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Microorganisms, Volume 7, Issue 2 (February 2019)

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Cover Story (view full-size image) Candida glabrata is an opportunistic human fungal pathogen that is capable of causing both [...] Read more.
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Open AccessArticle Refined versus Extra Virgin Olive Oil High-Fat Diet Impact on Intestinal Microbiota of Mice and Its Relation to Different Physiological Variables
Microorganisms 2019, 7(2), 61; https://doi.org/10.3390/microorganisms7020061
Received: 27 January 2019 / Revised: 16 February 2019 / Accepted: 20 February 2019 / Published: 23 February 2019
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Abstract
Extra virgin olive oil (EVOO) has been reported to have a distinct influence on gut microbiota in comparison to other fats, with its physiological benefits widely studied. However, a large proportion of the population consumes olive oil after a depurative process that not [...] Read more.
Extra virgin olive oil (EVOO) has been reported to have a distinct influence on gut microbiota in comparison to other fats, with its physiological benefits widely studied. However, a large proportion of the population consumes olive oil after a depurative process that not only mellows its taste, but also deprives it of polyphenols and other minority components. In this study, we compare the influence on the intestinal microbiota of a diet high in this refined olive oil (ROO) with other fat-enriched diets. Swiss Webster mice were fed standard or a high-fat diet enriched with EVOO, ROO, or butter (BT). Physiological parameters were also evaluated. At the end of the feeding period, DNA was extracted from feces and the 16S rRNA was pyrosequenced. The group fed ROO behaved differently to the EVOO group in half the families with statistically significant differences among the diets, with higher comparative levels in three families—Desulfovibrionaceae, Spiroplasmataceae, and Helicobacteraceae—correlating with total cholesterol. These results are again indicative of a link between specific diets, certain physiological parameters and the prevalence of some taxa, but also support the possibility that polyphenols and minor components of EVOO are involved in some of the proposed effects of this fat through the modulation of the intestinal microbiota Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
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Open AccessCorrection Correction: Hokynar, K. et al. Chlamydia-Like Organisms (CLOs) in Finnish Ixodes ricinus Ticks and Human Skin. Microorganisms 2016, 4, 28
Microorganisms 2019, 7(2), 60; https://doi.org/10.3390/microorganisms7020060
Received: 11 February 2019 / Accepted: 18 February 2019 / Published: 23 February 2019
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Abstract
The authors wish to make the following modification to this paper [...] Full article
Open AccessArticle What an Escherichia coli Mutant Can Teach Us About the Antibacterial Effect of Chlorophyllin
Microorganisms 2019, 7(2), 59; https://doi.org/10.3390/microorganisms7020059
Received: 31 December 2018 / Revised: 8 February 2019 / Accepted: 19 February 2019 / Published: 22 February 2019
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Abstract
Due to the increasing development of antibiotic resistances in recent years, scientists search intensely for new methods to control bacteria. Photodynamic treatment with porphyrins such as chlorophyll derivatives is one of the most promising methods to handle bacterial infestation, but their use is [...] Read more.
Due to the increasing development of antibiotic resistances in recent years, scientists search intensely for new methods to control bacteria. Photodynamic treatment with porphyrins such as chlorophyll derivatives is one of the most promising methods to handle bacterial infestation, but their use is dependent on illumination and they seem to be more effective against Gram-positive bacteria than against Gram-negatives. In this study, we tested chlorophyllin against three bacterial model strains, the Gram-positive Bacillus subtilis 168, the Gram-negative Escherichia coli DH5α and E. coli strain NR698 which has a deficient outer membrane, simulating a Gram-negative “without” its outer membrane. Illuminated with a standardized light intensity of 12 mW/cm2, B. subtilis showed high sensitivity already at low chlorophyllin concentrations (≤105 cfu/mL: ≤0.1 mg/L, 106–108 cfu/mL: 0.5 mg/L), whereas E. coli DH5α was less sensitive (≤105 cfu/mL: 2.5 mg/L, 106 cfu/mL: 5 mg/L, 107–108 cfu/mL: ineffective at ≤25 mg/L chlorophyllin). E. coli NR698 was almost as sensitive as B. subtilis against chlorophyllin, pointing out that the outer membrane plays a significant role in protection against photodynamic chlorophyllin impacts. Interestingly, E. coli NR698 and B. subtilis can also be inactivated by chlorophyllin in darkness, indicating a second, light-independent mode of action. Thus, chlorophyllin seems to be more than a photosensitizer, and a promising substance for the control of bacteria, which deserves further investigation. Full article
(This article belongs to the Special Issue Strategies and Weapons to Fight Antimicrobial Resistance)
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Open AccessReview Can Gut Microbiota and Lifestyle Help Us in the Handling of Anorexia Nervosa Patients?
Microorganisms 2019, 7(2), 58; https://doi.org/10.3390/microorganisms7020058
Received: 16 January 2019 / Revised: 8 February 2019 / Accepted: 20 February 2019 / Published: 22 February 2019
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Abstract
Gut microbiota is composed of different microorganisms that play an important role in the host. New research shows that bidirectional communications happen between intestinal microbiota and the brain, which is known as the gut–brain axis. This communication is significant and could have a [...] Read more.
Gut microbiota is composed of different microorganisms that play an important role in the host. New research shows that bidirectional communications happen between intestinal microbiota and the brain, which is known as the gut–brain axis. This communication is significant and could have a negative or positive effect depending on the state of the gut microbiota. Anorexia nervosa (AN) is a mental illness associated with metabolic, immunologic, biochemical, sensory abnormalities, and extremely low body weight. Different studies have shown a dysbiosis in patients with AN. Due to the gut–brain axis, it was observed that some of the symptoms could be improved in these patients by boosting their gut microbiota. This paper highlights some evidence connecting the role of microbiota in the AN onset and disease progress. Finally, a proposal is done to include the microbiota analysis as part of the recovery protocol used to treat AN patients. When conducting clinical studies of gut microbiota in AN patients, dysbiosis is expected to be found. Then the prescription of a personalized treatment rich in prebiotics and probiotics could be proposed to reverse the dysbiosis. Full article
(This article belongs to the Special Issue Gut Microbiota Diversity Relates to Lifestyle)
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Open AccessArticle Rotations with Indian Mustard and Wild Rocket Suppressed Cucumber Fusarium Wilt Disease and Changed Rhizosphere Bacterial Communities
Microorganisms 2019, 7(2), 57; https://doi.org/10.3390/microorganisms7020057
Received: 20 January 2019 / Revised: 20 February 2019 / Accepted: 20 February 2019 / Published: 21 February 2019
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Abstract
Crop monocropping usually results in an enrichment of soil-borne pathogens in soil. Crop rotation is an environmentally friendly method for controlling soil-borne diseases. Plant rhizosphere microorganisms, especially plant-beneficial microorganisms, play a major role in protecting plants from pathogens, but responses of these microorganisms [...] Read more.
