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Microorganisms
Volume 6
Issue 2
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Microorganisms, Volume 6, Issue 2 (June 2018) – 28 articles

Cover Story (view full-size image): Mars is currently considered relatively inhospitable due to its freezing temperatures, among other factors. Should life currently exist on the planet, it would likely consist of subsurface microorganisms capable of surviving and/or metabolizing at cold temperatures. Methanogens are found in a wide variety of environments on Earth, ranging from seafloor hydrothermal vents to arctic permafrost. Two non-psychrophilic species of methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii, have been shown capable of active growth following long-term exposure (~4 years) to freezing temperatures. View the paper here.
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21 pages, 317 KiB  
Review
Mucus-Pathogen Interactions in the Gastrointestinal Tract of Farmed Animals
by Macarena P. Quintana-Hayashi, Médea Padra, János Tamás Padra, John Benktander and Sara K. Lindén
Microorganisms 2018, 6(2), 55; https://doi.org/10.3390/microorganisms6020055 - 18 Jun 2018
Cited by 51 | Viewed by 7345
Abstract
Gastrointestinal infections cause significant challenges and economic losses in animal husbandry. As pathogens becoming resistant to antibiotics are a growing concern worldwide, alternative strategies to treat infections in farmed animals are necessary in order to decrease the risk to human health and increase [...] Read more.
Gastrointestinal infections cause significant challenges and economic losses in animal husbandry. As pathogens becoming resistant to antibiotics are a growing concern worldwide, alternative strategies to treat infections in farmed animals are necessary in order to decrease the risk to human health and increase animal health and productivity. Mucosal surfaces are the most common route used by pathogens to enter the body. The mucosal surface that lines the gastrointestinal tract is covered by a continuously secreted mucus layer that protects the epithelial surface. The mucus layer is the first barrier the pathogen must overcome for successful colonization, and is mainly composed of densely glycosylated proteins called mucins. The vast array of carbohydrate structures present on the mucins provide an important setting for host-pathogen interactions. This review summarizes the current knowledge on gastrointestinal mucins and their role during infections in farmed animals. We examine the interactions between mucins and animal pathogens, with a focus on how pathogenic bacteria can modify the mucin environment in the gut, and how this in turn affects pathogen adhesion and growth. Finally, we discuss analytical challenges and complexities of the mucus-based defense, as well as its potential to control infections in farmed animals. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
12 pages, 842 KiB  
Opinion
Bacteriophages as New Human Viral Pathogens
by George Tetz and Victor Tetz
Microorganisms 2018, 6(2), 54; https://doi.org/10.3390/microorganisms6020054 - 16 Jun 2018
Cited by 59 | Viewed by 11399
Abstract
The pathogenesis of numerous human multifaceted devastating diseases, including a variety of neurodegenerative and autoimmune diseases, is associated with alterations in the gut microbiota; however, the underlying mechanisms are not completely understood. Our recent human metagenome and phagobiota proteome analyses and studies in [...] Read more.
The pathogenesis of numerous human multifaceted devastating diseases, including a variety of neurodegenerative and autoimmune diseases, is associated with alterations in the gut microbiota; however, the underlying mechanisms are not completely understood. Our recent human metagenome and phagobiota proteome analyses and studies in relevant animal models suggested that bacterial viruses might be implicated in the progression and maintenance of at least some pathologies, including those associated with protein misfolding. Here, for the first time, we propose the concept of bacteriophages as human pathogens. We suggest that bacterial viruses have different ways to directly and indirectly interact with eukaryotic cells and proteins, leading to human diseases. Furthermore, we suggest different causes of bacteriophages infection on the basis of the unique ways of interplay of phages, microbiota, and the human host. This concept opens a discussion of the role of bacteriophages as previously overlooked pathogenic factors and suggests that bacterial viruses have to be further explored as a diagnostic and treatment target for therapeutic intervention. Full article
(This article belongs to the Special Issue Microbiome Gut Brain Axis)
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18 pages, 848 KiB  
Review
Mucus: An Underestimated Gut Target for Environmental Pollutants and Food Additives
by Kévin Gillois, Mathilde Lévêque, Vassilia Théodorou, Hervé Robert and Muriel Mercier-Bonin
Microorganisms 2018, 6(2), 53; https://doi.org/10.3390/microorganisms6020053 - 15 Jun 2018
Cited by 60 | Viewed by 10081
Abstract
Synthetic chemicals (environmental pollutants, food additives) are widely used for many industrial purposes and consumer-related applications, which implies, through manufactured products, diet, and environment, a repeated exposure of the general population with growing concern regarding health disorders. The gastrointestinal tract is the first [...] Read more.
