 10.3390/microorganisms5030056
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 57: The Skin Bacterium Propionibacterium
           acnes Employs Two Variants of Hyaluronate Lyase with Distinct Properties

    • Authors: Seven Nazipi, Kristian Stødkilde, Carsten Scavenius, Holger Brüggemann
      First page: 57
      Abstract: Hyaluronic acid (HA) and other glycosaminoglycans are extracellular matrix components in the human epidermis and dermis. One of the most prevalent skin microorganisms, Propionibacterium acnes, possesses HA-degrading activity, possibly conferred by the enzyme hyaluronate lyase (HYL). In this study, we identified the HYL of P. acnes and investigated the genotypic and phenotypic characteristics. Investigations include the generation of a P. acnes hyl knockout mutant and HYL activity assays to determine the substrate range and formed products. We found that P. acnes employs two distinct variants of HYL. One variant, HYL-IB/II, is highly active, resulting in complete HA degradation; it is present in strains of the phylotypes IB and II. The other variant, HYL-IA, has low activity, resulting in incomplete HA degradation; it is present in type IA strains. Our findings could explain some of the observed differences between P. acnes phylotype IA and IB/II strains. Whereas type IA strains are primarily found on the skin surface and associated with acne vulgaris, type IB/II strains are more often associated with soft and deep tissue infections, which would require elaborate tissue invasion strategies, possibly accomplished by a highly active HYL-IB/II.
      Citation: Microorganisms
      PubDate: 2017-09-12
      DOI: 10.3390/microorganisms5030057
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 58: Rapid and Highly Sensitive
           Non-Competitive Immunoassay for Specific Detection of Nodularin

    • Authors: Sultana Akter, Markus Vehniäinen, Harri Kankaanpää, Urpo Lamminmäki
      First page: 58
      Abstract: Nodularin (NOD) is a cyclic penta-peptide hepatotoxin mainly produced by Nodularia spumigena, reported from the brackish water bodies of various parts of the world. It can accumulate in the food chain and, for safety reasons, levels of NOD not only in water bodies but also in food matrices are of interest. Here, we report on a non-competitive immunoassay for the specific detection of NOD. A phage display technique was utilized to interrogate a synthetic antibody phage library for binders recognizing NOD bound to an anti-ADDA (3-Amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4(E),6(E)-dienoic acid) monoclonal antibody (Mab). One of the obtained immunocomplex binders, designated SA32C11, showed very high specificity towards nodularin-R (NOD-R) over to the tested 10 different microcystins (microcystin-LR, -dmLR, -RR, -dmRR, -YR, -LY, -LF, -LW, -LA, -WR). It was expressed in Escherichia coli as a single chain antibody fragment (scFv) fusion protein and used to establish a time-resolved fluorometry-based assay in combination with the anti-ADDA Mab. The detection limit (blank + 3SD) of the immunoassay, with a total assay time of 1 h 10 min, is 0.03 µg/L of NOD-R. This represents the most sensitive immunoassay method for the specific detection of NOD reported so far. The assay was tested for its performance to detect NOD using spiked (0.1 to 3 µg/L of NOD-R) water samples including brackish sea and coastal water and the recovery ranged from 79 to 127%. Furthermore, a panel of environmental samples, including water from different sources, fish and other marine tissue specimens, were analyzed for NOD using the assay. The assay has potential as a rapid screening tool for the analysis of a large number of water samples for the presence of NOD. It can also find applications in the analysis of the bioaccumulation of NOD in marine organisms and in the food chain.
      Citation: Microorganisms
      PubDate: 2017-09-12
      DOI: 10.3390/microorganisms5030058
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 59: Effect of Environmental Factors on
           Intra-Specific Inhibitory Activity of Carnobacterium maltaromaticum

    • Authors: Peipei Zhang, Mandeep Kaur, John Bowman, David Ratkowsky, Mark Tamplin
      First page: 59
      Abstract: Carnobacterium maltaromaticum is frequently associated with foods having extended shelf-life due to its inhibitory activity to other bacteria. The quantification of such inhibition interactions affected by various environmental factors is limited. This study investigated the effect of environmental factors relevant to vacuum-packaged beef on inhibition between two model isolates of C. maltaromaticum, D0h and D8c, specifically D8c sensitivity to D0h inhibition and D0h inhibitor production. The effects of temperature (−1, 7, 15, 25 °C), atmosphere (aerobic and anaerobic), pH (5.5, 6, 6.5), lactic acid (0, 25, 50 mM) and glucose (0, 0.56, 5.55 mM) on D8c sensitivity (diameter of an inhibition zone) were measured. The effects of pH, glucose, lactic acid and atmosphere on D0h inhibitor production were measured at 25 °C. Sensitivity of D8c was the highest at 15 °C, under aerobic atmosphere, at higher concentrations of undissociated lactic acid and glucose, and at pH 5.5 (p < 0.001). pH significantly affected D0h inhibitor production (p < 0.001), which was the highest at pH 6.5. The effect of lactic acid depended upon pH level; at relatively low pH (5.5), lactic acid decreased the production rate (arbitrary inhibition unit (AU)/mL/h). This study provides a quantitative description of intra-species interactions, studied in in vitro environments that are relevant to vacuum-packaged beef.
      Citation: Microorganisms
      PubDate: 2017-09-14
      DOI: 10.3390/microorganisms5030059
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 60: Proteomic Characterization of Armillaria
           mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary
           Metabolism Profiles

    • Authors: Cassandra Collins, Rachel Hurley, Nada Almutlaqah, Grainne O’Keeffe, Thomas Keane, David Fitzpatrick, Rebecca Owens
      First page: 60
      Abstract: Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein), indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM) enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.
      Citation: Microorganisms
      PubDate: 2017-09-17
      DOI: 10.3390/microorganisms5030060
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 61: Microbial Community Structure and
           Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine

    • Authors: Malin Bomberg, Jarno Mäkinen, Marja Salo, Mona Arnold
      First page: 61
      Abstract: Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L−1 sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance.
      Citation: Microorganisms
      PubDate: 2017-09-20
      DOI: 10.3390/microorganisms5030061
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 62: Diagnostic Value of Endotracheal
           Aspirates Sonication on Ventilator-Associated Pneumonia Microbiologic