Crop monocropping usually results in an enrichment of soil-borne pathogens in soil. Crop rotation is an environmentally friendly method for controlling soil-borne diseases. Plant rhizosphere microorganisms, especially plant-beneficial microorganisms, play a major role in protecting plants from pathogens, but responses of these microorganisms to crop rotation remain unclear. Here, we evaluated the effects of rotations with Indian mustard (Brassica juncea) and wild rocket (Diplotaxis tenuifolia (L.) DC.) on cucumber Fusarium wilt disease caused by Fusarium oxysporum f.sp. cucumerinum (FOC). Cucumber rhizosphere bacterial community composition was analyzed by high-throughput amplicon sequencing. Bacteria, Pseudomonas spp., 2,4-diacetylphloroglucinol (an antifungal secondary metabolite) producer and FOC abundances were estimated by real-time PCR. Rotations with Indian mustard and wild rocket suppressed cucumber Fusarium wilt disease and cucumber rhizosphere FOC abundance. Crop rotations increased cucumber rhizosphere bacteria, Pseudomonas spp. and 2,4-diacetylphloroglucinol producer abundances. Moreover, crop rotations changed cucumber rhizosphere bacterial community composition and increased bacterial community diversity. However, crop rotations decreased soil inorganic nitrogen content and inhibited cucumber seedling growth. Overall, rotations with Indian mustard and wild rocket suppressed cucumber Fusarium wilt disease, which might be linked to the increased rhizosphere bacterial diversity and abundances of potential plant-beneficial microorganisms (such as Pseudomonas spp. and 2,4-diacetylphloroglucinol producer). Full article
(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle In Silico Analysis of Genetic VapC Profiles from the Toxin-Antitoxin Type II VapBC Modules among Pathogenic, Intermediate, and Non-Pathogenic Leptospira
Microorganisms 2019, 7(2), 56; https://doi.org/10.3390/microorganisms7020056
Received: 29 January 2019 / Revised: 9 February 2019 / Accepted: 15 February 2019 / Published: 20 February 2019
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Abstract
Pathogenic Leptospira spp. is the etiological agent of leptospirosis. The high diversity among Leptospira species provides an array to look for important mediators involved in pathogenesis. Toxin-antitoxin (TA) systems represent an important survival mechanism on stress conditions. vapBC modules have been found [...] Read more.
Pathogenic Leptospira spp. is the etiological agent of leptospirosis. The high diversity among Leptospira species provides an array to look for important mediators involved in pathogenesis. Toxin-antitoxin (TA) systems represent an important survival mechanism on stress conditions. vapBC modules have been found in nearly one thousand genomes corresponding to about 40% of known TAs. In the present study, we investigated TA profiles of some strains of Leptospira using a TA database and compared them through protein alignment of VapC toxin sequences among Leptospira spp. genomes. Our analysis identified significant differences in the number of putative vapBC modules distributed in pathogenic, saprophytic, and intermediate strains: four in L. interrogans, three in L. borgpetersenii, eight in L. biflexa, and 15 in L. licerasiae. The VapC toxins show low identity among amino acid sequences within the species. Some VapC toxins appear to be exclusively conserved in unique species, others appear to be conserved among pathogenic or saprophytic strains, and some appear to be distributed randomly. The data shown here indicate that these modules evolved in a very complex manner, which highlights the strong need to identify and characterize new TAs as well as to understand their regulation networks and the possible roles of TA systems in pathogenic bacteria. Full article
(This article belongs to the Special Issue Toxin-Antitoxin Systems I)
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Open AccessReview Plasmid-Mediated Colistin Resistance in Salmonella enterica: A Review
Microorganisms 2019, 7(2), 55; https://doi.org/10.3390/microorganisms7020055
Received: 31 January 2019 / Revised: 13 February 2019 / Accepted: 15 February 2019 / Published: 19 February 2019
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Abstract
Colistin is widely used in food-animal production. Salmonella enterica is a zoonotic pathogen, which can pass from animal to human microbiota through the consumption of contaminated food, and cause disease, often severe, especially in young children, elderly and immunocompromised individuals. Recently, plasmid-mediated colistin [...] Read more.
Colistin is widely used in food-animal production. Salmonella enterica is a zoonotic pathogen, which can pass from animal to human microbiota through the consumption of contaminated food, and cause disease, often severe, especially in young children, elderly and immunocompromised individuals. Recently, plasmid-mediated colistin resistance was recognised; mcr-like genes are being identified worldwide. Colistin is not an antibiotic used to treat Salmonella infections, but has been increasingly used as one of the last treatment options for carbapenem resistant Enterobacteria in human infections. The finding of mobilizable mcr-like genes became a global concern due to the possibility of horizontal transfer of the plasmid that often carry resistance determinants to beta-lactams and/or quinolones. An understanding of the origin and dissemination of mcr-like genes in zoonotic pathogens such as S. enterica will facilitate the management of colistin use and target interventions to prevent further spread. The main objective of this review was to collect epidemiological data about mobilized colistin resistance in S. enterica, describing the mcr variants, identified serovars, origin of the isolate, country and other resistance genes located in the same genetic platform. Full article
(This article belongs to the Special Issue Multidrug-Resistant Pathogens)
Open AccessArticle Merkel Cell Polyomavirus Is Associated with Anal Infections in Men Who Have Sex with Men
Microorganisms 2019, 7(2), 54; https://doi.org/10.3390/microorganisms7020054
Received: 21 December 2018 / Revised: 13 February 2019 / Accepted: 14 February 2019 / Published: 19 February 2019
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Abstract
Background: Viral infections of the anal/rectal tract of men who have sex with men (MSM) have been poorly studied. Methods: In total, 158 swab samples (81 anal/rectal, 65 throat/oral and 12 urethral) were collected from 126 MSM. DNA was isolated and subjected to [...] Read more.
