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Microorganisms, Volume 6, Issue 3 (September 2018)

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Cover Story (view full-size image) Lactobacillus gorillae is a common lactobacillus among gorillas. This particular bacterium is [...] Read more.
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Open AccessReview Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes
Microorganisms 2018, 6(3), 95; https://doi.org/10.3390/microorganisms6030095
Received: 22 August 2018 / Revised: 1 September 2018 / Accepted: 5 September 2018 / Published: 17 September 2018
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Abstract
In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living
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In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown. Full article
(This article belongs to the Special Issue Plant Control of Symbiotic Microbe Behavior and Reproduction)
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Open AccessArticle Conservation Implications of Shifting Gut Microbiomes in Captive-Reared Endangered Voles Intended for Reintroduction into the Wild
Microorganisms 2018, 6(3), 94; https://doi.org/10.3390/microorganisms6030094
Received: 30 June 2018 / Revised: 5 September 2018 / Accepted: 11 September 2018 / Published: 12 September 2018
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Abstract
The Amargosa vole is a highly endangered rodent endemic to a small stretch of the Amargosa River basin in Inyo County, California. It specializes on a single, nutritionally marginal food source in nature. As part of a conservation effort to preserve the species,
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The Amargosa vole is a highly endangered rodent endemic to a small stretch of the Amargosa River basin in Inyo County, California. It specializes on a single, nutritionally marginal food source in nature. As part of a conservation effort to preserve the species, a captive breeding population was established to serve as an insurance colony and a source of individuals to release into the wild as restored habitat becomes available. The colony has successfully been maintained on commercial diets for multiple generations, but there are concerns that colony animals could lose gut microbes necessary to digest a wild diet. We analyzed feces from colony-reared and recently captured wild-born voles on various diets, and foregut contents from colony and wild voles. Unexpectedly, fecal microbial composition did not greatly differ despite drastically different diets and differences observed were mostly in low-abundance microbes. In contrast, colony vole foregut microbiomes were dominated by Allobaculum sp. while wild foreguts were dominated by Lactobacillus sp. If these bacterial community differences result in beneficial functional differences in digestion, then captive-reared Amargosa voles should be prepared prior to release into the wild to minimize or eliminate those differences to maximize their chance of success. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle Thermostable Xylanase Production by Geobacillus sp. Strain DUSELR13, and Its Application in Ethanol Production with Lignocellulosic Biomass
Microorganisms 2018, 6(3), 93; https://doi.org/10.3390/microorganisms6030093
Received: 5 August 2018 / Revised: 29 August 2018 / Accepted: 31 August 2018 / Published: 5 September 2018
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Abstract
The aim of the current study was to optimize the production of xylanase, and its application for ethanol production using the lignocellulosic biomass. A highly thermostable crude xylanase was obtained from the Geobacillus sp. strain DUSELR13 isolated from the deep biosphere of Homestake
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The aim of the current study was to optimize the production of xylanase, and its application for ethanol production using the lignocellulosic biomass. A highly thermostable crude xylanase was obtained from the Geobacillus sp. strain DUSELR13 isolated from the deep biosphere of Homestake gold mine, Lead, SD. Geobacillus sp. strain DUSELR13 produced 6 U/mL of the xylanase with the beechwood xylan. The xylanase production was improved following the optimization studies, with one factor at a time approach, from 6 U/mL to 19.8 U/mL with xylan. The statistical optimization with response surface methodology further increased the production to 31 U/mL. The characterization studies revealed that the crude xylanase complex had an optimum pH of 7.0, with a broad pH range of 5.0–9.0, and an optimum temperature of 75 °C. The ~45 kDa xylanase protein was highly thermostable with t1/2 of 48, 38, and 13 days at 50, 60, and 70 °C, respectively. The xylanase activity increased with the addition of Cu+2, Zn+2, K+, and Fe+2 at 1 mM concentration, and Ca+2, Zn+2, Mg+2, and Na+ at 10 mM concentration. The comparative analysis of the crude xylanase against its commercial counterpart Novozymes Cellic HTec and Dupont, Accellerase XY, showed that it performed better at higher temperature, hydrolyzing 65.4% of the beechwood at 75 °C. The DUSEL R13 showed the mettle to hydrolyze, and utilize the pretreated, and untreated lignocellulosic biomass: prairie cord grass (PCG), and corn stover (CS) as the substrate, and gave a maximum yield of 20.5 U/mL with the untreated PCG. When grown in co-culture with Geobacillus thermoglucosidasius, it produced 3.53 and 3.72 g/L ethanol, respectively with PCG, and CS. With these characteristics the xylanase under study could be an industrial success for the high temperature bioprocesses. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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Open AccessArticle Gut Bacterial Communities in Geographically Distant Populations of Farmed Sea Bream (Sparus aurata) and Sea Bass (Dicentrarchus labrax)
Microorganisms 2018, 6(3), 92; https://doi.org/10.3390/microorganisms6030092
Received: 18 July 2018 / Revised: 28 August 2018 / Accepted: 31 August 2018 / Published: 1 September 2018
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Abstract
This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order
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This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order to detect the core gut microbiota of these commercially important fish species. Data analyses resulted in no significant geographic impact in the gut microbial communities within the two host species, while strong similarities between them were also present. Our survey revealed the existence of a core gut microbiota within and between the two host species independent of diet and geographic location consisting of the Delftia, Pseudomonas, Pelomonas, Propionibacterium, and Atopostipes genera. Full article
(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)
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Open AccessCommunication Microbial Community and Potential Pathogen Shifts Along an Ornamental Fish Supply Chain
Microorganisms 2018, 6(3), 91; https://doi.org/10.3390/microorganisms6030091
Received: 21 July 2018 / Revised: 14 August 2018 / Accepted: 16 August 2018 / Published: 25 August 2018
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Abstract
There is broad interest in disease spread through the pet trade, but empirical research on hosts and pathogens in transit along actual trade routes is notably absent. Using next-generation DNA sequencing, and partnering with the ornamental fish industry, we tracked shifts in microbial