    • Authors: Laia Fernández-Barat, Ana Motos, Otavio Ranzani, Gianluigi Bassi, Elisabet Aguilera Xiol, Tarek Senussi, Chiara Travierso, Chiara Chiurazzi, Francesco Idone, Laura Muñoz, Jordi Vila, Miquel Ferrer, Paolo Pelosi, Francesco Blasi, Massimo Antonelli, Antoni Torres
      First page: 62
      Abstract: Microorganisms are able to form biofilms within respiratory secretions. Methods to disaggregate such biofilms before utilizing standard, rapid, or high throughput diagnostic technologies may aid in pathogen detection during ventilator associated pneumonia (VAP) diagnosis. Our aim was to determine if sonication of endotracheal aspirates (ETA) would increase the sensitivity of qualitative, semi-quantitative, and quantitative bacterial cultures in an animal model of pneumonia caused by Pseudomonas aeruginosa or by methicillin resistant Staphylococcus aureus (MRSA). Material and methods: P. aeruginosa or MRSA was instilled into the lungs or the oropharynx of pigs in order to induce severe VAP. Time point assessments for qualitative and quantitative bacterial cultures of ETA and bronchoalveolar lavage (BAL) samples were performed at 24, 48, and 72 h after bacterial instillation. In addition, at 72 h (autopsy), lung tissue was harvested to perform quantitative bacterial cultures. Each ETA sample was microbiologically processed with and without applying sonication for 5 min at 40 KHz before bacterial cultures. Sensitivity and specificity were determined using BAL as a gold-standard. Correlation with BAL and lung bacterial burden was also determined before and after sonication. Assessment of biofilm clusters and planktonic bacteria was performed through both optical microscopy utilizing Gram staining and Confocal Laser Scanning Microscopy utilizing the LIVE/DEAD®BacLight kit. Results: 33 pigs were included, 27 and 6 from P. aeruginosa and MRSA pneumonia models, respectively. Overall, we obtained 85 ETA, 69 (81.2%) from P. aeruginosa and 16 (18.8%) from MRSA challenged pigs. Qualitative cultures did not significantly change after sonication, whereas quantitative ETA cultures did significantly increase bacterial counting. Indeed, sonication consistently increased bacterial burden in ETAs at 24, 48, and 72 h after bacterial challenge. Sonication also improved sensitivity of ETA quantitative cultures and maintained specificity at levels previously reported and accepted for VAP diagnosis. Conclusion: The use of sonication in ETA respiratory samples needs to be clinically validated since sonication could potentially improve pathogen detection before standard, rapid, or high throughput diagnostic methods used in routine microbial diagnostics.
      Citation: Microorganisms
      PubDate: 2017-09-20
      DOI: 10.3390/microorganisms5030062
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 63: Bioprospecting for Exopolysaccharides
           from Deep-Sea Hydrothermal Vent Bacteria: Relationship between Bacterial
           Diversity and Chemical Diversity

    • Authors: Christine Delbarre-Ladrat, Marcia Leyva Salas, Corinne Sinquin, Agata Zykwinska, Sylvia Colliec-Jouault
      First page: 63
      Abstract: Many bacteria biosynthesize structurally diverse exopolysaccharides (EPS) and excrete them into their surrounding environment. The EPS functional features have found many applications in industries such as cosmetics and pharmaceutics. In particular, some EPS produced by marine bacteria are composed of uronic acids, neutral sugars, and N-acetylhexosamines, and may also bear some functional sulfate groups. This suggests that they can share common structural features with glycosaminoglycans (GAG) like the two EPS (HE800 and GY785) originating from the deep sea. In an attempt to discover new EPS that may be promising candidates as GAG-mimetics, fifty-one marine bacterial strains originating from deep-sea hydrothermal vents were screened. The analysis of the EPS chemical structure in relation to bacterial species showed that Vibrio, Alteromonas, and Pseudoalteromonas strains were the main producers. Moreover, they produced EPS with distinct structural features, which might be useful for targeting marine bacteria that could possibly produce structurally GAG-mimetic EPS.
      Citation: Microorganisms
      PubDate: 2017-09-20
      DOI: 10.3390/microorganisms5030063
      Issue No: Vol. 5, No. 3 (2017)
  • Microorganisms, Vol. 5, Pages 14: Identification and Characterization of
           Spontaneous Auxotrophic Mutants in Fusarium langsethiae

    • Authors: Olga Gavrilova, Anna Skritnika, Tatiana Gagkaeva
      First page: 14
      Abstract: Analysis of 49 strains of Fusarium langsethiae originating from northern Europe (Russia, Finland, Sweden, UK, Norway, and Latvia) revealed the presence of spontaneous auxotrophic mutants that reflect natural intraspecific diversity. Our investigations detected that 49.0% of F. langsethiae strains were auxotrophic mutants for biotin, and 8.2% of the strains required thiamine as a growth factor. They failed to grow on vitamin-free media. For both prototrophic and auxotrophic strains, no growth defect was observed in rich organic media. Without essential vitamins, a significant reduction in the growth of the auxotrophic strains results in a decrease of the formation of T-2 toxin and diacetoxyscirpenol. In addition, all analysed F. langsethiae strains were distinguished into two subgroups based on PCR product sizes. According to our results, 26 and 23 strains of F. langsethiae belong to subgroups I and II respectively. We determined that the deletion in the intergenic spacer (IGS) region of the rDNA of F. langsethiae belonging to subgroup II is linked with temperature sensitivity and causes a decrease in strain growth at 30 °C. Four thiamine auxotrophic strains were found in subgroup I, while 21 biotin auxotrophic strains were detected in subgroups II. To the best of our knowledge, the spontaneous mutations in F. langsethiae observed in the present work have not been previously reported.
      PubDate: 2017-03-31
      DOI: 10.3390/microorganisms5020014
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 15: Approaches to Dispersing Medical