Background: Viral infections of the anal/rectal tract of men who have sex with men (MSM) have been poorly studied. Methods: In total, 158 swab samples (81 anal/rectal, 65 throat/oral and 12 urethral) were collected from 126 MSM. DNA was isolated and subjected to real-time PCR assays for the detection of the sexually transmitted (ST) pathogens Chlamydia trachomatis, Neisseria gonorrhoeae and Mycoplasmas ssp, human papillomavirus (HPV) and six human polyomaviruses (HPyVs; JCPyV, BKPyV, Merkel cell PyV–MCPyV-, HPyV-6, HPyV-7 and HPyV-9). Results: C. trachomatis (31/126, 24.6%) and M. genitalium (30/126, 23.8%) were the most frequently detected ST pathogens. Thirty-one/126 (24.6%) patients were positive for at least one HPyV. The significantly (p < 0.05) prevalent HPyV in the anal tract was MCPyV, which was amplified in 27/81 (33.3%) samples, followed by HPyV-6, which was amplified in 6/81 (7.4%) swabs. Coinfections with MCPyV and C. trachomatis or Mycoplasmas were found in 4/21 (19.0%) and 5/21 (23.8%) anal/rectal swabs, respectively. Three/4 MCPyV-C. trachomatis coinfected patients were symptomatic. Conclusions: Based on the high prevalence of MCPyV in the anal/rectal swabs from MSM patients and on the well-known oncogenic properties of MCPyV, sexual transmission and possible involvement of HPyVs in the pathogenesis of diseases of the anal canal should be further studied. Full article
(This article belongs to the Section Medical Microbiology)
Open AccessReview Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry
Microorganisms 2019, 7(2), 53; https://doi.org/10.3390/microorganisms7020053
Received: 30 November 2018 / Revised: 1 February 2019 / Accepted: 3 February 2019 / Published: 15 February 2019
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Abstract
Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation [...] Read more.
Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation produce hydrogen. Hydrogen is also produced by a number of abiotic processes including radiolysis, serpentinization, graphitization, and cataclasis of silicate minerals. Both biotic and abiotically generated hydrogen may become available for consumption by microorganisms, but biotic production and consumption are usually tightly coupled. Understanding the microbiology of hydrogen cycling is relevant to subsurface engineered environments where hydrogen-cycling microorganisms are implicated in gas consumption and production and corrosion in a number of industries including carbon capture and storage, energy gas storage, and radioactive waste disposal. The same hydrogen-cycling microorganisms and processes are important in natural sites with elevated hydrogen and can provide insights into early life on Earth and life on other planets. This review draws together what is known about microbiology in natural environments with elevated hydrogen, and highlights where similar microbial populations could be of relevance to subsurface industry. Full article
(This article belongs to the Special Issue Subsurface Geomicrobiology)
Open AccessArticle ATP- and Polyphosphate-Dependent Glucokinases from Aerobic Methanotrophs
Microorganisms 2019, 7(2), 52; https://doi.org/10.3390/microorganisms7020052
Received: 26 December 2018 / Revised: 1 February 2019 / Accepted: 12 February 2019 / Published: 14 February 2019
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Abstract
The genes encoding adenosine triphosphate (ATP)- and polyphosphate (polyP)-dependent glucokinases (Glk) were identified in the aerobic obligate methanotroph Methylomonas sp. 12. The recombinant proteins were obtained by the heterologous expression of the glk genes in Esherichia coli. ATP-Glk behaved as a multimeric [...] Read more.
The genes encoding adenosine triphosphate (ATP)- and polyphosphate (polyP)-dependent glucokinases (Glk) were identified in the aerobic obligate methanotroph Methylomonas sp. 12. The recombinant proteins were obtained by the heterologous expression of the glk genes in Esherichia coli. ATP-Glk behaved as a multimeric protein consisting of di-, tri-, tetra-, penta- and hexamers with a subunit molecular mass of 35.5 kDa. ATP-Glk phosphorylated glucose and glucosamine using ATP (100% activity), uridine triphosphate (UTP) (85%) or guanosine triphosphate (GTP) (71%) as a phosphoryl donor and exhibited the highest activity in the presence of 5 mM Mg2+ at pH 7.5 and 65 °C but was fully inactivated after a short-term incubation at this temperature. According to a gel filtration in the presence of polyP, the polyP-dependent Glk was a dimeric protein (2 × 28 kDa). PolyP-Glk phosphorylated glucose, mannose, 2-deoxy-D-glucose, glucosamine and N-acetylglucosamine using polyP as the phosphoryl donor but not using nucleoside triphosphates. The Km values of ATP-Glk for glucose and ATP were about 78 μM, and the Km values of polyP-Glk for glucose and polyP(n=45) were 450 and 21 μM, respectively. The genomic analysis of methanotrophs showed that ATP-dependent glucokinase is present in all sequenced methanotrophs, with the exception of the genera Methylosinus and Methylocystis, whereas polyP-Glks were found in all species of the genus Methylomonas and in Methylomarinum vadi only. This work presents the first characterization of polyphosphate specific glucokinase in a methanotrophic bacterium. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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Open AccessArticle Effects of Bifidobacterium bifidum in Mice Infected with Citrobacter rodentium
Microorganisms 2019, 7(2), 51; https://doi.org/10.3390/microorganisms7020051
Received: 12 December 2018 / Revised: 7 February 2019 / Accepted: 11 February 2019 / Published: 14 February 2019
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Abstract
In vitro and in vivo studies suggest that selected Bifidobacterium bifidum strains sustain intestinal homeostasis. This study aimed to examine whether the administration of B. bifidum MIMBb75 (BB75) attenuates Citrobacter rodentium infection, a murine model for enteric infection and inflammatory bowel disease in [...] Read more.