Synthetic chemicals (environmental pollutants, food additives) are widely used for many industrial purposes and consumer-related applications, which implies, through manufactured products, diet, and environment, a repeated exposure of the general population with growing concern regarding health disorders. The gastrointestinal tract is the first physical and biological barrier against these compounds, and thus their first target. Mounting evidence indicates that the gut microbiota represents a major player in the toxicity of environmental pollutants and food additives; however, little is known on the toxicological relevance of the mucus/pollutant interplay, even though mucus is increasingly recognized as essential in gut homeostasis. Here, we aimed at describing how environmental pollutants (heavy metals, pesticides, and other persistent organic pollutants) and food additives (emulsifiers, nanomaterials) might interact with mucus and mucus-related microbial species; that is, “mucophilic” bacteria such as mucus degraders. This review highlights that intestinal mucus, either directly or through its crosstalk with the gut microbiota, is a key, yet underestimated gut player that must be considered for better risk assessment and management of environmental pollution. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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10 pages, 1344 KiB  
Review
Chemical Elicitors of Antibiotic Biosynthesis in Actinomycetes
by Anton P. Tyurin, Vera A. Alferova and Vladimir A. Korshun
Microorganisms 2018, 6(2), 52; https://doi.org/10.3390/microorganisms6020052 - 8 Jun 2018
Cited by 22 | Viewed by 6678
Abstract
Whole genome sequencing of actinomycetes has uncovered a new immense realm of microbial chemistry and biology. Most biosynthetic gene clusters present in genomes were found to remain “silent” under standard cultivation conditions. Some small molecules—chemical elicitors—can be used to induce the biosynthesis of [...] Read more.
Whole genome sequencing of actinomycetes has uncovered a new immense realm of microbial chemistry and biology. Most biosynthetic gene clusters present in genomes were found to remain “silent” under standard cultivation conditions. Some small molecules—chemical elicitors—can be used to induce the biosynthesis of antibiotics in actinobacteria and to expand the chemical diversity of secondary metabolites. Here, we outline a brief account of the basic principles of the search for regulators of this type and their application. Full article
(This article belongs to the Special Issue Actinobacteria and Myxobacteria—Important Resources for Novel Antibiotics)
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12 pages, 1615 KiB  
Article
Development of Versatile Vectors for Heterologous Expression in Bacillus
by Øivind Larsen and Gro Elin Kjæreng Bjerga
Microorganisms 2018, 6(2), 51; https://doi.org/10.3390/microorganisms6020051 - 7 Jun 2018
Cited by 8 | Viewed by 5686
Abstract
The discovery of new enzymes for industrial application relies on a robust discovery pipeline. Such a pipeline should facilitate efficient molecular cloning, recombinant expression and functional screening procedures. Previously, we have developed a vector set for heterologous expression in Escherichia coli. Here, [...] Read more.
The discovery of new enzymes for industrial application relies on a robust discovery pipeline. Such a pipeline should facilitate efficient molecular cloning, recombinant expression and functional screening procedures. Previously, we have developed a vector set for heterologous expression in Escherichia coli. Here, we supplement the catalogue with vectors for expression in Bacillus. The vectors are made compatible with a versatile cloning procedure based on type IIS restriction enzymes and T4 DNA ligase, and encompass an effective counter-selection procedure and complement the set of vectors with options for secreted expression. We validate the system with expression of recombinant subtilisins, which are generally challenging to express in a heterologous system. The complementarity of the E. coli and Bacillus systems allows rapid switching between the two commonly used hosts without comprehensive intermediate cloning steps. The vectors described are not limited to the expression of certain enzymes, but could also be applied for the expression of other enzymes for more generalized enzyme discovery or development. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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15 pages, 1144 KiB  
Review
Antifungal Peptides of the AFP Family Revisited: Are These Cannibal Toxins?
by Vera Meyer and Sascha Jung
Microorganisms 2018, 6(2), 50; https://doi.org/10.3390/microorganisms6020050 - 2 Jun 2018
Cited by 25 | Viewed by 5840
Abstract
The emergence and spread of pathogenic fungi resistant to currently used antifungal drugs represents a serious challenge for medicine and agriculture. The use of smart antimicrobials, so-called “dirty drugs” which affect multiple cellular targets, is one strategy to prevent resistance. Of special interest [...] Read more.
The emergence and spread of pathogenic fungi resistant to currently used antifungal drugs represents a serious challenge for medicine and agriculture. The use of smart antimicrobials, so-called “dirty drugs” which affect multiple cellular targets, is one strategy to prevent resistance. Of special interest is the exploitation of the AFP family of antimicrobial peptides, which include its founding member AFP from Aspergillus giganteus. This latter is a highly potent inhibitor of chitin synthesis and affects plasma membrane integrity in many human and plant pathogenic fungi. A transcriptomic meta-analysis of the afp-encoding genes in A. giganteus and A. niger predicts a role for these proteins during asexual sporulation, autophagy, and nutrient recycling, suggesting that AFPs are molecules important for the survival of A. niger and A. giganteus under nutrient limitation. In this review, we discuss parallels which exist between AFPs and bacterial cannibal toxins and provide arguments that the primary function of AFPs could be to kill genetically identical siblings. We hope that this review inspires computational and experimental biologists studying alternative explanations for the nature and function of antimicrobial peptides beyond the general assumption that they are mere defense molecules to fight competitors. Full article
(This article belongs to the Special Issue Antimicrobial Proteins in Filamentous Fungi)
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18 pages, 3209 KiB  
Article
A Sensitive and Rapid Method to Determine the Adhesion Capacity of Probiotics and Pathogenic Microorganisms to Human Gastrointestinal Mucins
by Bélinda Ringot-Destrez, Zéa D’Alessandro, Jean-Marie Lacroix, Muriel Mercier-Bonin, Renaud Léonard and Catherine Robbe-Masselot
Microorganisms 2018, 6(2), 49; https://doi.org/10.3390/microorganisms6020049 - 29 May 2018
Cited by 18 | Viewed by 5836
Abstract
Mucus is the habitat for the microorganisms, bacteria and yeast that form the commensal flora. Mucins, the main macromolecules of mucus, and more specifically, the glycans that cover them, play essential roles in microbial gastrointestinal colonization. Probiotics and pathogens must also colonize mucus [...] Read more.