    • Authors: Derek Fleming, Kendra Rumbaugh
      First page: 15
      Abstract: Biofilm-associated infections pose a complex problem to the medical community, in that residence within the protection of a biofilm affords pathogens greatly increased tolerances to antibiotics and antimicrobials, as well as protection from the host immune response. This results in highly recalcitrant, chronic infections and high rates of morbidity and mortality. Since as much as 80% of human bacterial infections are biofilm-associated, many researchers have begun investigating therapies that specifically target the biofilm architecture, thereby dispersing the microbial cells into their more vulnerable, planktonic mode of life. This review addresses the current state of research into medical biofilm dispersal. We focus on three major classes of dispersal agents: enzymes (including proteases, deoxyribonucleases, and glycoside hydrolases), antibiofilm peptides, and dispersal molecules (including dispersal signals, anti-matrix molecules, and sequestration molecules). Throughout our discussion, we provide detailed lists and summaries of some of the most prominent and extensively researched dispersal agents that have shown promise against the biofilms of clinically relevant pathogens, and we catalog which specific microorganisms they have been shown to be effective against. Lastly, we discuss some of the main hurdles to development of biofilm dispersal agents, and contemplate what needs to be done to overcome them.
      PubDate: 2017-04-01
      DOI: 10.3390/microorganisms5020015
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 16: Insights on Klebsiella pneumoniae
           Biofilms Assembled on Different Surfaces Using Phenotypic and Genotypic

    • Authors: Maria Bandeira, Vítor Borges, João Gomes, Aida Duarte, Luisa Jordao
      First page: 16
      Abstract: Klebsiella pneumoniae is a prominent etiological agent of healthcare associated infections (HAIs). In this context, multidrug-resistant and biofilm-producing bacteria are of special public health concern due to the difficulties associated with treatment of human infections and eradication from hospital environments. Here, in order to study the impact of medical devices-associated materials on the biofilm dynamics, we performed biofilm phenotypic analyses through a classic and a new scanning electron microscopy (SEM) technique for three multidrug-resistant K. pneumoniae isolates growing on polystyrene and silicone. We also applied whole-genome sequencing (WGS) to search for genetic clues underlying biofilm phenotypic differences. We found major differences in the extracellular polymeric substances (EPS) content among the three strains, which were further corroborated by in-depth EPS composition analysis. WGS analysis revealed a high nucleotide similarity within the core-genome, but relevant differences in the accessory genome that may account for the detected biofilm phenotypic dissimilarities, such as genes already associated with biofilm formation in other pathogenic bacteria (e.g., genes coding haemogglutinins and haemolysins). These data reinforce that the research efforts to defeat bacterial biofilms should take into account that their dynamics may be contingent on the medical devices-associated materials.
      PubDate: 2017-04-03
      DOI: 10.3390/microorganisms5020016
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 17: Probiotic Microorganisms: A Closer Look

    • Authors: Julio Villena, Haruki Kitazawa
      First page: 17
      Abstract: n/a
      PubDate: 2017-04-08
      DOI: 10.3390/microorganisms5020017
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 18: High Prevalence of blaNDM-1, blaVIM,
           qacE, and qacEΔ1 Genes and Their Association with Decreased
           Susceptibility to Antibiotics and Common Hospital Biocides in Clinical
           Isolates of Acinetobacter baumannii

    • Authors: Fatma Gomaa, Zeinab Helal, Mazhar Khan
      First page: 18
      Abstract: The objective of this study was to evaluate the susceptibility of metallo-β-lactamase (MBL)-producing Acinetobacter baumannii (A. baumannii) clinical isolates to biocides. We also determined the prevalence and correlation of efflux pump genes, class 1 integron and MBL encoding genes. In addition, blaVIM, blaNDM-1, qacE and qacEΔ1 nucleotide sequence analysis was performed and compared to sequences retrieved from GenBank at the National Center for Biotechnology Information database. A. baumannii had a resistance rate to carbapenem of 71.4% and 39.3% and was found to be a MBL producer. The minimum inhibitory concentrations (MICs) of chlorhexidine and cetrimide were higher than the recommended concentrations for disinfection in 54.5% and 77.3% of MBL-positive isolates respectively and their MICs were significantly higher among qac gene-positive isolates. Coexistence of qac genes was detected in 68.1% and 50% of the isolates with blaVIM and blaNDM-1 respectively. There was a significant correlation between the presence of qac genes and MBL-encoding blaVIM and blaNDM-1 genes. Each of the blaNDM-1, blaVIM, qacE and qacEΔ1 DNA sequences showed homology with each other and with similar sequences reported from other countries. The high incidence of Verona integron-encoded metallo-β-lactamases (VIM) and New-Delhi-metallo-β-lactamase (NDM) and qac genes in A. baumannii highlights emerging therapeutic challenges for being readily transferable between clinically relevant bacteria. In addition reduced susceptibility to chlorhexidine and cetrimide and the potential for cross resistance to some antibiotics necessitates the urgent need for healthcare facilities to periodically evaluate biocides efficacy, to address the issue of antiseptic resistance and to initiate a “biocidal stewardship”.
      PubDate: 2017-04-12
      DOI: 10.3390/microorganisms5020018
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 19: The Status of Biofilms in Penile

    • Authors: Matthew Faller, Tobias Kohler
      First page: 19
      Abstract: Erectile dysfunction is prevalent among men and will continue to become more so with the aging population. Of the available treatment options, implantable prosthetic devices are typically thought of as a third line treatment even though they have the highest satisfaction rate and continually improving success rates. Infection and mechanical failure are the most common reasons for implant revision in the past. Since the development of more reliable devices, bacterial biofilms are coming to the forefront of discussion as causes of required revision. Biofilms are problematic as they are ubiquitous and exceedingly difficult to prevent or treat.
      PubDate: 2017-04-18
      DOI: 10.3390/microorganisms5020019
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 20: Tellurite and Tellurate Reduction by the
           Aerobic Anoxygenic Phototroph Erythromonas ursincola, Strain KR99 Is
           Carried out by a Novel Membrane Associated Enzyme