In vitro and in vivo studies suggest that selected Bifidobacterium bifidum strains sustain intestinal homeostasis. This study aimed to examine whether the administration of B. bifidum MIMBb75 (BB75) attenuates Citrobacter rodentium infection, a murine model for enteric infection and inflammatory bowel disease in humans. C57Bl6/J mice were randomized to receive BB75 daily starting before or after C. rodentium infection. BB75 load and infection kinetics were monitored. On day 10 post-infection (p.i.), histological parameters of the large intestine were assessed. Barrier integrity was evaluated by pathogen translocation to secondary organs and in vivo permeability test. Fecal C. rodentium load peaked at 1010 CFU/g at day 10 p.i., with clearance at day 24 p.i., regardless of probiotic treatment. BB75 administration resulted in 107 cells/g of feces with no effect of timing of administration. BB75 treatment did not attenuate C. rodentium-induced crypt hyperplasia nor inflammation. C. rodentium and BB75 can co-exist in the gut with no mutual displacement. However, BB75 cannot counteract C. rodentium pathology. Our findings provide insight for the understanding of probiotics behavior and their clinical relevance in intestinal inflammation. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
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Open AccessArticle Phylogenomic Analyses of Bradyrhizobium Reveal Uneven Distribution of the Lateral and Subpolar Flagellar Systems, Which Extends to Rhizobiales
Microorganisms 2019, 7(2), 50; https://doi.org/10.3390/microorganisms7020050
Received: 19 December 2018 / Revised: 10 February 2019 / Accepted: 11 February 2019 / Published: 13 February 2019
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Abstract
Dual flagellar systems have been described in several bacterial genera, but the extent of their prevalence has not been fully explored. Bradyrhizobium diazoefficiens USDA 110T possesses two flagellar systems, the subpolar and the lateral flagella. The lateral flagellum of Bradyrhizobium displays no [...] Read more.
Dual flagellar systems have been described in several bacterial genera, but the extent of their prevalence has not been fully explored. Bradyrhizobium diazoefficiens USDA 110T possesses two flagellar systems, the subpolar and the lateral flagella. The lateral flagellum of Bradyrhizobium displays no obvious role, since its performance is explained by cooperation with the subpolar flagellum. In contrast, the lateral flagellum is the only type of flagella present in the related Rhizobiaceae family. In this work, we have analyzed the phylogeny of the Bradyrhizobium genus by means of Genome-to-Genome Blast Distance Phylogeny (GBDP) and Average Nucleotide Identity (ANI) comparisons of 128 genomes and divided it into 13 phylogenomic groups. While all the Bradyrhizobium genomes encode the subpolar flagellum, none of them encodes only the lateral flagellum. The simultaneous presence of both flagella is exclusive of the B. japonicum phylogenomic group. Additionally, 292 Rhizobiales order genomes were analyzed and both flagellar systems are present together in only nine genera. Phylogenetic analysis of 150 representative Rhizobiales genomes revealed an uneven distribution of these flagellar systems. While genomes within and close to the Rhizobiaceae family only possess the lateral flagellum, the subpolar flagellum is exclusive of more early-diverging families, where certain genera also present both flagella. Full article
(This article belongs to the collection Feature Papers in Environmental Microbiology)
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Open AccessReview PES Pathogens in Severe Community-Acquired Pneumonia
Microorganisms 2019, 7(2), 49; https://doi.org/10.3390/microorganisms7020049
Received: 17 January 2019 / Revised: 9 February 2019 / Accepted: 9 February 2019 / Published: 12 February 2019
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Abstract
Worldwide, there is growing concern about the burden of pneumonia. Severe community-acquired pneumonia (CAP) is frequently complicated by pulmonary and extra-pulmonary complications, including sepsis, septic shock, acute respiratory distress syndrome, and acute cardiac events, resulting in significantly increased intensive care admission rates and [...] Read more.
Worldwide, there is growing concern about the burden of pneumonia. Severe community-acquired pneumonia (CAP) is frequently complicated by pulmonary and extra-pulmonary complications, including sepsis, septic shock, acute respiratory distress syndrome, and acute cardiac events, resulting in significantly increased intensive care admission rates and mortality rates. Streptococcus pneumoniae (Pneumococcus) remains the most common causative pathogen in CAP. However, several bacteria and respiratory viruses are responsible, and approximately 6% of cases are due to the so-called PES (Pseudomonas aeruginosa, extended-spectrum β-lactamase Enterobacteriaceae, and methicillin-resistant Staphylococcus aureus) pathogens. Of these, P. aeruginosa and methicillin-resistant Staphylococcus aureus are the most frequently reported and require different antibiotic therapy to that for typical CAP. It is therefore important to recognize the risk factors for these pathogens to improve the outcomes in patients with CAP. Full article
(This article belongs to the Special Issue Multidrug-Resistant Pathogens)
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Open AccessReview Extracellular Vesicles in Epstein-Barr Virus’ Life Cycle and Pathogenesis
Microorganisms 2019, 7(2), 48; https://doi.org/10.3390/microorganisms7020048
Received: 28 January 2019 / Revised: 8 February 2019 / Accepted: 9 February 2019 / Published: 11 February 2019
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Extracellular vesicles (EVs), including exosomes and microvesicles, are evolutionarily conserved phospholidpid membrane-bound entities secreted from most eukaryotic cell types. They carry bioactive cargos such as protein and nucleic acids derived from their cells of origin. Over the past 10 years, they have been [...] Read more.
Extracellular vesicles (EVs), including exosomes and microvesicles, are evolutionarily conserved phospholidpid membrane-bound entities secreted from most eukaryotic cell types. They carry bioactive cargos such as protein and nucleic acids derived from their cells of origin. Over the past 10 years, they have been attracting increased attention in many fields of life science, representing a new route for intercellular communication. In this review article, we will discuss the current knowledge of both normal and virally modified EVs in the regulation of Epstein-Barr virus (EBV)’s life cycle and its associated pathogenesis. Full article
(This article belongs to the Special Issue Recent Advances in Understanding Epstein-Barr Virus)
Open AccessArticle Root-Associated Endophytic Bacterial Community Composition of Pennisetum sinese from Four Representative Provinces in China
Microorganisms 2019, 7(2), 47; https://doi.org/10.3390/microorganisms7020047
Received: 24 December 2018 / Revised: 16 January 2019 / Accepted: 30 January 2019 / Published: 11 February 2019
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Abstract
Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of [...] Read more.
Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies. Full article
(This article belongs to the Special Issue Plant Control of Symbiotic Microbe Behavior and Reproduction)
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Open AccessArticle Dynamics of Hydrology and Anaerobic Hydrocarbon Degrader Communities in A Tar-Oil Contaminated Aquifer
Microorganisms 2019, 7(2), 46; https://doi.org/10.3390/microorganisms7020046
Received: 21 December 2018 / Revised: 30 January 2019 / Accepted: 6 February 2019 / Published: 9 February 2019
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Abstract
Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such [...] Read more.