Mucus is the habitat for the microorganisms, bacteria and yeast that form the commensal flora. Mucins, the main macromolecules of mucus, and more specifically, the glycans that cover them, play essential roles in microbial gastrointestinal colonization. Probiotics and pathogens must also colonize mucus to have lasting positive or deleterious effects. The question of which mucin-harboured glycan motifs favour the adhesion of specific microorganisms remains very poorly studied. In the current study, a simple test based on the detection of fluorescent-labeled microorganisms raised against microgram amounts of mucins spotted on nitrocellulose was developed. The adhesion of various probiotic, commensal and pathogenic microorganisms was evaluated on a panel of human purified gastrointestinal mucins and compared with that of commercially available pig gastric mucins (PGM) and of mucins secreted by the colonic cancer cell line HT29-MTX. The latter two proved to be very poor indicators of adhesion capacity on intestinal mucins. Our results show that the nature of the sialylated cores of O-glycans, determined by MALDI MS-MS analysis, potentially enables sialic acid residues to modulate the adhesion of microorganisms either positively or negatively. Other identified factors affecting the adhesion propensity were O-glycan core types and the presence of blood group motifs. This test should help to select probiotics with enhanced adhesion capabilities as well as deciphering the role of specific mucin glycotopes on microbial adhesion. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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8 pages, 1425 KiB  
Article
Comparing the Recombinant Protein Production Potential of Planktonic and Biofilm Cells
by Alexandra Soares, Luciana Calheiros Gomes and Filipe José Mergulhão
Microorganisms 2018, 6(2), 48; https://doi.org/10.3390/microorganisms6020048 - 24 May 2018
Cited by 9 | Viewed by 4064
Abstract
Recombinant protein production in bacterial cells is commonly performed using planktonic cultures. However, the natural state for many bacteria is living in communities attached to surfaces forming biofilms. In this work, a flow cell system was used to compare the production of a [...] Read more.
Recombinant protein production in bacterial cells is commonly performed using planktonic cultures. However, the natural state for many bacteria is living in communities attached to surfaces forming biofilms. In this work, a flow cell system was used to compare the production of a model recombinant protein (enhanced green fluorescent protein, eGFP) between planktonic and biofilm cells. The fluorometric analysis revealed that when the system was in steady state, the average specific eGFP production from Escherichia coli biofilm cells was 10-fold higher than in planktonic cells. Additionally, epifluorescence microscopy was used to determine the percentage of eGFP-expressing cells in both planktonic and biofilm populations. In steady state, the percentage of planktonic-expressing cells oscillated around 5%, whereas for biofilms eGFP-expressing cells represented on average 21% of the total cell population. Therefore, the combination of fluorometric and microscopy data allowed us to conclude that E. coli biofilm cells can have a higher recombinant protein production capacity when compared to their planktonic counterparts. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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17 pages, 1346 KiB  
Review
Polyionic Tags as Enhancers of Protein Solubility in Recombinant Protein Expression
by Vasiliki Paraskevopoulou and Franco H. Falcone
Microorganisms 2018, 6(2), 47; https://doi.org/10.3390/microorganisms6020047 - 23 May 2018
Cited by 84 | Viewed by 13019
Abstract
Since the introduction of recombinant protein expression in the second half of the 1970s, the growth of the biopharmaceutical field has been rapid and protein therapeutics has come to the foreground. Biophysical and structural characterisation of recombinant proteins is the essential prerequisite for [...] Read more.
Since the introduction of recombinant protein expression in the second half of the 1970s, the growth of the biopharmaceutical field has been rapid and protein therapeutics has come to the foreground. Biophysical and structural characterisation of recombinant proteins is the essential prerequisite for their successful development and commercialisation as therapeutics. Despite the challenges, including low protein solubility and inclusion body formation, prokaryotic host systems and particularly Escherichia coli, remain the system of choice for the initial attempt of production of previously unexpressed proteins. Several different approaches have been adopted, including optimisation of growth conditions, expression in the periplasmic space of the bacterial host or co-expression of molecular chaperones, to assist correct protein folding. A very commonly employed approach is also the use of protein fusion tags that enhance protein solubility. Here, a range of experimentally tested peptide tags, which present specific advantages compared to protein fusion tags and the concluding remarks of these experiments are reviewed. Finally, a concept to design solubility-enhancing peptide tags based on a protein’s pI is suggested. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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10 pages, 228 KiB  
Review
The Genus Wallemia—From Contamination of Food to Health Threat
by Janja Zajc and Nina Gunde-Cimerman
Microorganisms 2018, 6(2), 46; https://doi.org/10.3390/microorganisms6020046 - 21 May 2018
Cited by 62 | Viewed by 7156
Abstract
The fungal genus Wallemia of the order Wallemiales (Wallemiomycotina, Basidiomycota) comprises the most xerotolerant, xerophilic and also halophilic species worldwide. Wallemia spp. are found in various osmotically challenged environments, such as dry, salted, or highly sugared foods, dry feed, hypersaline waters of solar [...] Read more.