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There is broad interest in disease spread through the pet trade, but empirical research on hosts and pathogens in transit along actual trade routes is notably absent. Using next-generation DNA sequencing, and partnering with the ornamental fish industry, we tracked shifts in microbial community and potential pathogen structure associated with Sailfin Tang (Zebrasoma desjardinii) along the United States (U.S.) leg of an international supply chain. We observed striking changes in microbial diversity and composition of potential pathogens, including increased dominance of vibrios of fishes in transit. Our pilot findings suggest that high investment in fishes early in the supply chain may not matter to their long-term health depending on end destination conditions. Full article
(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)
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Open AccessReview Dietary Nutrients, Proteomes, and Adhesion of Probiotic Lactobacilli to Mucin and Host Epithelial Cells
Microorganisms 2018, 6(3), 90; https://doi.org/10.3390/microorganisms6030090
Received: 15 June 2018 / Revised: 13 August 2018 / Accepted: 14 August 2018 / Published: 21 August 2018
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Abstract
The key role of diet and environment in human health receives increasing attention. Thus functional foods, probiotics, prebiotics, and synbiotics with beneficial effects on health and ability to prevent diseases are in focus. The efficacy of probiotic bacteria has been connected with their
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The key role of diet and environment in human health receives increasing attention. Thus functional foods, probiotics, prebiotics, and synbiotics with beneficial effects on health and ability to prevent diseases are in focus. The efficacy of probiotic bacteria has been connected with their adherence to the host epithelium and residence in the gut. Several in vitro techniques are available for analyzing bacterial interactions with mucin and intestinal cells, simulating adhesion to the host in vivo. Proteomics has monitored and identified proteins of probiotic bacteria showing differential abundance elicited in vitro by exposure to food components, including potential prebiotics (e.g., certain carbohydrates, and plant polyphenols). While adhesion of probiotic bacteria influenced by various environmental factors relevant to the gastrointestinal tract has been measured previously, this was rarely correlated with changes in the bacterial proteome induced by dietary nutrients. The present mini-review deals with effects of selected emerging prebiotics, food components and ingredients on the adhesion of probiotic lactobacilli to mucin and gut epithelial cells and concomitant abundancy changes of specific bacterial proteins. Applying this in vitro synbiotics-like approach enabled identification of moonlighting and other surface-located proteins of Lactobacillus acidophilus NCFM that are possibly associated with the adhesive mechanism. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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Open AccessArticle Influence of Season and Diet on Fiber Digestion and Bacterial Community Structure in the Rumen of Muskoxen (Ovibos moschatus)
Microorganisms 2018, 6(3), 89; https://doi.org/10.3390/microorganisms6030089
Received: 28 June 2018 / Revised: 8 August 2018 / Accepted: 14 August 2018 / Published: 20 August 2018
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Abstract
We studied the relationship between fiber digestion and the composition of the bacterial community in the rumen of muskoxen at the start and the end of the annual window of plant growth from spring to fall. Eight ruminally cannulated castrated males were fed
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We studied the relationship between fiber digestion and the composition of the bacterial community in the rumen of muskoxen at the start and the end of the annual window of plant growth from spring to fall. Eight ruminally cannulated castrated males were fed brome hay or triticale straw (69.6% vs. 84.6% neutral detergent fiber, respectively) that were similar in fiber content to the sedges consumed by wild muskoxen (64.5 to 71.7% neutral detergent fiber). Muskoxen digested fiber from both forages faster and to a greater extent when straw rather than hay was consumed. Fiber digestion was therefore inducible by diet 4 in each season. We used 16S rRNA sequences from ruminal contents to study how season and diet affected the bacterial community and how the latter related to fiber digestion. We found that Bacteroidetes and Firmicutes accounted for 90% of the sequences at the level of Phylum, which is typical for the mammal gut microbiome. Using partial least square regressions, it was found that between 48% and 72% of the variation in fiber digestion was associated with 36–43 genera of bacteria. The main fibrolytic bacteria typical of domestic ruminants were generally not among the most important bacteria associated with fiber digestion in muskoxen. This reveals that muskoxen rely upon on a large suite of bacterial genera that are largely distinct from those used by other ruminants to digest the cell walls of plants that vary widely in both abundance and nutritional quality through the year. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle The Protean Acremonium. A. sclerotigenum/egyptiacum: Revision, Food Contaminant, and Human Disease
Microorganisms 2018, 6(3), 88; https://doi.org/10.3390/microorganisms6030088
Received: 2 June 2018 / Revised: 12 August 2018 / Accepted: 13 August 2018 / Published: 16 August 2018
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Abstract
Acremonium is known to be regularly isolated from food and also to be a cause of human disease. Herein, we resolve some sources of confusion that have strongly hampered the accurate interpretation of these and other isolations. The recently designated type species of
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Acremonium is known to be regularly isolated from food and also to be a cause of human disease. Herein, we resolve some sources of confusion that have strongly hampered the accurate interpretation of these and other isolations. The recently designated type species of the genus Acremonium, A. alternatum, is known only from a single isolate, but it is the closest known relative of what may be one of the planet’s most successful organisms, Acremonium sclerotigenum/egyptianum, shown herein to be best called by its earliest valid name, A. egyptiacum. The sequencing of ribosomal internal transcribed spacer (ITS) regions, actin genes, or both for 72 study isolates within this group allowed the full range of morphotypes and ITS barcode types to be elucidated, along with information on temperature tolerance and habitat. The results showed that nomenclatural confusion and frequent misidentifications facilitated by morphotaxonomy, along with misidentified early sequence deposits, have obscured the reality that this species is, in many ways, the definitive match of the historical concept of Acremonium: a pale orange or dull greenish-coloured monophialidic hyphomycete, forming cylindrical, ellipsoidal, or obovoid conidia in sticky heads or obovoid conidia in dry chains, and acting ecologically as a soil organism, marine organism, plant pathogen, plant endophyte, probable insect pathogen, human opportunistic pathogen, food contaminant, probable dermatological communicable disease agent, and heat-tolerant spoilage organism. Industrially, it is already in exploratory use as a producer of the antibiotic ascofuranone, active against trypanosomes, cryptosporidia, and microsporidia, and additional applications are in development. The genus-level clarification of the phylogeny of A. egyptiacum shows other historic acremonia belong to separate genera, and two are here described, Parasarocladium for the Acremonium radiatum complex and Kiflimonium for the Acremonium curvulum complex. Full article
