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Microorganisms, Volume 6, Issue 1 (March 2018)

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Cover Story (view full-size image) It is now over a decade since recA and tly gene loci were adopted for sequence typing and [...] Read more.
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Editorial

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Open AccessEditorial Acknowledgement to Reviewers of Microorganisms in 2017
Microorganisms 2018, 6(1), 7; doi:10.3390/microorganisms6010007
Received: 12 January 2018 / Accepted: 12 January 2018 / Published: 12 January 2018
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Abstract
Peer review is an essential part in the publication process, ensuring that Microorganisms maintains high quality standards for its published papers [...]
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Research

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Open AccessArticle Unusually High Incidences of Staphylococcus aureus Infection within Studies of Ventilator Associated Pneumonia Prevention Using Topical Antibiotics: Benchmarking the Evidence Base
Microorganisms 2018, 6(1), 2; doi:10.3390/microorganisms6010002
Received: 7 December 2017 / Revised: 29 December 2017 / Accepted: 2 January 2018 / Published: 4 January 2018
Cited by 1 | PDF Full-text (1437 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Selective digestive decontamination (SDD, topical antibiotic regimens applied to the respiratory tract) appears effective for preventing ventilator associated pneumonia (VAP) in intensive care unit (ICU) patients. However, potential contextual effects of SDD on Staphylococcus aureus infections in the ICU remain unclear. The S.
[...] Read more.
Selective digestive decontamination (SDD, topical antibiotic regimens applied to the respiratory tract) appears effective for preventing ventilator associated pneumonia (VAP) in intensive care unit (ICU) patients. However, potential contextual effects of SDD on Staphylococcus aureus infections in the ICU remain unclear. The S. aureus ventilator associated pneumonia (S. aureus VAP), VAP overall and S. aureus bacteremia incidences within component (control and intervention) groups within 27 SDD studies were benchmarked against 115 observational groups. Component groups from 66 studies of various interventions other than SDD provided additional points of reference. In 27 SDD study control groups, the mean S. aureus VAP incidence is 9.6% (95% CI; 6.9–13.2) versus a benchmark derived from 115 observational groups being 4.8% (95% CI; 4.2–5.6). In nine SDD study control groups the mean S. aureus bacteremia incidence is 3.8% (95% CI; 2.1–5.7) versus a benchmark derived from 10 observational groups being 2.1% (95% CI; 1.1–4.1). The incidences of S. aureus VAP and S. aureus bacteremia within the control groups of SDD studies are each higher than literature derived benchmarks. Paradoxically, within the SDD intervention groups, the incidences of both S. aureus VAP and VAP overall are more similar to the benchmarks. Full article
(This article belongs to the Special Issue Staphylococcus aureus Infection and Antimicrobial Resistance)
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Open AccessArticle Pichia pastoris is a Suitable Host for the Heterologous Expression of Predicted Class I and Class II Hydrophobins for Discovery, Study, and Application in Biotechnology
Microorganisms 2018, 6(1), 3; doi:10.3390/microorganisms6010003
Received: 13 November 2017 / Revised: 15 December 2017 / Accepted: 29 December 2017 / Published: 5 January 2018
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Abstract
The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing
[...] Read more.
The heterologous expression of proteins is often a crucial first step in not only investigating their function, but also in their industrial application. The functional assembly and aggregation of hydrophobins offers intriguing biotechnological applications from surface modification to drug delivery, yet make developing systems for their heterologous expression challenging. In this article, we describe the development of Pichia pastoris KM71H strains capable of solubly producing the full set of predicted Cordyceps militaris hydrophobins CMil1 (Class IA), CMil2 (Class II), and CMil3 (IM) at mg/L yields with the use of 6His-tags not only for purification but for their detection. This result further demonstrates the feasibility of using P. pastoris as a host organism for the production of hydrophobins from all Ascomycota Class I subdivisions (a classification our previous work defined) as well as Class II. We highlight the specific challenges related to the production of hydrophobins, notably the challenge in detecting the protein that will be described, in particular during the screening of transformants. Together with the literature, our results continue to show that P. pastoris is a suitable host for the soluble heterologous expression of hydrophobins with a wide range of properties. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle Increase of Salt Tolerance in Carbon-Starved Cells of Rhodopseudomonas palustris Depending on Photosynthesis or Respiration
Microorganisms 2018, 6(1), 4; doi:10.3390/microorganisms6010004
Received: 1 December 2017 / Revised: 22 December 2017 / Accepted: 3 January 2018 / Published: 6 January 2018
Cited by 1 | PDF Full-text (806 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after
[...] Read more.
Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after carbon starvation under photosynthetic conditions in comparison with anaerobic and aerobic dark conditions. Tolerance to a treatment with high concentration of salt (2.5 M NaCl for 1 h) was largely increased after starvation under anaerobically light and aerobically dark conditions. The starved cells under the conditions of photosynthesis or aerobic respiration contained high levels of cellular ATP, but starvation under the anaerobic dark conditions resulted in a decrease of cellular ATP contents. To observe the large increase of the salt tolerance, incubation of starved cells for more than 18 h under illumination was needed. These results suggest that the ATP-dependent rearrangement of cells induced salt tolerance. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessArticle Enzymatic Preparation of 2,5-Furandicarboxylic Acid (FDCA)—A Substitute of Terephthalic Acid—By the Joined Action of Three Fungal Enzymes
Microorganisms 2018, 6(1), 5; doi:10.3390/microorganisms6010005
Received: 6 December 2017 / Revised: 5 January 2018 / Accepted: 6 January 2018 / Published: 9 January 2018
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Abstract
Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different
[...] Read more.
Enzymatic oxidation of 5-hydroxymethylfurfural (HMF) and its oxidized derivatives was studied using three fungal enzymes: wild-type aryl alcohol oxidase (AAO) from three fungal species, wild-type peroxygenase from Agrocybe aegerita (AaeUPO), and recombinant galactose oxidase (GAO). The effect of pH on different reaction steps was evaluated and apparent kinetic data (Michaelis-Menten constants, turnover numbers, specific constants) were calculated for different enzyme-substrate ratios and enzyme combinations. Finally, the target product, 2,5-furandicarboxylic acid (FDCA), was prepared in a multi-enzyme cascade reaction combining three fungal oxidoreductases at micro-scale. Furthermore, an oxidase-like reaction is proposed for heme-containing peroxidases, such as UPO, horseradish peroxidase, or catalase, causing the conversion of 5-formyl-2-furancarboxylic acid into FDCA in the absence of exogenous hydrogen peroxide. Full article
(This article belongs to the Special Issue Filamentous Fungi in White Biotechnology)
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Open AccessArticle Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli Using Amplicon-Based Next-Generation Sequencing and Automated Analysis
Microorganisms 2018, 6(1), 6; doi:10.3390/microorganisms6010006
Received: 27 November 2017 / Revised: 5 January 2018 / Accepted: 9 January 2018 / Published: 11 January 2018
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Abstract
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing
[...] Read more.
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods. Retrospectively, ESBL-producing bacteria and resistance genes were detected directly from eSwab medium by an accelerated workflow without prior enrichment cultures by an amplicon-based next-generation sequencing (NGS) method, and culture. A total of 27 (18.1%) samples were positive in either test. Sensitivity for CTX-M detection was 96.3% for the phenotypic method and 85.2% for the NGS method, and the specificity was 100% for both methods, as confirmed by micro-array. This resulted in a positive predictive value (PPV) of 100% for both methods, and a negative predictive value (NPV) of 99.2% and 96.8% for the phenotypic method and the NGS method, respectively. Time to result was four days and 14 h for the phenotypic method and the NGS method, respectively. In conclusion, the sensitivity without enrichment shows promising results for further use of amplicon-based NGS for screening during outbreaks. Full article
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Open AccessArticle Biogenic Weathering: Solubilization of Iron from Minerals by Epilithic Freshwater Algae and Cyanobacteria
Microorganisms 2018, 6(1), 8; doi:10.3390/microorganisms6010008
Received: 8 December 2017 / Revised: 29 December 2017 / Accepted: 9 January 2018 / Published: 15 January 2018
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Abstract
A sandstone outcrop exposed to freshwater seepage supports a diverse assemblage of photosynthetic microbes. Dominant taxa are two cyanophytes (Oscillatoria sp., Rivularia sp.) and a unicellular green alga (Palmellococcus sp.). Less abundant taxa include a filamentous green alga, Microspora, and
[...] Read more.