The fungal genus Wallemia of the order Wallemiales (Wallemiomycotina, Basidiomycota) comprises the most xerotolerant, xerophilic and also halophilic species worldwide. Wallemia spp. are found in various osmotically challenged environments, such as dry, salted, or highly sugared foods, dry feed, hypersaline waters of solar salterns, salt crystals, indoor and outdoor air, and agriculture aerosols. Recently, eight species were recognized for the genus Wallemia, among which four are commonly associated with foods: W. sebi, W. mellicola, W. muriae and W. ichthyophaga. To date, only strains of W. sebi, W. mellicola and W. muriae have been reported to be related to human health problems, as either allergological conditions (e.g., farmer’s lung disease) or rare subcutaneous/cutaneous infections. Therefore, this allergological and infective potential, together with the toxins that the majority of Wallemia spp. produce even under saline conditions, defines these fungi as filamentous food-borne pathogenic fungi. Full article
(This article belongs to the Special Issue Human Pathogenic Filamentous Fungi from Food/Water and Mycotoxins from Water)
9 pages, 230 KiB  
Review
Risk Mitigation for Immunocompromised Consumers of Mucormycete Spoiled and Fermented Foods: Germane Guidance and Remaining Needs
by Abigail B. Snyder and Randy W. Worobo
Microorganisms 2018, 6(2), 45; https://doi.org/10.3390/microorganisms6020045 - 18 May 2018
Cited by 14 | Viewed by 5375
Abstract
Mucoralean invasive fungal infections, while unusual among the general population, have a high mortality rate among immunocompromised individuals who become infected. They are also common spoilage organisms in cultured dairy products, some fresh produce, and baked goods. Additionally, Mucor and Rhizopus spp. are [...] Read more.
Mucoralean invasive fungal infections, while unusual among the general population, have a high mortality rate among immunocompromised individuals who become infected. They are also common spoilage organisms in cultured dairy products, some fresh produce, and baked goods. Additionally, Mucor and Rhizopus spp. are utilized in the production of traditional fermented foods including mold ripened cheeses and fermented soy products. The risk that consumption of these foods poses to immunocompromised consumers has been previously identified. However, actionable guidance on implementation of appropriate dietary restrictions and microbial specification targets for food manufacturers serving these populations is scarce and is limited by insufficient data regarding traceback analysis in cases of invasive fungal infections where food is the suspected transmission vector. Culture-dependent and molecular subtyping methods, including whole genome sequencing, will improve identification of the point source. In turn, the empirically determined information on root-cause can best direct the development of appropriate food safety policies and programs. Full article
(This article belongs to the Special Issue Human Pathogenic Filamentous Fungi from Food/Water and Mycotoxins from Water)
15 pages, 2929 KiB  
Article
Binding of Helicobacter pylori to Human Gastric Mucins Correlates with Binding of TFF1
by Ciara Dunne, Julie Naughton, Gina Duggan, Catherine Loughrey, Michelle Kilcoyne, Lokesh Joshi, Stephen Carrington, Helen Earley, Steffen Backert, Catherine Robbe Masselot, Felicity E. B. May and Marguerite Clyne
Microorganisms 2018, 6(2), 44; https://doi.org/10.3390/microorganisms6020044 - 18 May 2018
Cited by 14 | Viewed by 5725
Abstract
Helicobacter pylori binds to the gastric mucin, MUC5AC, and to trefoil factor, TFF1, which has been shown to interact with gastric mucin. We examined the interactions of TFF1 and H. pylori with purified gastrointestinal mucins from different animal species and from humans printed [...] Read more.
Helicobacter pylori binds to the gastric mucin, MUC5AC, and to trefoil factor, TFF1, which has been shown to interact with gastric mucin. We examined the interactions of TFF1 and H. pylori with purified gastrointestinal mucins from different animal species and from humans printed on a microarray platform to investigate whether TFF1 may play a role in locating H. pylori in gastric mucus. TFF1 bound almost exclusively to human gastric mucins and did not interact with human colonic mucins. There was a strong correlation between binding of TFF1 and H. pylori to human gastric mucins, and between binding of both TFF1 and H. pylori to gastric mucins with that of Griffonia simplicifolia lectin-II, which is specific for terminal non-reducing α- or β-linked N-acetyl-d-glucosamine. These results suggest that TFF1 may help to locate H. pylori in a discrete layer of gastric mucus and hence restrain their interactions with epithelial cells. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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9 pages, 259 KiB  
Brief Report
Effect of UVC Radiation on Hydrated and Desiccated Cultures of Slightly Halophilic and Non-Halophilic Methanogenic Archaea: Implications for Life on Mars
by Navita Sinha and Timothy A. Kral
Microorganisms 2018, 6(2), 43; https://doi.org/10.3390/microorganisms6020043 - 12 May 2018
Cited by 4 | Viewed by 3885
Abstract
Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic [...] Read more.