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Open AccessReview Messing with the Sentinels—The Interaction of Staphylococcus aureus with Dendritic Cells
Microorganisms 2018, 6(3), 87; https://doi.org/10.3390/microorganisms6030087
Received: 6 July 2018 / Revised: 12 August 2018 / Accepted: 14 August 2018 / Published: 15 August 2018
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Abstract
Staphylococcus aureus (S. aureus) is a dangerous pathogen as well as a frequent colonizer, threatening human health worldwide. Protection against S. aureus infection is challenging, as the bacteria have sophisticated strategies to escape the host immune response. To maintain equilibrium with
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Staphylococcus aureus (S. aureus) is a dangerous pathogen as well as a frequent colonizer, threatening human health worldwide. Protection against S. aureus infection is challenging, as the bacteria have sophisticated strategies to escape the host immune response. To maintain equilibrium with S. aureus, both innate and adaptive immune effector mechanisms are required. Dendritic cells (DCs) are critical players at the interface between the two arms of the immune system, indispensable for inducing specific T cell responses. In this review, we highlight the importance of DCs in mounting innate as well as adaptive immune responses against S. aureus with emphasis on their role in S. aureus-induced respiratory diseases. We also review what is known about mechanisms that S. aureus has adopted to evade DCs or manipulate these cells to its advantage. Full article
(This article belongs to the Special Issue Staphylococcus aureus Infection and Antimicrobial Resistance)
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Open AccessArticle Characteristics of Gorilla-Specific Lactobacillus Isolated from Captive and Wild Gorillas
Microorganisms 2018, 6(3), 86; https://doi.org/10.3390/microorganisms6030086
Received: 30 June 2018 / Revised: 11 August 2018 / Accepted: 14 August 2018 / Published: 14 August 2018
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Abstract
Lactic acid bacteria (LAB) reside in a wide range of mammals, such as autochthonous intestinal bacteria. In this paper, we present the phenotypic and phylogenetic characteristics of gorilla-specific LAB. Lactobacillus gorillae—previously isolated from the wild and captive western lowland gorillas (Gorilla
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Lactic acid bacteria (LAB) reside in a wide range of mammals, such as autochthonous intestinal bacteria. In this paper, we present the phenotypic and phylogenetic characteristics of gorilla-specific LAB. Lactobacillus gorillae—previously isolated from the wild and captive western lowland gorillas (Gorilla gorilla gorilla)—were successfully isolated from wild mountain gorillas (Gorilla gorilla beringei) in addition to other captive and wild western lowland gorillas. The strains from wild gorillas could ferment D-xylose, arbutine, cellobiose, and trehalose better than those from captive gorillas. By contrast, tolerance to NaCl was higher in isolates from captive gorillas than in those from wild gorillas. This tendency may have been induced by regular foods in zoos, which contain sufficient amount of salts but less amount of indigestible fiber and plant secondary metabolites compared to foods in the wild. All strains of L. gorillae showed inhibitory activities to enteric pathogenic bacteria; however, the activity was significantly higher for strains from wild gorillas than for those from captive gorillas. This may have been induced by the captive condition with routine veterinary intervention. Since L. gorillae can grow in the gastrointestinal tract of gorillas in captivity, the strains from wild mountain gorillas are potential probiotics for gorillas under captive conditions. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle New 19-Residue Peptaibols from Trichoderma Clade Viride
Microorganisms 2018, 6(3), 85; https://doi.org/10.3390/microorganisms6030085
Received: 2 July 2018 / Revised: 7 August 2018 / Accepted: 10 August 2018 / Published: 12 August 2018
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Abstract
Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues
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Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues of peptaibols, i.e., α-aminoisobutyric acid (Aib), isovaline (Iva), and the C-terminal 1,2-amino alcohol make them unique among peptides. In this study, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS. The examined strains appeared to produce 19-residue peptaibols, most of which are unknown from literature, but their amino acid sequences are similar to those of trikoningins, tricholongins, trichostrigocins, trichorzianins, and trichorzins. A new group of peptaibols detected in T. koningiopsis are described here under the name “Koningiopsin”. Trikoningin KA V, the closest peptaibol compound to the peptaibols produced by these two strains, was selected for structural investigation by short MD simulation, which revealed that many residues show high preference for left handed helix formation. The bioactivity of the peptaibol mixtures produced by T. koningiopsis and T. gamsii was tested on agar plates against bacteria, yeasts, and filamentous fungi. The results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures. Full article
(This article belongs to the Special Issue Antimicrobial Proteins in Filamentous Fungi)
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Open AccessReview Diversity of Myxobacteria—We Only See the Tip of the Iceberg
Microorganisms 2018, 6(3), 84; https://doi.org/10.3390/microorganisms6030084
Received: 6 June 2018 / Revised: 6 August 2018 / Accepted: 8 August 2018 / Published: 11 August 2018
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Abstract
The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites
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The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites for decades. To date, about 600 substances could be described, many of them with antibacterial, antifungal, or cytostatic activity. But, recent cultivation-independent studies on marine, terrestrial, or uncommon habitats unequivocally demonstrate that the number of uncultured myxobacteria is much higher than would be expected from the number of cultivated strains. Although several highly promising myxobacterial taxa have been identified recently, this so-called Great Plate Count Anomaly must be overcome to get broader access to new secondary metabolite producers. In the last years it turned out that especially new species, genera, and families of myxobacteria are promising sources for new bioactive metabolites. Therefore, the cultivation of the hitherto uncultivable ones is our biggest challenge. Full article