    • Authors: Chris Maltman, Lynda Donald, Vladimir Yurkov
      First page: 20
      Abstract: Erythromonas ursincola, strain KR99 isolated from a freshwater thermal spring of Kamchatka Island in Russia, resists and reduces very high levels of toxic tellurite under aerobic conditions. Reduction is carried out by a constitutively expressed membrane associated enzyme, which was purified and characterized. The tellurite reductase has a molecular weight of 117 kDa, and is comprised of two subunits (62 and 55 kDa) in a 1:1 ratio. Optimal activity occurs at pH 7.0 and 28 °C. Tellurite reduction has a Vmax of 5.15 µmol/min/mg protein and a Km of 3.36 mM. The enzyme can also reduce tellurate with a Vmax and Km of 1.08 µmol/min/mg protein and 1.44 mM, respectively. This is the first purified membrane associated Te oxyanion reductase.
      PubDate: 2017-04-19
      DOI: 10.3390/microorganisms5020020
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 21: Hyperbaric Oxygen Therapy is Ineffective
           as an Adjuvant to Daptomycin with Rifampicin Treatment in a Murine Model
           of Staphylococcus aureus in Implant-Associated Osteomyelitis

    • Authors: Nis Jørgensen, Kasper Hansen, Caroline Andreasen, Michael Pedersen, Kurt Fuursted, Rikke Meyer, Eskild Petersen
      First page: 21
      Abstract: Implant-associated infections caused by bacterial biofilms are difficult to treat. Surgical intervention is often necessary to cure the patient, as the antibiotic recalcitrance of biofilms renders them untreatable with conventional antibiotics. Intermittent hyperbaric oxygen treatment (HBOT) has been proposed as an adjuvant to conventional antibiotic treatment and it has been speculated that combining HBOT with antibiotics could improve treatment outcomes for biofilm infections. In this study we addressed whether HBOT could improve treatment outcomes of daptomycin and rifampicin combination therapy. The effect of HBOT on the treatment outcomes of daptomycin and rifampicin against implant-associated osteomyelitis was quantified in a murine model. In total, 80 mice were randomized into two groups receiving antibiotics, either alone or in combination with daily intermittent HBOT (304 kPa for 60 min) following injection of antibiotics. Treatment was initiated 11 days after animals were infected with Staphylococcus aureus and treatment duration was 14 days. We found that HBOT did not improve the cure rate and did not reduce the bacterial load on the implant surface or in the surrounding tissue. Cure rates of daptomycin + rifampicin were 40% in infected tibias and 75% for implants while cure rates for HBOT-daptomycin + rifampicin were 50% and 85%, respectively, which were not significantly higher (Fisher’s exact test). While it is encouraging that the combination of daptomycin and rifampicin is very effective, our study demonstrates that this efficacy cannot be improved by adjuvant HBOT.
      PubDate: 2017-04-25
      DOI: 10.3390/microorganisms5020021
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 22: Melanisation of Aspergillus terreus—Is
           Butyrolactone I Involved in the Regulation of Both DOPA and DHN Types of
           Pigments in Submerged Culture'

    • Authors: Elina Palonen, Sheetal Raina, Annika Brandt, Jussi Meriluoto, Tajalli Keshavarz, Juhani Soini
      First page: 22
      Abstract: Pigments and melanins of fungal spores have been investigated for decades, revealing important roles in the survival of the fungus in hostile environments. The key genes and the encoded enzymes for pigment and melanin biosynthesis have recently been found in Ascomycota, including Aspergillus spp. In Aspergillus terreus, the pigmentation has remained mysterious with only one class of melanin biogenesis being found. In this study, we examined an intriguing, partially annotated gene cluster of A. terreus strain NIH2624, utilizing previously sequenced transcriptome and improved gene expression data of strain MUCL 38669, under the influence of a suggested quorum sensing inducing metabolite, butyrolactone I. The core polyketide synthase (PKS) gene of the cluster was predicted to be significantly longer on the basis of the obtained transcriptional data, and the surrounding cluster was positively regulated by butyrolactone I at the late growth phase of submerged culture, presumably during sporulation. Phylogenetic analysis of the extended PKS revealed remarkable similarity with a group of known pigments of Fusarium spp., indicating a similar function for this PKS. We present a hypothesis of this PKS cluster to biosynthesise a 1,8-dihydroxynaphthalene (DHN)-type of pigment during sporulation with the influence of butyrolactone I under submerged culture.
      PubDate: 2017-05-04
      DOI: 10.3390/microorganisms5020022
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 23: Lactic Fermentation as an Efficient Tool
           to Enhance the Antioxidant Activity of Tropical Fruit Juices and Teas

    • Authors: Amandine Fessard, Ashish Kapoor, Jessica Patche, Sophie Assemat, Mathilde Hoarau, Emmanuel Bourdon, Theeshan Bahorun, Fabienne Remize
      First page: 23
      Abstract: Tropical fruits like pineapple, papaya, mango, and beverages such as green or black teas, represent an underestimated source of antioxidants that could exert health-promoting properties. Most food processing technologies applied to fruit beverages or teas result in an impairment of inherent nutritional properties. Conversely, we hypothesise that lactic acid fermentation may constitute a promising route to maintain and even improve the nutritional qualities of processed fruits. Using specific growth media, lactic acid bacteria were selected from the fruit phyllosphere diversity and fruit juice, with the latter undergoing acidification kinetics analyses and characterised for exopolysaccharide production. Strains able to ferment tropical fruit juices or teas into pleasant beverages, within a short time, were of particular interest. Strains Weissella cibaria 64 and Leuconostoc mesenteroides 12b, able to increase antioxidant activity, were specifically studied as potential starters for lactic fermented pineapple juice.
      PubDate: 2017-05-10
      DOI: 10.3390/microorganisms5020023
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 24: Dairy Propionibacteria: Versatile