Aquifers are typically perceived as rather stable habitats, characterized by low biogeochemical and microbial community dynamics. Upon contamination, aquifers shift to a perturbed ecological status, in which specialized populations of contaminant degraders establish and mediate aquifer restoration. However, the ecological controls of such degrader populations, and possible feedbacks between hydraulic and microbial habitat components, remain poorly understood. Here, we provide evidence of such couplings, via 4 years of annual sampling of groundwater and sediments across a high-resolution depth-transect of a hydrocarbon plume. Specialized anaerobic degrader populations are known to be established at the reactive fringes of the plume. Here, we show that fluctuations of the groundwater table were paralleled by pronounced dynamics of biogeochemical processes, pollutant degradation, and plume microbiota. Importantly, a switching in maximal relative abundance between dominant degrader populations within the Desulfobulbaceae and Desulfosporosinus spp. was observed after hydraulic dynamics. Thus, functional redundancy amongst anaerobic hydrocarbon degraders could have been relevant in sustaining biodegradation processes after hydraulic fluctuations. These findings contribute to an improved ecological perspective of contaminant plumes as a dynamic microbial habitat, with implications for both monitoring and remediation strategies in situ. Full article
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Open AccessArticle The Foodborne Strain Lactobacillus fermentum MBC2 Triggers pept-1-Dependent Pro-Longevity Effects in Caenorhabditis elegans
Microorganisms 2019, 7(2), 45; https://doi.org/10.3390/microorganisms7020045
Received: 21 December 2018 / Revised: 21 January 2019 / Accepted: 7 February 2019 / Published: 7 February 2019
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Abstract
Lactic acid bacteria (LAB) are involved in several food fermentations and many of them provide strain-specific health benefits. Herein, the probiotic potential of the foodborne strain Lactobacillus fermentum MBC2 was investigated through in vitro and in vivo approaches. Caenorhabditis elegans was used as [...] Read more.
Lactic acid bacteria (LAB) are involved in several food fermentations and many of them provide strain-specific health benefits. Herein, the probiotic potential of the foodborne strain Lactobacillus fermentum MBC2 was investigated through in vitro and in vivo approaches. Caenorhabditis elegans was used as an in vivo model to analyze pro-longevity and anti-aging effects. L. fermentum MBC2 showed a high gut colonization capability compared to E. coli OP50 (OP50) or L. rhamnosus GG (LGG). Moreover, analysis of pumping rate, lipofuscin accumulation, and body bending showed anti-aging effects in L. fermentum MBC2-fed worms. Studies on PEPT-1 mutants demonstrated that pept-1 gene was involved in the anti-aging processes mediated by this bacterial strain through DAF-16, whereas the oxidative stress protection was PEPT-1 independent. Moreover, analysis of acid tolerance, bile tolerance, and antibiotic susceptibility were evaluated. L. fermentum MBC2 exerted beneficial effects on nematode lifespan, influencing energy metabolism and oxidative stress resistance, resulted in being tolerant to acidic pH and able to adhere to Caco-2 cells. Overall, these findings provide new insight for application of this strain in the food industry as a newly isolated functional starter. Furthermore, these results will also shed light on C. elegans molecular players involved in host-microbe interactions. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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Open AccessReview Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe–Plant–Animal Interactions
Microorganisms 2019, 7(2), 44; https://doi.org/10.3390/microorganisms7020044
Received: 14 December 2018 / Revised: 23 January 2019 / Accepted: 2 February 2019 / Published: 6 February 2019
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Abstract
The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human [...] Read more.
The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment. Full article
(This article belongs to the Special Issue Macro and Microorganism Interactions)
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Open AccessArticle Environmental Aspects of the Use of Hedera helix Extract in Bioremediation Process
Microorganisms 2019, 7(2), 43; https://doi.org/10.3390/microorganisms7020043
Received: 30 December 2018 / Revised: 25 January 2019 / Accepted: 2 February 2019 / Published: 5 February 2019
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Abstract
This paper analyzes the impact of saponins from English ivy leaves on the properties of environmental bacterial strains and hydrocarbon degradation ability. For this purpose, two bacterial strains, Raoultella ornitinolytica M03 and Acinetobacter calcoaceticus M1B, have been used in toluene, 4-chlorotoluene, and α,α,α-trifluorotoluene [...] Read more.
This paper analyzes the impact of saponins from English ivy leaves on the properties of environmental bacterial strains and hydrocarbon degradation ability. For this purpose, two bacterial strains, Raoultella ornitinolytica M03 and Acinetobacter calcoaceticus M1B, have been used in toluene, 4-chlorotoluene, and α,α,α-trifluorotoluene biodegradation supported by Hedera helix extract. Moreover, theeffects of ivy exposition on cell properties and extract toxicity were investigated. The extract was found to cause minor differences in cell surface hydrophobicity, membrane permeability, and Zeta potential, although it adhered to the cell surface. Acinetobacter calcoaceticus M1B was more affected by the ivy extract; thus, the cells were more metabolically active and degraded saponins at greater amounts. Although the extract influenced positively the cells’ viability in the presence of hydrocarbons, it could have been used by the bacteria as a carbon source, thus slowing down hydrocarbon degradation. These results show that the use of ivy saponins for hydrocarbon remediation is environmentally acceptable but should be carefully analyzed to assess the efficiency of the selected saponins-rich extract in combination with selected bacterial strains. Full article
(This article belongs to the Special Issue Bioremediation - The Natural Solution)
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Open AccessArticle Optimization of In Vitro Mycobacterium avium and Mycobacterium intracellulare Growth Assays for Therapeutic Development
Microorganisms 2019, 7(2), 42; https://doi.org/10.3390/microorganisms7020042
Received: 17 December 2018 / Revised: 12 January 2019 / Accepted: 20 January 2019 / Published: 1 February 2019
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Abstract
Infection with nontuberculous mycobacteria (NTM) is a complication of lung disease in immunocompromised patients, including those with human immunodeficiency virus and acquired immune deficiency syndrome (HIV/AIDS), chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF). The most widespread, disease-causing NTM is Mycobacterium avium [...] Read more.