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Open AccessArticle Exploring the Impact of the Biofloc Rearing System and an Oral WSSV Challenge on the Intestinal Bacteriome of Litopenaeus vannamei
Microorganisms 2018, 6(3), 83; https://doi.org/10.3390/microorganisms6030083
Received: 4 July 2018 / Revised: 3 August 2018 / Accepted: 4 August 2018 / Published: 8 August 2018
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Abstract
We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition
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We provide a global overview of the intestinal bacteriome of Litopenaeus vannamei in two rearing systems and after an oral challenge by the White spot syndrome virus (WSSV). By using a high-throughput 16S rRNA gene sequencing technology, we identified and compared the composition and abundance of bacterial communities from the midgut of shrimp reared in the super-intensive biofloc technology (BFT) and clear seawater system (CWS). The predominant bacterial group belonged to the phylum Proteobacteria, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes. Within Proteobacteria, the family Vibrionaceae, which includes opportunistic shrimp pathogens, was more abundant in CWS than in BFT-reared shrimp. Whereas the families Rhodobacteraceae and Enterobacteriaceae accounted for almost 20% of the bacterial communities of shrimp cultured in BFT, they corresponded to less than 3% in CWS-reared animals. Interestingly, the WSSV challenge dramatically changed the bacterial communities in terms of composition and abundance in comparison to its related unchallenged group. Proteobacteria remained the dominant phylum. Vibrionaceae was the most affected in BFT-reared shrimp (from 11.35 to 20.80%). By contrast, in CWS-reared animals the abundance of this family decreased from 68.23 to 23.38%. Our results provide new evidence on the influence of both abiotic and biotic factors on the gut bacteriome of aquatic species of commercial interest. Full article
(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)
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Open AccessArticle The Species-Specific Responses of Freshwater Diatoms to Elevated Temperatures Are Affected by Interspecific Interactions
Microorganisms 2018, 6(3), 82; https://doi.org/10.3390/microorganisms6030082
Received: 11 June 2018 / Revised: 30 July 2018 / Accepted: 3 August 2018 / Published: 7 August 2018
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Abstract
Numerous experimental simulations with different warming scenarios have been conducted to predict how algae will respond to warming, but their conclusions are sometimes contradictory to each other. This might be due to a failure to consider interspecific interactions. In this study, the dominant
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Numerous experimental simulations with different warming scenarios have been conducted to predict how algae will respond to warming, but their conclusions are sometimes contradictory to each other. This might be due to a failure to consider interspecific interactions. In this study, the dominant diatom species in a seasonal succession were isolated and verified to adapt to different temperature ranges by constant temperature experiment. Both unialgal and mixed cultures were exposed to two fluctuant temperature treatments that simulated the temperature variations from early spring to summer, with one treatment 4 °C higher (warming scenario) than the other. We found that the specific response of diatoms to warming was affected by interspecific interactions. Spring warming had no significant effect on eurythermal species and had a positive effect on the abundance of warm-adapted diatom species, but interspecific interactions reduced this promotional effect. Cold-adapted species had a negative response to spring warming in the presence of other diatom species but had a positive response to early spring warming in the absence of interspecific interactions. In addition, warming resulted in the growth of all diatom species peaking earlier in unialgal cultures, but this effect could be weakened or amplified by interspecies interactions in mixed cultures. Our results suggest that the specific diatom species with different optimal growth temperature ranges responding to warming were expected if there were no interspecific interactions. However, in natural environments, the inevitable and complex interspecific interactions will influence the responses of diatoms to warming. This important factor should not be ignored in the prediction of organism responses to climate warming. Full article
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Open AccessArticle Directed Evolution of Saccharomyces cerevisiae for Increased Selenium Accumulation
Microorganisms 2018, 6(3), 81; https://doi.org/10.3390/microorganisms6030081
Received: 28 June 2018 / Revised: 20 July 2018 / Accepted: 2 August 2018 / Published: 6 August 2018
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Abstract
Selenium-enriched yeast (selenium yeast) are one of the most popular sources of selenium supplementation used in the agriculture and human nutritional supplements industries. To enhance the production efficiency of selenium yeast, we sought to develop a method to identify, and ultimately select for,
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Selenium-enriched yeast (selenium yeast) are one of the most popular sources of selenium supplementation used in the agriculture and human nutritional supplements industries. To enhance the production efficiency of selenium yeast, we sought to develop a method to identify, and ultimately select for, strains of yeast with enhanced selenium accumulation capabilities. Selenite resistance of four genetically diverse strains of Saccharomyces cerevisiae was assayed in various conditions, including varying carbon sources, nitrogen sources, and phosphate amounts, and they were correlated with selenium accumulation in a commercially relevant selenium-containing growth medium. Glycerol- and selenite-containing media was used to select for six yeast isolates with enhanced selenite resistance. One isolate was found to accumulate 10-fold greater selenium (0.13 to 1.4 mg Se g−1 yeast) than its parental strain. Glycerol- and selenium-containing medium can be used to select for strains of yeast with enhanced selenium accumulation capability. The methods identified can lead to isolation of industrial yeast strains with enhanced selenium accumulation capabilities that can result in greater cost efficiency of selenium yeast production. Additionally, the selection method does not involve the construction of transgenic yeast, and thus produces yeasts suitable for use in human food and nutrient supplements. Full article
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Open AccessArticle Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source
Microorganisms 2018, 6(3), 80; https://doi.org/10.3390/microorganisms6030080
Received: 25 May 2018 / Revised: 1 August 2018 / Accepted: 2 August 2018 / Published: 5 August 2018
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This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started