    • Authors: Houem Rabah, Fillipe Rosa do Carmo, Gwénaël Jan
      First page: 24
      Abstract: Dairy propionibacteria are used as cheese ripening starters, as biopreservative and as beneficial additives, in the food industry. The main species, Propionibacterium freudenreichii, is known as GRAS (Generally Recognized As Safe, USA, FDA). In addition to another dairy species, Propionibacterium acidipropionici, they are included in QPS (Qualified Presumption of Safety) list. Additional to their well-known technological application, dairy propionibacteria increasingly attract attention for their promising probiotic properties. The purpose of this review is to summarize the probiotic characteristics of dairy propionibacteria reported by the updated literature. Indeed, they meet the selection criteria for probiotic bacteria, such as the ability to endure digestive stressing conditions and to adhere to intestinal epithelial cells. This is a prerequisite to bacterial persistence within the gut. The reported beneficial effects are ranked according to property’s type: microbiota modulation, immunomodulation, and cancer modulation. The proposed molecular mechanisms are discussed. Dairy propionibacteria are described as producers of nutraceuticals and beneficial metabolites that are responsible for their versatile probiotic attributes include short chain fatty acids (SCFAs), conjugated fatty acids, surface proteins, and 1,4-dihydroxy-2-naphtoic acid (DHNA). These metabolites possess beneficial properties and their production depends on the strain and on the growth medium. The choice of the fermented food matrix may thus determine the probiotic properties of the ingested product. This review approaches dairy propionibacteria, with an interest in both technological abilities and probiotic attributes.
      PubDate: 2017-05-13
      DOI: 10.3390/microorganisms5020024
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 25: Microbial Diversity in Extreme Marine
           Habitats and Their Biomolecules

    • Authors: Annarita Poli, Ilaria Finore, Ida Romano, Alessia Gioiello, Licia Lama, Barbara Nicolaus
      First page: 25
      Abstract: Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.
      PubDate: 2017-05-16
      DOI: 10.3390/microorganisms5020025
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 26: Adding Value to Goat Meat: Biochemical
           and Technological Characterization of Autochthonous Lactic Acid Bacteria
           to Achieve High-Quality Fermented Sausages

    • Authors: Miriam Nediani, Luis García, Lucila Saavedra, Sandra Martínez, Soledad López Alzogaray, Silvina Fadda
      First page: 26
      Abstract: Quality and safety are important challenges in traditional fermented sausage technology. Consequently, the development of a tailored starter culture based on indigenous microbiota constitutes an interesting alternative. In the present study, spontaneously fermented goat meat sausages were created and analyzed using a physicochemical and microbiological approach. Thereafter 170 lactic acid bacteria (LAB) strains were isolated and preliminary characterized by phenotypic assays. The hygienic and technological properties, and growth and fermentative potential of isolates using a goat-meat-based culture medium were evaluated. All strains proved to have bioprotective features due to their acidogenic metabolism. Almost all grew optimally in meat environments. LAB isolates presented proteolytic activity against meat proteins and enriched amino acid contents of the goat-meat-based model. The most efficient strains were four different Lactobacillus sakei isolates, as identified by genotyping and RAPD analysis. L. sakei strains are proposed as optimal candidates to improve the production of fermented goat meat sausages, creating a new added-value fermented product.
      PubDate: 2017-05-17
      DOI: 10.3390/microorganisms5020026
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 27: From Genome to Phenotype: An Integrative
           Approach to Evaluate the Biodiversity of Lactococcus lactis

    • Authors: Valérie Laroute, Hélène Tormo, Christel Couderc, Muriel Mercier-Bonin, Pascal Le Bourgeois, Muriel Cocaign-Bousquet, Marie-Line Daveran-Mingot
      First page: 27
      Abstract: Lactococcus lactis is one of the most extensively used lactic acid bacteria for the manufacture of dairy products. Exploring the biodiversity of L. lactis is extremely promising both to acquire new knowledge and for food and health-driven applications. L. lactis is divided into four subspecies: lactis, cremoris, hordniae and tructae, but only subsp. lactis and subsp. cremoris are of industrial interest. Due to its various biotopes, Lactococcus subsp. lactis is considered the most diverse. The diversity of L. lactis subsp. lactis has been assessed at genetic, genomic and phenotypic levels. Multi-Locus Sequence Type (MLST) analysis of strains from different origins revealed that the subsp. lactis can be classified in two groups: “domesticated” strains with low genetic diversity, and “environmental” strains that are the main contributors of the genetic diversity of the subsp. lactis. As expected, the phenotype investigation of L. lactis strains reported here revealed highly diverse carbohydrate metabolism, especially in plant- and gut-derived carbohydrates, diacetyl production and stress survival. The integration of genotypic and phenotypic studies could improve the relevance of screening culture collections for the selection of strains dedicated to specific functions and applications.
      PubDate: 2017-05-19
      DOI: 10.3390/microorganisms5020027
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 28: Regulatory and Safety Requirements for
           Food Cultures

    • Authors: Svend Laulund, Anette Wind, Patrick Derkx, Véronique Zuliani
      First page: 28
      Abstract: The increased use of food cultures to ferment perishable raw materials has potentiated the need for regulations to assess and assure the safety of food cultures and their uses. These regulations differ from country to country, all aimed at assuring the safe use of food cultures which has to be guaranteed by the food culture supplier. Here we highlight national differences in regulations and review a list of methods and methodologies to assess the safety of food cultures at strain level, at production, and in the final product.
      PubDate: 2017-05-23
      DOI: 10.3390/microorganisms5020028
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 29: Toxin Variability Estimations of 68
           Alexandrium ostenfeldii (Dinophyceae) Strains from The Netherlands Reveal
           a Novel Abundant Gymnodimine

    • Authors: Helge Martens, Urban Tillmann, Kirsi Harju, Carmela Dell’Aversano, Luciana Tartaglione, Bernd Krock
      First page: 29
      Abstract: Alexandrium ostenfeldii is a toxic dinoflagellate that has recently bloomed in Ouwerkerkse Kreek, The Netherlands, and which is able to cause a serious threat to shellfish consumers and aquacultures. We used a large set of 68 strains to the aim of fully characterizing the toxin profiles of the Dutch A. ostenfeldii in consideration of recent reports of novel toxins. Alexandrium ostenfeldii is known as a causative species of paralytic shellfish poisoning, and consistently in the Dutch population we determined the presence of several paralytic shellfish toxins (PST) including saxitoxin (STX), GTX2/3 (gonyautoxins), B1 and C1/C2. We also examined the production of spiroimine toxins by the Dutch A. ostenfeldii strains. An extensive liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed a high intraspecific variability of spirolides (SPX) and gymnodimines (GYM). Spirolides included 13-desMethyl-spirolide C generally as the major compound and several other mostly unknown SPX-like compounds that were detected and characterized. Besides spirolides, the presence of gymnodimine A and 12-Methyl-gymnodimine A was confirmed, together with two new gymnodimines. One of these was tentatively identified as an analogue of gymnodimine D and was the most abundant gymnodimine (calculated cell quota up to 274 pg cell−1, expressed as GYM A equivalents). Our multi-clonal approach adds new analogues to the increasing number of compounds in these toxin classes and revealed a high strain variability in cell quota and in toxin profile of toxic compounds within a single population.
      PubDate: 2017-05-26
      DOI: 10.3390/microorganisms5020029
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 30: Table Olive Fermentation Using Starter
           Cultures with Multifunctional Potential