Infection with nontuberculous mycobacteria (NTM) is a complication of lung disease in immunocompromised patients, including those with human immunodeficiency virus and acquired immune deficiency syndrome (HIV/AIDS), chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF). The most widespread, disease-causing NTM is Mycobacterium avium complex (MAC), which colonizes the lungs as a combination of Mycobacterium avium, Mycobacterium intracellulare, and other mycobacterial species. While combination drug therapy exists for MAC colonization, there is no cure. Therapeutic development to treat MAC has been difficult because of the slow-growing nature of the bacterial complex, limiting the ability to characterize the bacteria’s growth in response to new therapeutics. The development of a technology that allows observation of both the MAC predominant strains and MAC could provide a means to develop new therapeutics to treat NTM. We have developed a new methodology in which M. avium and M. intracellulare can be optimally grown in short term culture to study each strain independently and in combination, as a monitor of growth kinetics and efficient therapeutic testing protocols. Full article
(This article belongs to the Special Issue Virulence Studies of Pathogenic Mycobacteria of Humans and Animal)
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Open AccessReview Potential Role for the Gut Microbiota in Modulating Host Circadian Rhythms and Metabolic Health
Microorganisms 2019, 7(2), 41; https://doi.org/10.3390/microorganisms7020041
Received: 17 January 2019 / Revised: 26 January 2019 / Accepted: 28 January 2019 / Published: 31 January 2019
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Abstract
This article reviews the current evidence associating gut microbiota with factors that impact host circadian-metabolic axis, such as light/dark cycles, sleep/wake cycles, diet, and eating patterns. We examine how gut bacteria possess their own daily rhythmicity in terms of composition, their localization to [...] Read more.
This article reviews the current evidence associating gut microbiota with factors that impact host circadian-metabolic axis, such as light/dark cycles, sleep/wake cycles, diet, and eating patterns. We examine how gut bacteria possess their own daily rhythmicity in terms of composition, their localization to intestinal niches, and functions. We review evidence that gut bacteria modulate host rhythms via microbial metabolites such as butyrate, polyphenolic derivatives, vitamins, and amines. Lifestyle stressors such as altered sleep and eating patterns that may disturb the host circadian system also influence the gut microbiome. The consequent disruptions to microbiota-mediated functions such as decreased conjugation of bile acids or increased production of hydrogen sulfide and the resultant decreased production of butyrate, in turn affect substrate oxidation and energy regulation in the host. Thus, disturbances in microbiome rhythms may at least partially contribute to an increased risk of obesity and metabolic syndrome associated with insufficient sleep and circadian misalignment. Good sleep and a healthy diet appear to be essential for maintaining gut microbial balance. Manipulating daily rhythms of gut microbial abundance and activity may therefore hold promise for a chrononutrition-based approach to consolidate host circadian rhythms and metabolic homeorhesis. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
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Open AccessReview Bioreactor-Scale Strategies for the Production of Recombinant Protein in the Yeast Yarrowia lipolytica
Microorganisms 2019, 7(2), 40; https://doi.org/10.3390/microorganisms7020040
Received: 17 January 2019 / Revised: 28 January 2019 / Accepted: 29 January 2019 / Published: 30 January 2019
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Abstract
Recombinant protein production represents a multibillion-dollar market. Therefore, it constitutes an important research field both in academia and industry. The use of yeast as a cell factory presents several advantages such as ease of genetic manipulation, growth at high cell density, and the [...] Read more.
Recombinant protein production represents a multibillion-dollar market. Therefore, it constitutes an important research field both in academia and industry. The use of yeast as a cell factory presents several advantages such as ease of genetic manipulation, growth at high cell density, and the possibility of post-translational modifications. Yarrowia lipolytica is considered as one of the most attractive hosts due to its ability to metabolize raw substrate, to express genes at a high level, and to secrete protein in large amounts. In recent years, several reviews have been dedicated to genetic tools developed for this purpose. Though the construction of efficient cell factories for recombinant protein synthesis is important, the development of an efficient process for recombinant protein production in a bioreactor constitutes an equally vital aspect. Indeed, a sports car cannot drive fast on a gravel road. The aim of this review is to provide a comprehensive snapshot of process tools to consider for recombinant protein production in bioreactor using Y. lipolytica as a cell factory, in order to facilitate the decision-making for future strain and process engineering. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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Open AccessReview Candida glabrata: A Lot More Than Meets the Eye
Microorganisms 2019, 7(2), 39; https://doi.org/10.3390/microorganisms7020039
Received: 19 December 2018 / Revised: 21 January 2019 / Accepted: 29 January 2019 / Published: 30 January 2019
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Abstract
Candida glabrata is an opportunistic human fungal pathogen that causes superficial mucosal and life-threatening bloodstream infections in individuals with a compromised immune system. Evolutionarily, it is closer to the non-pathogenic yeast Saccharomyces cerevisiae than to the most prevalent Candida bloodstream pathogen, C. albicans [...] Read more.
Candida glabrata is an opportunistic human fungal pathogen that causes superficial mucosal and life-threatening bloodstream infections in individuals with a compromised immune system. Evolutionarily, it is closer to the non-pathogenic yeast Saccharomyces cerevisiae than to the most prevalent Candida bloodstream pathogen, C. albicans. C. glabrata is a haploid budding yeast that predominantly reproduces clonally. In this review, we summarize interactions of C. glabrata with the host immune, epithelial and endothelial cells, and the ingenious strategies it deploys to acquire iron and phosphate from the external environment. We outline various attributes including cell surface-associated adhesins and aspartyl proteases, biofilm formation and stress response mechanisms, that contribute to the virulence of C. glabrata. We further discuss how, C. glabrata, despite lacking morphological switching and secreted proteolytic activity, is able to disarm macrophage, dampen the host inflammatory immune response and replicate intracellularly. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Fungal Virulence and Commensalism)
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Open AccessArticle The Form of N Supply Determines Plant Growth Promotion by P-Solubilizing Microorganisms in Maize
Microorganisms 2019, 7(2), 38; https://doi.org/10.3390/microorganisms7020038
Received: 28 December 2018 / Revised: 16 January 2019 / Accepted: 26 January 2019 / Published: 29 January 2019
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Abstract
Phosphate-(P)-solubilizing microorganisms (PSM) are important drivers of P cycling in natural and agro-ecosystems. Their use as plant inoculants to improve P acquisition of crops has been investigated for decades. However, limited reproducibility of the expected effects, particularly under field conditions, remains a major [...] Read more.