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This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started with two different inocula were used. These reactors initially showed great differences depending on inoculum source, but eventually showed similar performance and overall microbial community structure. At the start of the present experiment, the substrate was complemented with milled feed wheat, added all at once or divided into two portions. The starting hypothesis was that process performance depends on initial inoculum source and microbial diversity, and thus that reactor performance is influenced by the feeding regime. In response to the substrate change, all reactors showed increases and decreases in volumetric and specific methane production, respectively. However, specific methane yield and development of the microbial community showed differences related to the initial inoculum source, confirming the hypothesis. However, the different feeding regimes had only minor effects on process performance and overall community structure, but still induced differences in the cellulose-degrading community and in cellulose degradation. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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Open AccessReview Opportunistic Water-Borne Human Pathogenic Filamentous Fungi Unreported from Food
Microorganisms 2018, 6(3), 79; https://doi.org/10.3390/microorganisms6030079
Received: 14 June 2018 / Revised: 2 August 2018 / Accepted: 2 August 2018 / Published: 3 August 2018
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Abstract
Clean drinking water and sanitation are fundamental human rights recognized by the United Nations (UN) General Assembly and the Human Rights Council in 2010 (Resolution 64/292). In modern societies, water is not related only to drinking, it is also widely used for personal
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Clean drinking water and sanitation are fundamental human rights recognized by the United Nations (UN) General Assembly and the Human Rights Council in 2010 (Resolution 64/292). In modern societies, water is not related only to drinking, it is also widely used for personal and home hygiene, and leisure. Ongoing human population and subsequent environmental stressors challenge the current standards on safe drinking and recreational water, requiring regular updating. Also, a changing Earth and its increasingly frequent extreme weather events and climatic changes underpin the necessity to adjust regulation to a risk-based approach. Although fungi were never introduced to water quality regulations, the incidence of fungal infections worldwide is growing, and changes in antimicrobial resistance patterns are taking place. The presence of fungi in different types of water has been thoroughly investigated during the past 30 years only in Europe, and more than 400 different species were reported from ground-, surface-, and tap-water. The most frequently reported fungi, however, were not waterborne, but are frequently related to soil, air, and food. This review focuses on waterborne filamentous fungi, unreported from food, that offer a pathogenic potential. Full article
Open AccessReview The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human
Microorganisms 2018, 6(3), 78; https://doi.org/10.3390/microorganisms6030078
Received: 29 June 2018 / Revised: 25 July 2018 / Accepted: 30 July 2018 / Published: 2 August 2018
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Abstract
Glycoproteins are major players in the mucus protective barrier in the gastrointestinal and other mucosal surfaces. In particular the mucus glycoproteins, or mucins, are responsible for the protective gel barrier. They are characterized by their high carbohydrate content, present in their variable number,
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Glycoproteins are major players in the mucus protective barrier in the gastrointestinal and other mucosal surfaces. In particular the mucus glycoproteins, or mucins, are responsible for the protective gel barrier. They are characterized by their high carbohydrate content, present in their variable number, tandem repeat domains. Throughout evolution the mucins have been maintained as integral components of the mucosal barrier, emphasizing their essential biological status. The glycosylation of the mucins is achieved through a series of biosynthetic pathways processes, which generate the wide range of glycans found in these molecules. Thus mucins are decorated with molecules having information in the form of a glycocode. The enteric microbiota interacts with the mucosal mucus barrier in a variety of ways in order to fulfill its many normal processes. How bacteria read the glycocode and link to normal and pathological processes is outlined in the review. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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Open AccessArticle Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (Lagopus muta japonica) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria
Microorganisms 2018, 6(3), 77; https://doi.org/10.3390/microorganisms6030077
Received: 26 June 2018 / Revised: 23 July 2018 / Accepted: 25 July 2018 / Published: 28 July 2018
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Abstract
Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of
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Preservation of indigenous gastrointestinal microbiota is critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we compared the cecal microbial composition of wild living Japanese rock ptarmigans (Lagopus muta japonica) in different locations of Japanese mountains, and the dominant cecal microbial structure of wild Japanese rock ptarmigans is elucidated. Coriobacteraceae and Lachnospraceae were the two dominant bacterial families in all samples analyzed. At the genus level, 10 genera Olsenella, Actinomyces, Megasphaera, Slackia, Cloacibacillus, Bifidobacterium,Escherichia,Dialister, Megamonas, and Bilophila were dominant. These results reveal the high level of coexistence of lactic acid bacteria (Olsenella and Bifidobacterium) and lactate-utilizing bacteria (Megasphaera). This coexistence should be taken into account for the successful breeding of captive Japanese rock ptarmigans in the national conservation program. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway
Microorganisms 2018, 6(3), 76; https://doi.org/10.3390/microorganisms6030076
Received: 31 May 2018 / Revised: 11 July 2018 / Accepted: 19 July 2018 / Published: 25 July 2018
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Abstract
Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic
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Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic animals. In this study, we metabarcoded the 16S rRNA region of faecal samples from muskoxen of Northeast Greenland, Northwest Greenland and Norway, and quantified the effects of physiological and temporal factors on bacterial composition. We found significant effects of body mass, year of sampling and location on the gut bacterial communities of North East Greenland muskoxen. These effects were however dwarfed by the effects of location, emphasizing the importance of the local ecology on the gut bacterial community. Habitat alterations and rising temperatures may therefore have a considerable impact on muskoxen health and reproductive success. Moreover, muskoxen are hunted and consumed in Greenland, Canada and Alaska; therefore, this study also screened for potential zoonoses of food safety interest. A total of 13 potentially zoonotic genera were identified, including the genera Erysipelothrix and Yersinia implicated in recent mass die-offs of the muskoxen themselves. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessReview Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How?