    • Authors: Stamatoula Bonatsou, Chrysoula Tassou, Efstathios Panagou, George-John Nychas
      First page: 30
      Abstract: Table olives are one of the most popular plant-derived fermented products. Their enhanced nutritional value due to the presence of phenolic compounds and monounsaturated fatty acids makes olives an important food commodity of the Mediterranean diet. However, despite its economic significance, table olive fermentation is mainly craft-based and empirically driven by the autochthonous microbiota of the olives depending on various intrinsic and extrinsic factors, leading to a spontaneous process and a final product of variable quality. The use of microorganisms previously isolated from olive fermentations and studied for their probiotic potential and technological characteristics as starter cultures may contribute to the reduction of spoilage risk resulting in a controlled fermentation process. This review focuses on the importance of the development and implementation of multifunctional starter cultures related to olives with desirable probiotic and technological characteristics for possible application on table olive fermentation with the main purpose being the production of a health promoting and sensory improved functional food.
      PubDate: 2017-05-28
      DOI: 10.3390/microorganisms5020030
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 31: Changes in Microbial (Bacteria and
           Archaea) Plankton Community Structure after Artificial Dispersal in
           Grazer-Free Microcosms

    • Authors: Hera Karayanni, Alexandra Meziti, Sofie Spatharis, Savvas Genitsaris, Claude Courties, Konstantinos Kormas
      First page: 31
      Abstract: Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.
      PubDate: 2017-06-03
      DOI: 10.3390/microorganisms5020031
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 32: Interaction of Candida Species with the

    • Authors: Andreas Kühbacher, Anke Burger-Kentischer, Steffen Rupp
      First page: 32
      Abstract: The human skin is commonly colonized by diverse fungal species. Some Candida species, especially C. albicans, do not only reside on the skin surface as commensals, but also cause infections by growing into the colonized tissue. However, defense mechanisms at the skin barrier level are very efficient, involving residential non-immune and immune cells as well as immune cells specifically recruited to the site of infection. Therefore, the skin is an effective barrier against fungal infection. While most studies about commensal and pathogenic interaction of Candida species with host epithelia focus on the interaction with mucosal surfaces such as the vaginal and gastrointestinal epithelia, less is known about the mechanisms underlying Candida interaction with the skin. In this review, we focus on the ecology and molecular pathogenesis of Candida species on the skin and give an overview of defense mechanisms against C. albicans in this context. We also discuss new research avenues in dermal infection, including the involvement of neurons, fibroblasts, and commensal bacteria in both mouse and human model systems.
      PubDate: 2017-06-07
      DOI: 10.3390/microorganisms5020032
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 33: Purine Acquisition and Synthesis by
           Human Fungal Pathogens

    • Authors: Jessica Chitty, James Fraser
      First page: 33
      Abstract: While members of the Kingdom Fungi are found across many of the world’s most hostile environments, only a limited number of species can thrive within the human host. The causative agents of the most common invasive fungal infections are Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans. During the infection process, these fungi must not only combat the host immune system while adapting to dramatic changes in temperature and pH, but also acquire sufficient nutrients to enable growth and dissemination in the host. One class of nutrients required by fungi, which is found in varying concentrations in their environmental niches and the human host, is the purines. These nitrogen-containing heterocycles are one of the most abundant organic molecules in nature and are required for roles as diverse as signal transduction, energy metabolism and DNA synthesis. The most common life-threatening fungal pathogens can degrade, salvage and synthesize de novo purines through a number of enzymatic steps that are conserved. While these enable them to adapt to the changing purine availability in the environment, only de novo purine biosynthesis is essential during infection and therefore an attractive antimycotic target.
      PubDate: 2017-06-08
      DOI: 10.3390/microorganisms5020033
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 34: Comment on: “Melanisation of
           Aspergillus terreus—Is Butyrolactone I Involved in the Regulation of
           Both DOPA and DHN Types of Pigments in Submerged Culture'
           Microorganisms 2017, 5, 22”

    • Authors: Elena Geib, Matthias Brock
      First page: 34
      Abstract: A recent article by Palonen et al. describes the effect of butyrolactone I on the expression of a secondary metabolite biosynthesis gene cluster from Aspergillus terreus that shows similarities to fusarubin biosynthesis gene clusters from Fusarium species. The authors claim that two different types of pigments are formed in Aspergillus terreus conidia, whereby one pigment is termed a DOPA-type melanin and the second a DHN-type melanin. Unfortunately, the terminology of the classification of melanin-types requires revision as Asp-melanin present in A. terreus conidia is clearly distinct from DOPA-melanins. In addition, some hypotheses in this manuscript are based on questionable data published previously, resulting in incorrect conclusions. Finally, as biochemical data are lacking and metabolite production is only deduced from bioinformatics and transcriptomic data, the production of a second pigment type in A. terreus conidia appears highly speculative.
      PubDate: 2017-06-21
      DOI: 10.3390/microorganisms5020034
      Issue No: Vol. 5, No. 2 (2017)
  • Microorganisms, Vol. 5, Pages 2: Acknowledgement to Reviewers of
           Microorganisms in 2016

    • Authors: Microorganisms Editorial Office
      First page: 2
      Abstract: n/a
      PubDate: 2017-01-11
      DOI: 10.3390/microorganisms5010002
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 3: Using Network Extracted Ontologies to
           Identify Novel Genes with Roles in Appressorium Development in the Rice
           Blast Fungus Magnaporthe oryzae

    • Authors: Ryan Ames
      First page: 3
      Abstract: Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.
      PubDate: 2017-01-17
      DOI: 10.3390/microorganisms5010003
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 4: Phylogenetic Heatmaps Highlight
           Composition Biases in Sequenced Reads