Phosphate-(P)-solubilizing microorganisms (PSM) are important drivers of P cycling in natural and agro-ecosystems. Their use as plant inoculants to improve P acquisition of crops has been investigated for decades. However, limited reproducibility of the expected effects, particularly under field conditions, remains a major challenge. This study demonstrates that the form of nitrogen fertilization has a significant impact on the performance of various fungal and bacterial PSM inoculants in maize grown on neutral to alkaline soils with limited P availability. Under these conditions, a high soil pH-buffering capacity frequently limits the efficiency of nutrient mobilization, mediated by plant roots and microorganisms via rhizosphere acidification. In a soil pH range between 7.0 and 8.0, nitrate fertilization promoting rhizosphere alkalinisation further aggravates this problem. Accordingly, in greenhouse experiments, six strains of Pseudomonas, Bacillus, Paenibacillus, Streptomyces, and Penicillium with proven P-solubilizing potential, completely failed to promote P acquisition in maize grown on a calcareous Loess sub-soil pH 7.6 with nitrate fertilization and rock phosphate (Rock-P) as a sparingly soluble P source. However, after replacement of nitrate fertilization by ammonium, stabilized with the nitrification inhibitor 3,4-dimethylpyrazole-phosphate (DMPP), five out of seven investigated PSM inoculants (comprising 12 fungal and bacterial PSM strains) exerted beneficial effects on plant growth and reached up to 88% of the shoot biomass production of a control supplied with soluble triple-superphosphate (TSP). Stabilized ammonium combined with PSM-inoculants improved P acquisition (Trichoderma harzianum T22, Pseudomonas sp. DMSZ 13134), while other strains particularly stimulated root growth (T. harzianum OMG16, Bacillus amyloliquefaciens FZB42), which promoted the acquisition also of other mineral nutrients, such as N, K, and Mn. A similar effect was recorded under field conditions on an alkaline clay-loam soil pH 8.6. The combination of stabilized ammonium with a range of consortium products based on T. harzianum OMG16, B. amyloliquefaciens, micronutrients, and humic acids completely compensated the effect of a TSP fertilization on field establishment, nutrient acquisition, and yield formation in maize, while non-stabilized urea-di-ammonium phosphate fertilization was largely ineffective. These findings suggest that the efficiency of PSM-plant interactions can be influenced by the form of N fertilization, offering promising perspectives for synergistic effects with stabilized ammonium fertilizers. Full article
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Open AccessArticle Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes
Microorganisms 2019, 7(2), 37; https://doi.org/10.3390/microorganisms7020037
Received: 31 December 2018 / Revised: 22 January 2019 / Accepted: 23 January 2019 / Published: 27 January 2019
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Abstract
Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues [...] Read more.
Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years. Full article
(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle Inhibitory Effect of 7-Demethoxytylophorine on Penicillium italicum and its Possible Mechanism
Microorganisms 2019, 7(2), 36; https://doi.org/10.3390/microorganisms7020036
Received: 30 December 2018 / Revised: 22 January 2019 / Accepted: 24 January 2019 / Published: 26 January 2019
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Abstract
7-demethoxytylophorine (DEM) is a phenanthroindolizidine alkaloid, which is reported to be effective in inhibiting leucocytes and regulation of human immunity. However, few studies reported the inhibitory effect of DEM against plant-pathogenic fungi, particularly postharvest pathogen Penicillium italicum (P. italicum). Current studies [...] Read more.
7-demethoxytylophorine (DEM) is a phenanthroindolizidine alkaloid, which is reported to be effective in inhibiting leucocytes and regulation of human immunity. However, few studies reported the inhibitory effect of DEM against plant-pathogenic fungi, particularly postharvest pathogen Penicillium italicum (P. italicum). Current studies have investigated the antifungal activity of DEM through membrane damage and energy deficit in P. italicum. The results showed that the DEM potentially inhibits the growth of P. italicum in a dose-dependent manner. In vitro (mycelial growth and spore germination) tests showed great minimal inhibitory concentration (MIC) (1.56 µg mL−1) and minimum fugicide concentration (MFC) (6.25 µg mL−1). Microscopic analyses showed that mycelial morphology of P. italicum was severely damaged following DEM treatment. Moreover, relative electrical conductivity and lysis ability assays showed that DEM treatment aids in destroying the integrity of plasma membranes that deplete reducing sugars and soluble proteins. The activity of malate dehydrogenase (MDH) and succinate dehydrogenase (SDH) demonstrated that DEM led to the disruption of TCA cycle in P. italicum mycelia. The results of this study led us to conclude that, DEM could be used as a natural antifungal agent for controlling postharvest blue mold disease of citrus fruits caused by P. italicum. Full article
(This article belongs to the Section Food Microbiology)
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Open AccessArticle The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence
Microorganisms 2019, 7(2), 35; https://doi.org/10.3390/microorganisms7020035
Received: 8 November 2018 / Revised: 13 January 2019 / Accepted: 21 January 2019 / Published: 26 January 2019
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Abstract
The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of [...] Read more.
The sea urchin Strongylocentrotus purpuratus (order Camarodonta, family Strongylocentrotidae) can be found dominating low intertidal pool biomass on the southern coast of Oregon, USA. In this case study, three adult sea urchins were collected from their shared intertidal pool, and the bacteriome of their pharynx, gut tissue, and gut digesta, including their tide pool water and algae, was determined using targeted high-throughput sequencing (HTS) of the 16S rRNA genes and bioinformatics tools. Overall, the gut tissue demonstrated Arcobacter and Sulfurimonas (Epsilonproteobacteria) to be abundant, whereas the gut digesta was dominated by Psychromonas (Gammaproteobacteria), Propionigenium (Fusobacteria), and Flavobacteriales (Bacteroidetes). Alpha and beta diversity analyses indicated low species richness and distinct microbial communities comprising the gut tissue and digesta, while the pharynx tissue had higher richness, more closely resembling the water microbiota. Predicted functional profiles showed Kyoto Encyclopedia of Genes and Genomes (KEGG) Level-2 categories of energy metabolism, membrane transport, cell motility, and signal transduction in the gut tissue, and the gut digesta represented amino acid, carbohydrate, vitamin and cofactor metabolisms, and replication and repair. Co-occurrence network analysis showed the potential relationships and key taxa, such as the highly abundant Arcobacter and Propionigenium, influencing population patterns and taxonomic organization between the gut tissue and digesta. These results demonstrate a trend of microbial community integration, allocation, predicted metabolic roles, and taxonomic co-occurrence patterns in the S. purpuratus gut ecosystem. Full article
(This article belongs to the Section Gut Microbiota)
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Open AccessArticle A Piscibacillus sp. Isolated from A Soda Lake Exhibits Anticancer Activity Against Breast Cancer MDA-MB-231 Cells
Microorganisms 2019, 7(2), 34; https://doi.org/10.3390/microorganisms7020034
Received: 17 October 2018 / Revised: 22 January 2019 / Accepted: 23 January 2019 / Published: 26 January 2019
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Abstract
Microorganisms thrive in extreme environments and are known for synthesizing valuable metabolites. Salt-loving microorganisms can flourish in saline environments which inhibit the growth of other microbial life, and they possess the potential to produce stable and novel biomolecules for the use in biotechnological [...] Read more.