Microorganisms 2018, 6(3), 75; https://doi.org/10.3390/microorganisms6030075
Received: 1 June 2018 / Revised: 3 July 2018 / Accepted: 12 July 2018 / Published: 23 July 2018
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Abstract
Akkermansia muciniphila is a mucin-degrading bacterium of the phylum Verrucomicrobia. Its abundance in the human intestinal tract is inversely correlated to several disease states. A. muciniphila resides in the mucus layer of the large intestine, where it is involved in maintaining intestinal integrity.
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Akkermansia muciniphila is a mucin-degrading bacterium of the phylum Verrucomicrobia. Its abundance in the human intestinal tract is inversely correlated to several disease states. A. muciniphila resides in the mucus layer of the large intestine, where it is involved in maintaining intestinal integrity. We explore the presence of Akkermansia-like spp. based on its 16S rRNA sequence and metagenomic signatures in the human body so as to understand its colonization pattern in time and space. A. muciniphila signatures were detected in colonic samples as early as a few weeks after birth and likely could be maintained throughout life. The sites where Akkermansia-like sequences (including Verrucomicrobia phylum and/or Akkermansia spp. sequences found in the literature) were detected apart from the colon included human milk, the oral cavity, the pancreas, the biliary system, the small intestine, and the appendix. The function of Akkermansia-like spp. in these sites may differ from that in the mucosal layer of the colon. A. muciniphila present in the appendix or in human milk could play a role in the re-colonization of the colon or breast-fed infants, respectively. In conclusion, even though A. muciniphila is most abundantly present in the colon, the presence of Akkermansia-like spp. along the digestive tract indicates that this bacterium might have more functions than those currently known. Full article
(This article belongs to the Special Issue Gut Bacteria-Mucus Interaction)
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Open AccessArticle Variability in Characterizing Escherichia coli from Cattle Feces: A Cautionary Tale
Microorganisms 2018, 6(3), 74; https://doi.org/10.3390/microorganisms6030074
Received: 15 June 2018 / Revised: 17 July 2018 / Accepted: 20 July 2018 / Published: 21 July 2018
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Abstract
Shiga toxin-producing Escherichia coli (STEC) are diverse bacteria, with seven serogroups (O26, O45, O103, O111, O121, O145, O157; “Top 7”) of interest due to their predominance in human disease. Confirmation of STEC relies on a combination of culturing, immunological and molecular assays, but
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Shiga toxin-producing Escherichia coli (STEC) are diverse bacteria, with seven serogroups (O26, O45, O103, O111, O121, O145, O157; “Top 7”) of interest due to their predominance in human disease. Confirmation of STEC relies on a combination of culturing, immunological and molecular assays, but no single gold standard for identification exists. In this study, we compared analysis of STEC between three independent laboratories (LAB) using different methodologies. In LAB A, colonies of Top 7 were picked after serogroup-specific immunomagnetic separation of feces from western-Canadian slaughter cattle. A fraction of each colony was tested by PCR (stx1, stx2, eae, O group), and Top 7 isolates were saved as glycerol stocks (n = 689). In LAB B, a subsample of isolates (n = 171) were evaluated for stx1 and stx2 using different primer sets. For this, approximately half of the PCR were performed using original DNA template provided by LAB A and half using DNA extracted from sub-cultured isolates. All Top 7 isolates were sub-cultured by LAB A and shipped to LAB C for traditional serotyping (TS) to determine O and H groups, with PCR-confirmation of virulence genes using a third set of primers. By TS, 76% of O groups (525/689) matched PCR-determined O groups. Lowest proportions (p < 0.05) of O group matches between PCR and TS (62.6% and 69.8%) occurred for O26 and O45 serogroups, respectively. PCR-detection of stx differed most between LAB A and LAB C. Excluding isolates where O groups by PCR and TS did not match, detection of stx1 was most consistent (p < 0.01) for O111 and O157:H7/NM. In contrast, for O45 and O103, stx1 was detected in >65% of isolates by LAB A and <5% by LAB C. Stx2 was only detected by LAB C in isolates of serogroups O121, O145, and O157:H7/NM. LAB B also detected stx2 in O26 and O157:H12/H29, while LAB A detected stx2 in all serogroups. Excluding O111 and O157:H7/NM, marked changes in stx detection were observed between initial isolation and sub-cultures of the same isolate. While multiple explanations exist for discordant O-typing between PCR and TS and for differences in stx detection across labs, these data suggest that assays for STEC classification may require re-evaluation and/or standardization. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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Open AccessReview Antiviral Compounds from Myxobacteria
Microorganisms 2018, 6(3), 73; https://doi.org/10.3390/microorganisms6030073
Received: 25 May 2018 / Revised: 13 July 2018 / Accepted: 17 July 2018 / Published: 19 July 2018
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Abstract
Viral infections including human immunodeficiency virus (HIV), cytomegalovirus (CMV), hepatitis B virus (HBV), and hepatitis C virus (HCV) pose an ongoing threat to human health due to the lack of effective therapeutic agents. The re-emergence of old viral diseases such as the recent
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Viral infections including human immunodeficiency virus (HIV), cytomegalovirus (CMV), hepatitis B virus (HBV), and hepatitis C virus (HCV) pose an ongoing threat to human health due to the lack of effective therapeutic agents. The re-emergence of old viral diseases such as the recent Ebola outbreaks in West Africa represents a global public health issue. Drug resistance and toxicity to target cells are the major challenges for the current antiviral agents. Therefore, there is a need for identifying agents with novel modes of action and improved efficacy. Viral-based illnesses are further aggravated by co-infections, such as an HIV patient co-infected with HBV or HCV. The drugs used to treat or manage HIV tend to increase the pathogenesis of HBV and HCV. Hence, novel antiviral drug candidates should ideally have broad-spectrum activity and no negative drug-drug interactions. Myxobacteria are in the focus of this review since they produce numerous structurally and functionally unique bioactive compounds, which have only recently been screened for antiviral effects. This research has already led to some interesting findings, including the discovery of several candidate compounds with broad-spectrum antiviral activity. The present review looks at myxobacteria-derived antiviral secondary metabolites. Full article