    • Authors: Sulbha Choudhari, Andrey Grigoriev
      First page: 4
      Abstract: Due to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs), a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups. This method is well suited for finding noise and biases when comparing metagenomics samples. We apply PGHMs to detect noise and bias in the data produced with different DNA extraction protocols, different sequencing platforms and different experimental frameworks. In parallel, we use principal component analysis displaying different clustering of sequences from each sample to support our findings and illustrate the utility of PGHMs. We considered contributions of the read length and GC-content variation and observed that in most cases biases were generally due to the GC-content of the reads.
      PubDate: 2017-01-24
      DOI: 10.3390/microorganisms5010004
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 5: Fluorescence Lectin Bar-Coding of
           Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate
           Forming Microorganisms

    • Authors: Thomas Neu, Ute Kuhlicke
      First page: 5
      Abstract: Microbial biofilm systems are defined as interface-associated microorganisms embedded into a self-produced matrix. The extracellular matrix represents a continuous challenge in terms of characterization and analysis. The tools applied in more detailed studies comprise extraction/chemical analysis, molecular characterization, and visualisation using various techniques. Imaging by laser microscopy became a standard tool for biofilm analysis, and, in combination with fluorescently labelled lectins, the glycoconjugates of the matrix can be assessed. By employing this approach a wide range of pure culture biofilms from different habitats were examined using the commercially available lectins. From the results, a binary barcode pattern of lectin binding can be generated. Furthermore, the results can be fine-tuned and transferred into a heat map according to signal intensity. The lectin barcode approach is suggested as a useful tool for investigating the biofilm matrix characteristics and dynamics at various levels, e.g. bacterial cell surfaces, adhesive footprints, individual microcolonies, and the gross biofilm or bio-aggregate. Hence fluorescence lectin bar-coding (FLBC) serves as a basis for a subsequent tailor-made fluorescence lectin-binding analysis (FLBA) of a particular biofilm. So far, the lectin approach represents the only tool for in situ characterization of the glycoconjugate makeup in biofilm systems.  Furthermore, lectin staining lends itself to other fluorescence techniques in order to correlate it with cellular biofilm constituents in general and glycoconjugate producers in particular.
      PubDate: 2017-02-10
      DOI: 10.3390/microorganisms5010005
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 6: Effects of Dietary Yogurt on the Healthy
           Human Gastrointestinal (GI) Microbiome

    • Authors: Daniel Lisko, G. Johnston, Carl Johnston
      First page: 6
      Abstract: The gastrointestinal (GI) tract performs key functions that regulate the relationship between the host and the microbiota. Research has shown numerous benefits of probiotic intake in the modulation of immune responses and human metabolic processes. However, unfavorable attention has been paid to temporal changes of the microbial composition and diversity of the GI tract. This study aimed to investigate the effects of yogurt consumption on the GI microbiome bacteria community composition, structure and diversity during and after a short-term period (42 days). We used a multi-approach combining classical fingerprinting techniques (T-RFLPs), Sanger analyses and Illumina MiSeq 16S rRNA gene amplicon sequencing to elucidate bacterial communities and Lactobacilli and Bifidobacteria populations within healthy adults that consume high doses of yogurt daily. Results indicated that overall GI microbial community and diversity was method-dependent, yet we found individual specific changes in bacterial composition and structure in healthy subjects that consumed high doses of yogurt throughout the study.
      PubDate: 2017-02-15
      DOI: 10.3390/microorganisms5010006
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 7: Presence of Calcium Lowers the Expansion
           of Bacillus subtilis Colony Biofilms

    • Authors: Eisha Mhatre, Anandaroopan Sundaram, Theresa Hölscher, Mike Mühlstädt, Jörg Bossert, Ákos Kovács
      First page: 7
      Abstract: Robust colony formation by Bacillus subtilis is recognized as one of the sessile, multicellular lifestyles of this bacterium. Numerous pathways and genes are responsible for the architecturally complex colony structure development. Cells in the biofilm colony secrete extracellular polysaccharides (EPS) and protein components (TasA and the hydrophobin BslA) that hold them together and provide a protective hydrophobic shield. Cells also secrete surfactin with antimicrobial as well as surface tension reducing properties that aid cells to colonize the solid surface. Depending on the environmental conditions, these secreted components of the colony biofilm can also promote the flagellum-independent surface spreading of B. subtilis, called sliding. In this study, we emphasize the influence of Ca2+ in the medium on colony expansion of B. subtilis. Interestingly, the availability of Ca2+ has no major impact on the induction of complex colony morphology. However, in the absence of this divalent ion, peripheral cells of the colony expand radially at later stages of development, causing colony size to increase. We demonstrate that the secreted extracellular compounds, EPS, BslA, and surfactin facilitate colony expansion after biofilm maturation. We propose that Ca2+ hinders biofilm colony expansion by modifying the amphiphilic properties of surfactin.
      PubDate: 2017-02-16
      DOI: 10.3390/microorganisms5010007
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 8: Genome Sequence of Rhodoferax antarcticus
           ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic
           Microbial Mat

    • Authors: Jennifer Baker, Carli Riester, Blair Skinner, Austin Newell, Wesley Swingley, Michael Madigan, Deborah Jung, Marie Asao, Min Chen, Patrick Loughlin, Hao Pan, Yuankui Lin, Yaqiong Li, Jacob Shaw, Mindy Prado, Chris Sherman, Joseph Tang, Robert Blankenship, Tingting Zhao, Jeffrey Touchman, W. Sattley
      First page: 8
      Abstract: Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3), but not light-harvesting complex 2 (LH2), were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.
      PubDate: 2017-02-21
      DOI: 10.3390/microorganisms5010008
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 9: Microbial Biofilms and Chronic Wounds

    • Authors: Amin Omar, J. Wright, Gregory Schultz, Robert Burrell, Patricia Nadworny
      First page: 9
      Abstract: Background is provided on biofilms, including their formation, tolerance mechanisms, structure, and morphology within the context of chronic wounds. The features of biofilms in chronic wounds are discussed in detail, as is the impact of biofilm on wound chronicity. Difficulties associated with the use of standard susceptibility tests (minimum inhibitory concentrations or MICs) to determine appropriate treatment regimens for, or develop new treatments for use in, chronic wounds are discussed, with alternate test methods specific to biofilms being recommended. Animal models appropriate for evaluating biofilm treatments are also described. Current and potential future therapies for treatment of biofilm-containing chronic wounds, including probiotic therapy, virulence attenuation, biofilm phenotype expression attenuation, immune response suppression, and aggressive debridement combined with antimicrobial dressings, are described.
      PubDate: 2017-03-07
      DOI: 10.3390/microorganisms5010009
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 10: Lactobacillus gasseri PA-3 Uses the
           Purines IMP, Inosine and Hypoxanthine and Reduces their Absorption in Rats