Methanogens have been considered models for life on Mars for many years. In order to survive any exposure at the surface of Mars, methanogens would have to endure Martian UVC radiation. In this research, we irradiated hydrated and desiccated cultures of slightly halophilic Methanococcus maripaludis and non-halophilic Methanobacterium formicicum for various time intervals with UVC (254 nm) radiation. The survivability of the methanogens was determined by measuring methane concentrations in the headspace gas samples of culture tubes after re-inoculation of the methanogens into their growth-supporting media following exposure to UVC radiation. Hydrated M. maripaludis survived 24 h of UVC exposure, while in a desiccated condition they endured for 16 h. M. formicicum also survived UVC radiation for 24 h in a liquid state; however, in a desiccated condition, the survivability of M. formicicum was only 12 h. Some of the components of the growth media could have served as shielding agents that protected cells from damage caused by exposure to ultraviolet radiation. Overall, these results suggest that limited exposure (12–24 h) to UVC radiation on the surface of Mars would not necessarily be a limiting factor for the survivability of M. maripaludis and M. formicicum. Full article
(This article belongs to the Special Issue Anaerobic Microorganisms in Mars)
19 pages, 488 KiB  
Review
Genetic Tools and Techniques for Recombinant Expression in Thermophilic Bacillaceae
by Eivind B. Drejer, Sigrid Hakvåg, Marta Irla and Trygve Brautaset
Microorganisms 2018, 6(2), 42; https://doi.org/10.3390/microorganisms6020042 - 10 May 2018
Cited by 37 | Viewed by 8486
Abstract
Although Escherichia coli and Bacillus subtilis are the most prominent bacterial hosts for recombinant protein production by far, additional species are being explored as alternatives for production of difficult-to-express proteins. In particular, for thermostable proteins, there is a need for hosts able to [...] Read more.
Although Escherichia coli and Bacillus subtilis are the most prominent bacterial hosts for recombinant protein production by far, additional species are being explored as alternatives for production of difficult-to-express proteins. In particular, for thermostable proteins, there is a need for hosts able to properly synthesize, fold, and excrete these in high yields, and thermophilic Bacillaceae represent one potentially interesting group of microorganisms for such purposes. A number of thermophilic Bacillaceae including B. methanolicus, B. coagulans, B. smithii, B. licheniformis, Geobacillus thermoglucosidasius, G. kaustophilus, and G. stearothermophilus are investigated concerning physiology, genomics, genetic tools, and technologies, altogether paving the way for their utilization as hosts for recombinant production of thermostable and other difficult-to-express proteins. Moreover, recent successful deployments of CRISPR/Cas9 in several of these species have accelerated the progress in their metabolic engineering, which should increase their attractiveness for future industrial-scale production of proteins. This review describes the biology of thermophilic Bacillaceae and in particular focuses on genetic tools and methods enabling use of these organisms as hosts for recombinant protein production. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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20 pages, 2605 KiB  
Article
Regulation of Camphor Metabolism: Induction and Repression of Relevant Monooxygenases in Pseudomonas putida NCIMB 10007
by Andrew Willetts, Pamela Masters and Carol Steadman
Microorganisms 2018, 6(2), 41; https://doi.org/10.3390/microorganisms6020041 - 7 May 2018
Cited by 4 | Viewed by 5288
Abstract
For the first time, the differential rates of synthesis of all the key monooxygenases involved in the catabolism by Pseudomonas putida NCIMB 10007 of bicyclic (rac)-camphor to ∆2,5-3,4,4-trimethylpimelyl-CoA, the first aliphatic pathway intermediate, have been determined to help establish [...] Read more.
For the first time, the differential rates of synthesis of all the key monooxygenases involved in the catabolism by Pseudomonas putida NCIMB 10007 of bicyclic (rac)-camphor to ∆2,5-3,4,4-trimethylpimelyl-CoA, the first aliphatic pathway intermediate, have been determined to help establish the relevant induction profile of each of the oxygen-dependent enzymes. The efficacy of both relevant substrates and pathway metabolites as inducers has been established. Further, inhibitors with characterised functionality have been used to indicate that the pertinent regulatory controls operate at the level of transcription of the corresponding genes. Full article
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9 pages, 220 KiB  
Review
Pediatric Methicillin-Resistant Staphylococcus aureus Osteoarticular Infections
by Ashlesha Kaushik and Helen Kest
Microorganisms 2018, 6(2), 40; https://doi.org/10.3390/microorganisms6020040 - 4 May 2018
Cited by 15 | Viewed by 5087
Abstract
Osteoarticular infections (OSI) are a significant cause of hospitalizations and morbidity in young children. The pediatric patient with OSI presents unique challenges in diagnosis and management due to higher morbidity, effect on growth plate with associated long-lasting sequelae, and challenges in early identification [...] Read more.
Osteoarticular infections (OSI) are a significant cause of hospitalizations and morbidity in young children. The pediatric patient with OSI presents unique challenges in diagnosis and management due to higher morbidity, effect on growth plate with associated long-lasting sequelae, and challenges in early identification and management. Methicillin-resistant Staphylococcus aureus (MRSA), first described in the 1960s, has evolved rapidly to emerge as a predominant cause of OSI in children, and therefore empiric treatment for OSI should include an antibiotic effective against MRSA. Characterizing MRSA strains can be done by antimicrobial susceptibility testing, detection of Panton–Valentine leukocidin (PVL) gene, staphylococcal cassette chromosome mec (SCCmec) typing, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Worldwide, community-onset methicillin-resistant staphylococcal disease is widespread and is mainly associated with a PVL-producing clone, ST8/USA300. Many studies have implied a correlation between PVL genes and more severe infection. We review MRSA OSI along with the pertinent aspects of its pathogenesis, clinical spectrum, diagnosis, and current guidelines for management. Full article
(This article belongs to the Special Issue Staphylococcus aureus Infection and Antimicrobial Resistance)
26 pages, 14577 KiB  
Review
The Role of Glycans in Bacterial Adhesion to Mucosal Surfaces: How Can Single-Molecule Techniques Advance Our Understanding?
by Cécile Formosa-Dague, Mickaël Castelain, Hélène Martin-Yken, Karen Dunker, Etienne Dague and Marit Sletmoen
Microorganisms 2018, 6(2), 39; https://doi.org/10.3390/microorganisms6020039 - 4 May 2018
Cited by 32 | Viewed by 7278
Abstract
Bacterial adhesion is currently the subject of increased interest from the research community, leading to fast progress in our understanding of this complex phenomenon. Resent research within this field has documented the important roles played by glycans for bacterial surface adhesion, either through [...] Read more.