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Open AccessArticle Evaluation of Antimicrobial, Enzyme Inhibitory, Antioxidant and Cytotoxic Activities of Partially Purified Volatile Metabolites of Marine Streptomyces sp.S2A
Microorganisms 2018, 6(3), 72; https://doi.org/10.3390/microorganisms6030072
Received: 30 April 2018 / Revised: 6 July 2018 / Accepted: 13 July 2018 / Published: 18 July 2018
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Abstract
In the present study, marine actinobacteria Streptomyces sp.S2A was isolated from the Gulf of Mannar, India. Identification was carried out by 16S rRNA analysis. Bioactive metabolites were extracted by solvent extraction method. The metabolites were assayed for antagonistic activity against bacterial and fungal
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In the present study, marine actinobacteria Streptomyces sp.S2A was isolated from the Gulf of Mannar, India. Identification was carried out by 16S rRNA analysis. Bioactive metabolites were extracted by solvent extraction method. The metabolites were assayed for antagonistic activity against bacterial and fungal pathogens, inhibition of α-glucosidase and α-amylase enzymes, antioxidant activity and cytotoxic activity against various cell lines. The actinobacterial extract showed significant antagonistic activity against four gram-positive and two gram-negative pathogens. Excellent reduction in the growth of fungal pathogens was also observed. The minimum inhibitory concentration of the partially purified extract (PPE) was determined as 31.25 μg/mL against Klebsiella pneumoniae, 15.62 μg/mL against Staphylococcus epidermidis, Staphylococcus aureus and Bacillus cereus. The lowest MIC was observed against Micrococcus luteus as 7.8 μg/mL. MIC against fungal pathogens was determined as 62.5 μg/mL against Bipolaris maydis and 15.62 μg/mL against Fusarium moniliforme. The α-glucosidase and α-amylase inhibitory potential of the fractions were carried out by microtiter plate method. IC50 value of active fraction for α-glucosidase and α-amylase inhibition was found to be 21.17 μg/mL and 20.46 μg/mL respectively. The antioxidant activity of partially purified extract (PPE) (DPPH, ABTS, FRAP and Metal chelating activity) were observed and were also found to have significant cytotoxic activity against HT-29, MDA and U-87MG cell lines. The compound analysis was performed using gas chromatography-mass spectrometry (GC-MS) and resulted in three constituents; pyrrolo[1–a]pyrazine-1,4-dione,hexahydro-3-(2-methylpropyl)-, being the main component (80%). Overall, the strain possesses a wide spectrum of antimicrobial, enzyme inhibitory, antioxidant and cytotoxic activities which affords the production of significant bioactive metabolites as potential pharmacological agents. Full article
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Open AccessArticle Detection of Legionella anisa in Water from Hospital Dental Chair Units and Molecular Characterization by Whole-Genome Sequencing
Microorganisms 2018, 6(3), 71; https://doi.org/10.3390/microorganisms6030071
Received: 19 June 2018 / Revised: 13 July 2018 / Accepted: 16 July 2018 / Published: 18 July 2018
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Abstract
This study aims to assess contamination with Legionella spp. in water from dental chair units (DCUs) of a hospital dental ward and to perform its molecular characterization by whole-genome sequencing (WGS). We collect eight water samples (250 mL) from four DCUs (sink and
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This study aims to assess contamination with Legionella spp. in water from dental chair units (DCUs) of a hospital dental ward and to perform its molecular characterization by whole-genome sequencing (WGS). We collect eight water samples (250 mL) from four DCUs (sink and water-syringe). Samples are tested for the presence of Legionella spp. (CFUs/mL) by culturing according to the Nederland Norm (NEN) 6265. Three DCUs are found positive for Legionella anisa, and four isolates are cultured (sink n = 2, water-syringe n = 1; two isolates from the same chair) with 1 × 102 CFU/mL. Whole-genome multi-locus sequence typing (wgMLST) results indicate that all strains belong to the same cluster with two to four allele differences. Classical culture combined with WGS allows the identification of a unique clone of L. anisa in several DCUs in the same hospital dental ward. This may indicate a common contamination source in the dental unit waterlines, which was fixed by replacing the chairs and main pipeline of the unit. Our results reveal tap water contamination in direct contact with patients and the usefulness of WGS to investigate bacterial molecular epidemiology. Full article
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Open AccessArticle Zoonotic Fecal Pathogens and Antimicrobial Resistance in Canadian Petting Zoos
Microorganisms 2018, 6(3), 70; https://doi.org/10.3390/microorganisms6030070
Received: 12 June 2018 / Revised: 9 July 2018 / Accepted: 11 July 2018 / Published: 16 July 2018
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Abstract
This study aimed to better understand the potential public health risk associated with zoonotic pathogens in agricultural fairs and petting zoos in Canada. Prevalence of Salmonella, Shiga toxin-producing Escherichia coli (STEC) O157:H7, and top six non-O157 STEC serogroups in feces (n
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This study aimed to better understand the potential public health risk associated with zoonotic pathogens in agricultural fairs and petting zoos in Canada. Prevalence of Salmonella, Shiga toxin-producing Escherichia coli (STEC) O157:H7, and top six non-O157 STEC serogroups in feces (n = 88), hide/feather (n = 36), and hand rail samples (n = 46) was assessed, as well as distributions of antimicrobial resistant (AMR) broad and extended-spectrum β-lactamase (ESBL)-producing E. coli. Prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in pig nasal swabs (n = 4), and Campylobacter, Cryptosporidium, and Giardia in feces was also assessed. Neither Salmonella nor MRSA were detected. Campylobacter spp. were isolated from 32% of fecal samples. Cryptosporidium and Giardia were detected in 2% and 15% of fecal samples, respectively. Only one fecal sample was positive for STEC O157, whereas 22% were positive for non-O157 STEC. Multi-drug resistance (MDR) to antibiotics classified as critically and highly important in human medicine was proportionally greatest in E. coli from cattle feces. The β-lactamase-producing E. coli from pig, horse/donkey feces, and hand rail samples, as well as the STEC E. coli from handrail swabs were MDR. The diversity and prevalence of zoonotic pathogens and AMR bacteria detected within agricultural fairs and petting zoos emphasize the importance of hygienic practices and sanitization with respect to reducing associated zoonotic risks. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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Open AccessArticle Inhibitory Effect of PgAFP and Protective Cultures on Aspergillus parasiticus Growth and Aflatoxins Production on Dry-Fermented Sausage and Cheese