    • Authors: Naruomi Yamada, Chizuru Saito-Iwamoto, Marie Nakamura, Misato Soeda, Yoshika Chiba, Hiroshi Kano, Yukio Asami
      First page: 10
      Abstract: Excessive intake of purine-rich foods elevates serum levels of uric acid. Animal and fish meats contain high amounts of inosine and its related purines, and the reduction of taking those purines is crucial for the improvement of serum uric acid levels. We previously showed that Lactobacillus gasseri PA-3 (PA-3) incorporates adenosine and its related purines and that oral treatment with PA-3 reduced adenosine absorption in rats. This study investigated whether PA-3 also incorporates IMP (inosine 5′-monophosphate), inosine, and hypoxanthine, and whether it reduces their absorption in rats. PA-3 was incubated in vitro with radioisotope (RI)-labeled IMP, inosine, and hypoxanthine, and the incorporation of these compounds by PA-3 was evaluated. In addition, rats were orally administered PA-3 along with RI-labeled inosine 5′-monophosphate, inosine, or hypoxanthine, and the ability of PA-3 to attenuate the absorption of these purines was determined. PA-3 incorporated all three purines and displayed greater proliferation in the presence than in the absence of these purines. Oral administration of PA-3 to rats reduced the absorption of IMP, inosine, and hypoxanthine. These results indicate that PA-3 reduces the absorption of purines contained in foods and it is expected that PA-3 contributes attenuation of the excessive intake of dietary purines.
      PubDate: 2017-03-08
      DOI: 10.3390/microorganisms5010010
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 11: The Food Production Environment and the
           Development of Antimicrobial Resistance in Human Pathogens of Animal

    • Authors: Manjusha Lekshmi, Parvathi Ammini, Sanath Kumar, Manuel F. Varela
      First page: 11
      Abstract: Food-borne pathogens are a serious human health concern worldwide, and the emergence of antibiotic-resistant food pathogens has further confounded this problem. Once-highly-efficacious antibiotics are gradually becoming ineffective against many important pathogens, resulting in severe treatment crises. Among several reasons for the development and spread of antimicrobial resistance, their overuse in animal food production systems for purposes other than treatment of infections is prominent. Many pathogens of animals are zoonotic, and therefore any development of resistance in pathogens associated with food animals can spread to humans through the food chain. Human infections by antibiotic-resistant pathogens such as Campylobacter spp., Salmonella spp., Escherichia coli and Staphylococcus aureus are increasing. Considering the human health risk due to emerging antibiotic resistance in food animal–associated bacteria, many countries have banned the use of antibiotic growth promoters and the application in animals of antibiotics critically important in human medicine. Concerted global efforts are necessary to minimize the use of antimicrobials in food animals in order to control the development of antibiotic resistance in these systems and their spread to humans via food and water.
      PubDate: 2017-03-14
      DOI: 10.3390/microorganisms5010011
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 12: Transcriptomic Complexity of Aspergillus
           terreus Velvet Gene Family under the Influence of Butyrolactone I

    • Authors: Elina Palonen, Sheetal Raina, Annika Brandt, Jussi Meriluoto, Tajalli Keshavarz, Juhani Soini
      First page: 12
      Abstract: Filamentous fungi of the Ascomycota phylum are known to contain a family of conserved conidiation regulating proteins with distinctive velvet domains. In Aspergilli, this velvet family includes four proteins, VeA, VelB, VelC and VosA, and is involved in conidiation and secondary metabolism along with a global regulator LaeA. In A. terreus, the overexpression of LaeA has been observed to increase the biogenesis of the pharmaceutically-important secondary metabolite, lovastatin, while the role of the velvet family has not been studied. The secondary metabolism and conidiation of A. terreus have also been observed to be increased by butyrolactone I in a quorum-sensing manner. An enlightenment of the interplay of these regulators will give potential advancement to the industrial use of this fungus, as well as in resolving the pathogenic features. In this study, the Aspergillus terreus MUCL 38669 transcriptome was strand-specifically sequenced to enable an in-depth gene expression analysis to further investigate the transcriptional role of butyrolactone I in these processes. The sequenced transcriptome revealed intriguing properties of the velvet family transcripts, including the regulator laeA, and uncovered the velC gene in A. terreus. The reliability refining microarray gene expression analysis disclosed a positive regulatory role for butyrolactone I in laeA expression, as well as an influence on the expression of the canonical conidiation-regulating genes under submerged culture. All of this supports the suggested regulative role of butyrolactone I in A. terreus secondary metabolism, as well as conidiation.
      PubDate: 2017-03-14
      DOI: 10.3390/microorganisms5010012
      Issue No: Vol. 5, No. 1 (2017)
  • Microorganisms, Vol. 5, Pages 13: Immune Response to Coccidioidomycosis
           and the Development of a Vaccine

    • Authors: Natalia Castro-Lopez, Chiung-Yu Hung
      First page: 13
      Abstract: Coccidioidomycosis is a fungal infection caused by Coccidioides posadasii and Coccidioides immitis. It is estimated that 150,000 new infections occur in the United States each year. The incidence of this infection continues to rise in endemic regions. There is an urgent need for the development of better therapeutic drugs and a vaccine against coccidioidomycosis. This review discusses the features of host innate and adaptive immune responses to Coccidioides infection. The focus is on the recent advances in the immune response and host-pathogen interactions, including the recognition of spherules by the host and defining the signal pathways that guide the development of the adaptive T-cell response to Coccidioides infection. Also discussed is an update on progress in developing a vaccine against these fungal pathogens.
      PubDate: 2017-03-16
      DOI: 10.3390/microorganisms5010013
      Issue No: Vol. 5, No. 1 (2017)
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-2016