Bacterial adhesion is currently the subject of increased interest from the research community, leading to fast progress in our understanding of this complex phenomenon. Resent research within this field has documented the important roles played by glycans for bacterial surface adhesion, either through interaction with lectins or with other glycans. In parallel with this increased interest for and understanding of bacterial adhesion, there has been a growth in the sophistication and use of sensitive force probes for single-molecule and single cell studies. In this review, we highlight how the sensitive force probes atomic force microscopy (AFM) and optical tweezers (OT) have contributed to clarifying the mechanisms underlying bacterial adhesion to glycosylated surfaces in general and mucosal surfaces in particular. We also describe research areas where these techniques have not yet been applied, but where their capabilities appear appropriate to advance our understanding. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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23 pages, 1890 KiB  
Review
Comparison of Yeasts as Hosts for Recombinant Protein Production
by Antonio Milton Vieira Gomes, Talita Souza Carmo, Lucas Silva Carvalho, Frederico Mendonça Bahia and Nádia Skorupa Parachin
Microorganisms 2018, 6(2), 38; https://doi.org/10.3390/microorganisms6020038 - 29 Apr 2018
Cited by 192 | Viewed by 29496
Abstract
Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts [...] Read more.
Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria Escherichia coli to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, Saccharomyces cerevisiae was the dominant yeast host for heterologous protein production. Lately, other yeasts such as Komagataella sp., Kluyveromyces lactis, and Yarrowia lipolytica have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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14 pages, 1854 KiB  
Article
Recombinant Inga Laurina Trypsin Inhibitor (ILTI) Production in Komagataella Phaffii Confirms Its Potential Anti-Biofilm Effect and Reveals an Anti-Tumoral Activity
by Fábio C. Carneiro, Simone S. Weber, Osmar N. Silva, Ana Cristina Jacobowski, Marcelo H. S. Ramada, Maria L. R. Macedo, Octávio L. Franco and Nádia S. Parachin
Microorganisms 2018, 6(2), 37; https://doi.org/10.3390/microorganisms6020037 - 28 Apr 2018
Cited by 4 | Viewed by 4524
Abstract
Protease inhibitors have a broad biotechnological application ranging from medical drugs to anti-microbial agents. The Inga laurina trypsin inhibitor (ILTI) previously showed a great in vitro inhibitory effect under the adherence of Staphylococcus species, being a strong candidate for use as an anti-biofilm [...] Read more.
Protease inhibitors have a broad biotechnological application ranging from medical drugs to anti-microbial agents. The Inga laurina trypsin inhibitor (ILTI) previously showed a great in vitro inhibitory effect under the adherence of Staphylococcus species, being a strong candidate for use as an anti-biofilm agent. Nevertheless, this is found in small quantities in its sources, which impairs its utilization at an industrial scale. Within this context, heterologous production using recombinant microorganisms is one of the best options to scale up the recombinant protein production. Thus, this work aimed at utilizing Komagataella phaffii to produce recombinant ILTI. For this, the vector pPIC9K+ILTI was constructed and inserted into the genome of the yeast K. phaffii, strain GS115. The protein expression was highest after 48 h using methanol 1%. A matrix-assisted laser desorption ionization–time-of-flight (MALDI–TOF) analysis was performed to confirm the production of the recombinant ILTI and its activity was investigated trough inhibitory assays using the synthetic substrate Nα-Benzoyl-D,L-arginine p-nitroanilide hydrochloride (BAPNA). Finally, recombinant ILTI (rILTI) was used in assays, showing that there was no significant difference between native and recombinant ILTI in its inhibitory activity in biofilm formation. Anti-tumor assay against Ehrlich ascites tumor (EAT) cells showed that rILTI has a potential anti-tumoral effect, showing the same effect as Melittin when incubated for 48 h in concentrations above 25 µg/mL. All together the results suggests broad applications for rILTI. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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16 pages, 337 KiB  
Review
Genotypic Features of Clinical and Bovine Escherichia coli O157 Strains Isolated in Countries with Different Associated-Disease Incidences
by Luis Pianciola and Marta Rivas
Microorganisms 2018, 6(2), 36; https://doi.org/10.3390/microorganisms6020036 - 27 Apr 2018
Cited by 21 | Viewed by 4400
Abstract
There is great geographical variation in the frequency of Escherichia coli O157 infections that correlates with important differences in the bovine reservoir of each country. Our group carried out a broad molecular characterization of human and bovine E. coli O157 strains circulating in [...] Read more.