Microorganisms 2018, 6(3), 69; https://doi.org/10.3390/microorganisms6030069
Received: 31 May 2018 / Revised: 29 June 2018 / Accepted: 11 July 2018 / Published: 13 July 2018
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Abstract
Aflatoxigenic molds can grow and produce aflatoxins on dry-fermented meat and cheese. The small, basic, cysteine-rich antifungal protein PgAFP displays a time-limited inhibitory ability against unwanted molds by increasing reactive oxygen species (ROS), which can lead to increased aflatoxin production. However, calcium abolishes
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Aflatoxigenic molds can grow and produce aflatoxins on dry-fermented meat and cheese. The small, basic, cysteine-rich antifungal protein PgAFP displays a time-limited inhibitory ability against unwanted molds by increasing reactive oxygen species (ROS), which can lead to increased aflatoxin production. However, calcium abolishes the inhibitory effect of PgAFP on certain Aspergillus spp. To maximize the antifungal effect, this protein may be combined with protective cultures. Yeasts and lactic acid bacteria may counteract the impact of calcium on PgAFP fungal inhibition. The objective of this work was to study the effect of PgAFP and different combined treatments with Debaryomyces hansenii and/or Pediococcus acidilactici against growth of and aflatoxin production by an aflatoxigenic strain of Aspergillus parasiticus in both culture media and dry-fermented foods with low or high calcium levels. Aflatoxins production was increased by PgAFP but dramatically reduced by P. acidilactici in low calcium culture medium, whereas in the Ca-enriched culture medium, all treatments tested led to low aflatoxins levels. To study whether PgAFP and the protective microorganisms interfere with ROS and aflatoxin production, the relative expression of genes foxA, which is involved in peroxisomal β-oxidation, and aflP, which is required for aflatoxin biosynthesis, were evaluated. The aflatoxin overproduction induced by PgAFP seems not to be linked to peroxisomal β-oxidation. The combination of PgAFP and D. hansenii provided a successful inhibitory effect on A. parasiticus growth as well as on aflatoxin production on sliced dry-fermented sausage and cheese ripened up to 15 days, whereas P. acidilactici did not further enhance the protective effect of the two former agents. Therefore, the combined treatment of PgAFP and D. hansenii seems to provide a promising protective mean against aflatoxin-producing A. parasiticus on dry-fermented foods. Full article
(This article belongs to the Special Issue Antimicrobial Proteins in Filamentous Fungi)
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Open AccessBrief Report Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll
Microorganisms 2018, 6(3), 68; https://doi.org/10.3390/microorganisms6030068
Received: 30 May 2018 / Revised: 4 July 2018 / Accepted: 10 July 2018 / Published: 12 July 2018
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Abstract
The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a
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The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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Open AccessArticle Transcription of IVIAT and Virulence Genes in Photobacterium damselae subsp. piscicida Infecting Solea senegalensis
Microorganisms 2018, 6(3), 67; https://doi.org/10.3390/microorganisms6030067
Received: 19 June 2018 / Revised: 9 July 2018 / Accepted: 10 July 2018 / Published: 12 July 2018
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Abstract
Photobacterium damselae subsp. piscicida (Phdp) is responsible for disease outbreaks in marine aquaculture worldwide. Solea senegalensis, a valuable fish species for aquaculture in the south of Europe, is frequently affected by this pathogen. It is well established that bacteria respond
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Photobacterium damselae subsp. piscicida (Phdp) is responsible for disease outbreaks in marine aquaculture worldwide. Solea senegalensis, a valuable fish species for aquaculture in the south of Europe, is frequently affected by this pathogen. It is well established that bacteria respond to environmental signals and, in the case of pathogens, this ability may determine the outcome of their interaction with the host. Determination of gene expression under in vivo conditions constitutes a valuable tool in the assessment of microbial pathogenesis. Considering that different hosts may represent different environments for the pathogen, expression of Phdp virulence and in vivo induced antigen (IVIAT) genes during S. senegalensis infection has been determined in the present work. Increased transcription of genes encoding proteins involved in iron acquisition (Irp1, Irp2, HutB and HutD), oxidative stress defence (AhpC and Sod), adhesion (PDP_0080), toxins (AIP56) and metabolism (Impdh, Shmt and AlaRS) were detected in Phdp infecting S. senegalensis head kidney or liver. The highest increases corresponded to genes involved in survival under iron limiting conditions and oxidative stress, indicating their essential role during infection of sole. Results obtained give insight into Phdp virulence strategies and contribute to the identification of promising targets for the control of photobacteriosis. Full article
(This article belongs to the Special Issue Marine Vibrios and Photobacteria: Taxonomy, Ecology and Pathogenesis)
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Open AccessReview Cellulases from Thermophiles Found by Metagenomics
Microorganisms 2018, 6(3), 66; https://doi.org/10.3390/microorganisms6030066
Received: 21 June 2018 / Revised: 4 July 2018 / Accepted: 5 July 2018 / Published: 10 July 2018
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Abstract
Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a
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Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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