Microorganisms thrive in extreme environments and are known for synthesizing valuable metabolites. Salt-loving microorganisms can flourish in saline environments which inhibit the growth of other microbial life, and they possess the potential to produce stable and novel biomolecules for the use in biotechnological applications, including anticancer compounds. Sambhar Lake is the largest inland soda lake in India and is an appropriate habitat for halophilic bacterial and archaeal strains in terms of diversity and potential production of bioactive compounds. In the present study, a moderately halo-alkaliphilic bacterial strain C12A1 was isolated from Sambhar Lake, located in Rajasthan, India. C12A1 was gram-positive, motile, rod-shaped, formed oval endospores, produced carotenoids, and exhibited optimal growth at 37 °C in 10–15% NaCl (pH 8). C12A1 was found to be able to hydrolyze skimmed milk, gelatin, and Tween 80 but unable to hydrolyze starch and carboxymethylcellulose. C12A1 showed 98.87% and 98.50% identity in 16S rRNA gene sequence to P. halophilus and P. salipiscarius, respectively. Nevertheless, C12A1 was clustered within the clade consisting of P. salipiscarius strains, but it showed a distinct lineage. Thus, C12A1 was designated as Piscibacillus sp. Cell proliferation assay results showed that C12A1 broth extract (BEP) decreased cell viability in breast cancer MDA-MB-231 cells, which was confirmed by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. Induction of cell toxicity was visualized by microscopy. Reverse Transcriptase PCR (RT-PCR) analysis demonstrated that BEP inhibited the expression of proliferative B-cell lymphoma-extra large (Bcl-xL) and cell cycle marker Cyclin-dependent kinase 2 (CDK2) at transcript levels. Similarly, cell migration and colony formation along with mesenchymal marker vimentin and stem cell marker BMI transcripts were found to be inhibited when cells were treated with the BEP. The anti-breast cancer potential of C12A1 indicates that microorganisms inhabiting saline-alkaline habitats, with Piscibacillus sp. in particular, are a promising source for discovery of novel bioactive substances. Full article
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Open AccessArticle Cave Drip Water-Related Samples as a Natural Environment for Aromatic Hydrocarbon-Degrading Bacteria
Microorganisms 2019, 7(2), 33; https://doi.org/10.3390/microorganisms7020033
Received: 30 November 2018 / Revised: 14 January 2019 / Accepted: 15 January 2019 / Published: 25 January 2019
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Abstract
Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic [...] Read more.
Restricted contact with the external environment has allowed the development of microbial communities adapted to the oligotrophy of caves. However, nutrients can be transported to caves by drip water and affect the microbial communities inside the cave. To evaluate the influence of aromatic compounds carried by drip water on the microbial community, two limestone caves were selected in Brazil. Drip-water-saturated and unsaturated sediment, and dripping water itself, were collected from each cave and bacterial 16S rDNA amplicon sequencing and denaturing gradient gel electrophoresis (DGGE) of naphthalene dioxygenase (ndo) genes were performed. Energy-dispersive X-ray spectroscopy (EDX) and atomic absorption spectroscopy (AAS) were performed to evaluate inorganic nutrients, and GC was performed to estimate aromatic compounds in the samples. The high frequency of Sphingomonadaceae in drip water samples indicates the presence of aromatic hydrocarbon-degrading bacteria. This finding was consistent with the detection of naphthalene and acenaphthene and the presence of ndo genes in drip-water-related samples. The aromatic compounds, aromatic hydrocarbon-degrading bacteria and 16S rDNA sequencing indicate that aromatic compounds may be one of the sources of energy and carbon to the system and the drip-water-associated bacterial community contains several potentially aromatic hydrocarbon-degrading bacteria. To the best of our knowledge, this is the first work to present compelling evidence for the presence of aromatic hydrocarbon-degrading bacteria in cave drip water. Full article
(This article belongs to the Special Issue Subsurface Geomicrobiology)
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Open AccessArticle High-Throughput Rapid and Inexpensive Assay for Quantitative Determination of Low Cell-Density Yeast Cultures
Microorganisms 2019, 7(2), 32; https://doi.org/10.3390/microorganisms7020032
Received: 14 December 2018 / Revised: 12 January 2019 / Accepted: 22 January 2019 / Published: 24 January 2019
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Abstract
A procedure for microbial cell density determination with a high-throughput densitometric assay was developed to allow a precise quantification of both free and sessile cells, such as those of a biofilm, with a large range from low to high cell densities. Densitometry was [...] Read more.
A procedure for microbial cell density determination with a high-throughput densitometric assay was developed to allow a precise quantification of both free and sessile cells, such as those of a biofilm, with a large range from low to high cell densities. Densitometry was chosen because it allows fast, rapid and cost-effective measures; it is non-disruptive; and has an easy learning curve. The method setup, and the further validation, was carried out with strains of Candida albicans, C. tropicalis and C. parapsilosis. Equations were developed at the level of the single strains, of the three species and finally a general one applicable to all three species. In the cross validation, with strains absent from the training set, the method was shown to be robust and flexible. The best results were obtained with species specific equations, although the global equation performed almost as well in terms of correlation between real and estimated density values. In all cases, a correlation around 0.98 between effective and predicted density was obtained with figures ranging from 102 to 108 cells mL−1. The entire analytical part of the procedure can be accomplished with a MS Excel macro provided free of charge. Full article
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