There is great geographical variation in the frequency of Escherichia coli O157 infections that correlates with important differences in the bovine reservoir of each country. Our group carried out a broad molecular characterization of human and bovine E. coli O157 strains circulating in Argentina using different methodologies. Our data allows us to conclude that in Argentina, a high homogeneity is observed in both cattle and human strains, with almost exclusive circulation of strains belonging to the hypervirulent clade 8 described by Manning. The aim of this review was to compare the genetic background of E. coli O157 strains isolated in countries that have conducted similar studies, to try to correlate specific O157 genotypes with the incidence and severity of E. coli O157 associated diseases. The characteristics of the strains that cause disease in humans reflect the predominant genotypes in cattle in each of the countries analyzed. The main features clearly linked to high incidence or severity of E. coli O157 infections are lineage-specific polymorphism assay-6 lineage I/II, clade 8 strains and probably, clade 6 strains, the stx2a/stx2c genotype, the presence of q933 and q21 simultaneously, and putative virulence factor EC_3286. In countries with an absence of these features in O157 strains, the overall incidence of O157 disease is low. Argentina, where these characteristics are detected in most strains, shows the highest incidence of hemolytic uremic syndrome (HUS) worldwide. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
32 pages, 16571 KiB  
Review
Harnessing the Power of Microbiome Assessment Tools as Part of Neuroprotective Nutrition and Lifestyle Medicine Interventions
by Miguel Toribio-Mateas
Microorganisms 2018, 6(2), 35; https://doi.org/10.3390/microorganisms6020035 - 25 Apr 2018
Cited by 20 | Viewed by 52554
Abstract
An extensive body of evidence documents the importance of the gut microbiome both in health and in a variety of human diseases. Cell and animal studies describing this relationship abound, whilst clinical studies exploring the associations between changes in gut microbiota and the [...] Read more.
An extensive body of evidence documents the importance of the gut microbiome both in health and in a variety of human diseases. Cell and animal studies describing this relationship abound, whilst clinical studies exploring the associations between changes in gut microbiota and the corresponding metabolites with neurodegeneration in the human brain have only begun to emerge more recently. Further, the findings of such studies are often difficult to translate into simple clinical applications that result in measurable health outcomes. The purpose of this paper is to appraise the literature on a select set of faecal biomarkers from a clinician’s perspective. This practical review aims to examine key physiological processes that influence both gastrointestinal, as well as brain health, and to discuss how tools such as the characterisation of commensal bacteria, the identification of potential opportunistic, pathogenic and parasitic organisms and the quantification of gut microbiome biomarkers and metabolites can help inform clinical decisions of nutrition and lifestyle medicine practitioners. Full article
(This article belongs to the Special Issue Microbiome Gut Brain Axis)
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24 pages, 3022 KiB  
Article
Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars
by Rebecca L. Mickol, Sarah K. Laird and Timothy A. Kral
Microorganisms 2018, 6(2), 34; https://doi.org/10.3390/microorganisms6020034 - 23 Apr 2018
Cited by 11 | Viewed by 5801
Abstract
Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable [...] Read more.
Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii, were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars. Full article
(This article belongs to the Special Issue Anaerobic Microorganisms in Mars)
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20 pages, 407 KiB  
Review
Intracellular Bacterial Infections: A Challenge for Developing Cellular Mediated Immunity Vaccines for Farmed Fish
by Hetron Mweemba Munang’andu
Microorganisms 2018, 6(2), 33; https://doi.org/10.3390/microorganisms6020033 - 22 Apr 2018
Cited by 40 | Viewed by 8199
Abstract
Aquaculture is one of the most rapidly expanding farming systems in the world. Its rapid expansion has brought with it several pathogens infecting different fish species. As a result, there has been a corresponding expansion in vaccine development to cope with the increasing [...] Read more.
Aquaculture is one of the most rapidly expanding farming systems in the world. Its rapid expansion has brought with it several pathogens infecting different fish species. As a result, there has been a corresponding expansion in vaccine development to cope with the increasing number of infectious diseases in aquaculture. The success of vaccine development for bacterial diseases in aquaculture is largely attributed to empirical vaccine designs based on inactivation of whole cell (WCI) bacteria vaccines. However, an upcoming challenge in vaccine design is the increase of intracellular bacterial pathogens that are not responsive to WCI vaccines. Intracellular bacterial vaccines evoke cellular mediated immune (CMI) responses that “kill” and eliminate infected cells, unlike WCI vaccines that induce humoral immune responses whose protective mechanism is neutralization of extracellular replicating pathogens by antibodies. In this synopsis, I provide an overview of the intracellular bacterial pathogens infecting different fish species in aquaculture, outlining their mechanisms of invasion, replication, and survival intracellularly based on existing data. I also bring into perspective the current state of CMI understanding in fish together with its potential application in vaccine development. Further, I highlight the immunological pitfalls that have derailed our ability to produce protective vaccines against intracellular pathogens for finfish. Overall, the synopsis put forth herein advocates for a shift in vaccine design to include CMI-based vaccines against intracellular pathogens currently adversely affecting the aquaculture industry. Full article
(This article belongs to the Special Issue Vaccine Informatics)
23 pages, 3273 KiB  
Article
Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators
by Federico Dorati, Glyn A. Barrett, Maria Sanchez-Contreras, Tanya Arseneault, Mateo San José, David J. Studholme, Jesús Murillo, Primitivo Caballero, Nicholas R. Waterfield, Dawn L. Arnold, Liz J. Shaw and Robert W. Jackson
Microorganisms 2018, 6(2), 32; https://doi.org/10.3390/microorganisms6020032 - 21 Apr 2018
Cited by 6 | Viewed by 7373
Abstract
Understanding the molecular mechanisms underpinning the ecological success of plant pathogens is critical to develop strategies for controlling diseases and protecting crops. Recent observations have shown that plant pathogenic bacteria, particularly Pseudomonas, exist in a range of natural environments away from their [...] Read more.
Understanding the molecular mechanisms underpinning the ecological success of plant pathogens is critical to develop strategies for controlling diseases and protecting crops. Recent observations have shown that plant pathogenic bacteria, particularly Pseudomonas, exist in a range of natural environments away from their natural plant host e.g., water courses, soil, non-host plants. This exposes them to a variety of eukaryotic predators such as nematodes, insects and amoebae present in the environment. Nematodes and amoeba in particular are bacterial predators while insect herbivores may act as indirect predators, ingesting bacteria on plant tissue. We therefore postulated that bacteria are probably under selective pressure to avoid or survive predation and have therefore developed appropriate coping mechanisms. We tested the hypothesis that plant pathogenic Pseudomonas syringae are able to cope with predation pressure and found that three pathovars show weak, but significant resistance or toxicity. To identify the gene systems that contribute to resistance or toxicity we applied a heterologous screening technique, called Rapid Virulence Annotation (RVA), for anti-predation and toxicity mechanisms. Three cosmid libraries for P. syringae pv. aesculi, pv. tomato and pv. phaseolicola, of approximately 2000 cosmids each, were screened in the susceptible/non-toxic bacterium Escherichia coli against nematode, amoebae and an insect. A number of potential conserved and unique genes were identified which included genes encoding haemolysins, biofilm formation, motility and adhesion. These data provide the first multi-pathovar comparative insight to how plant pathogens cope with different predation pressures and infection of an insect gut and provide a foundation for further study into the function of selected genes and their role in ecological success. Full article
(This article belongs to the Section Environmental Microbiology)
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16 pages, 11233 KiB  
Article
Production and Characterization of an Extracellular Acid Protease from Thermophilic Brevibacillus sp. OA30 Isolated from an Algerian Hot Spring
by Mohamed Amine Gomri, Agustín Rico-Díaz, Juan-José Escuder-Rodríguez, Tedj El Moulouk Khaldi, María-Isabel González-Siso and Karima Kharroub
Microorganisms 2018, 6(2), 31; https://doi.org/10.3390/microorganisms6020031 - 12 Apr 2018
Cited by 12 | Viewed by 6520
Abstract
Proteases have numerous biotechnological applications and the bioprospection for newly-thermostable proteases from the great biodiversity of thermophilic microorganisms inhabiting hot environments, such as geothermal sources, aims to discover more effective enzymes for processes at higher temperatures. We report in this paper the production [...] Read more.
Proteases have numerous biotechnological applications and the bioprospection for newly-thermostable proteases from the great biodiversity of thermophilic microorganisms inhabiting hot environments, such as geothermal sources, aims to discover more effective enzymes for processes at higher temperatures. We report in this paper the production and the characterization of a purified acid protease from strain OA30, a moderate thermophilic bacterium isolated from an Algerian hot spring. Phenotypic and genotypic study of strain OA30 was followed by the production of the extracellular protease in a physiologically-optimized medium. Strain OA30 showed multiple extracellular proteolytic enzymes and protease 32-F38 was purified by chromatographic methods and its biochemical characteristics were studied. Strain OA30 was affiliated with Brevibacillus thermoruber species. Protease 32-F38 had an estimated molecular weight of 64.6 kDa and was optimally active at 50 °C. It showed a great thermostability after 240 min and its optimum pH was 6.0. Protease 32-F38 was highly stable in the presence of different detergents and solvents and was inhibited by metalloprotease inhibitors. The results of this work suggest that protease 32-F38 might have interesting biotechnological applications. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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25 pages, 13990 KiB  
Review
Translation and Translational Control in Dinoflagellates
by Sougata Roy, Rosemary Jagus and David Morse
Microorganisms 2018, 6(2), 30; https://doi.org/10.3390/microorganisms6020030 - 7 Apr 2018
Cited by 26 | Viewed by 5966
Abstract
Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. [...] Read more.
Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here. Full article
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2 pages, 143 KiB  
Editorial
Special Issue: Response of Microbial Communities to Environmental Changes
by Ulrich Stingl
Microorganisms 2018, 6(2), 29; https://doi.org/10.3390/microorganisms6020029 - 30 Mar 2018
Cited by 2 | Viewed by 3496
Abstract
Environmental issues such as eutrophication, ocean acidification, sea level rise, saltwater intrusion, increase in carbon dioxide levels, or rise of average global temperatures, among many others, are impacting and changing whole ecosystems [...]
Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
2 pages, 174 KiB  
Editorial
Symbiotic Plant-Bacterial Endospheric Interactions
by Sharon Lafferty Doty
Microorganisms 2018, 6(2), 28; https://doi.org/10.3390/microorganisms6020028 - 22 Mar 2018
Cited by 5 | Viewed by 3570
Abstract
While plant-microbe symbioses involving root nodules (Rhizobia and Frankia) or the root-soil interface (rhizosphere) have been well studied, the intimate interaction of microbial endophytes with the plant host is a relatively new field of research.[...] Full article
(This article belongs to the Special Issue Symbiotic Plant-Bacterial Endospheric Interactions)
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