A sandstone outcrop exposed to freshwater seepage supports a diverse assemblage of photosynthetic microbes. Dominant taxa are two cyanophytes (Oscillatoria sp., Rivularia sp.) and a unicellular green alga (Palmellococcus sp.). Less abundant taxa include a filamentous green alga, Microspora, and the desmid Cosmarium. Biologic activity is evidenced by measured levels of chlorophyll and lipids. Bioassay methods confirm the ability of these microbes to dissolve and metabolize Fe from ferruginous minerals. Chromatographic analysis reveals citric acid as the likely chelating agent; this low molecular weight organic acid is detectable in interstitial fluid in the sandstone, measured as 0.0756 mg/mL. Bioassays using a model organism, Synechoccus elongates strain UTEX 650, show that Fe availability varies among different ferruginous minerals. In decreasing order of Fe availability: magnetite > limonite > biotite > siderite > hematite. Biotite was selected for detailed study because it is the most abundant iron-bearing mineral in the sandstone. SEM images support the microbiologic evidence, showing weathering of biotite compared to relatively undamaged grains of other silicate minerals. Full article
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Open AccessArticle Therapeutic Management of Pseudomonas aeruginosa Bloodstream Infection Non-Susceptible to Carbapenems but Susceptible to “Old” Cephalosporins and/or to Penicillins
Microorganisms 2018, 6(1), 9; doi:10.3390/microorganisms6010009
Received: 13 November 2017 / Revised: 1 January 2018 / Accepted: 11 January 2018 / Published: 16 January 2018
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Abstract
It is unknown as to whether other beta-lactams can be used for bloodstream infections (BSI) resulting from Pseudomonas aeruginosa (PA) which are non-susceptible to one or more carbapenem. We conducted a retrospective cohort study at the Assaf Harofeh Medical Center (AHMC) from January
[...] Read more.
It is unknown as to whether other beta-lactams can be used for bloodstream infections (BSI) resulting from Pseudomonas aeruginosa (PA) which are non-susceptible to one or more carbapenem. We conducted a retrospective cohort study at the Assaf Harofeh Medical Center (AHMC) from January 2010 to August 2014. Adult patients with PA-BSI non-susceptible to a group 2 carbapenem but susceptible to ceftazidime or piperacillin (with or without tazobactam), were enrolled. We compared the outcomes of patients who received an appropriate beta-lactam antibiotic (“cases”) to those who received an appropriate non-beta-lactam antibiotic (“controls”). Whole genome sequencing was performed for one of the isolates. Twenty-six patients with PA-BSI met inclusion criteria: 18 received a beta-lactam and 8 a non-beta-lactam (three a fluoroquinolone, two colistin, one a fluoroquinolone and an aminoglycoside, one a fluoroquinolone and colistin, and one colistin and an aminoglycoside). All clinical outcomes were similar between the groups. There were large variations in the phenotypic susceptibilities of the strains. A detailed molecular investigation of one isolate revealed a strain that belonged to MLST-137, with the presence of multiple efflux pumps, OXA-50, and a chromosomally mediated Pseudomonas-derived cephalosporinase (PDC). The oprD gene was intact. Non-carbapenem-β-lactams may still be effective alternatives for short duration therapy (up to 14 days) for BSI caused by a carbapenem non-susceptible (but susceptible to ceftazidime, piperacillin, and/or piperacillin-tazobactam) PA strain. This observation requires further confirmatory analyses. Future molecular investigations should be performed, in order to further analyze additional potential mechanisms for this prevalent phenotype. Full article
Open AccessArticle Investigating Potential Chromosomal Rearrangements during Laboratory Culture of Neisseria gonorrhoeae
Microorganisms 2018, 6(1), 10; doi:10.3390/microorganisms6010010
Received: 1 December 2017 / Revised: 19 December 2017 / Accepted: 19 January 2018 / Published: 20 January 2018
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Abstract
Comparisons of genome sequence data between different strains and isolates of Neisseria spp., such as Neisseria gonorrhoeae, reveal that over the evolutionary history of these organisms, large scale chromosomal rearrangements have occurred. Factors within the genomes, such as repetitive sequences and prophage,
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Comparisons of genome sequence data between different strains and isolates of Neisseria spp., such as Neisseria gonorrhoeae, reveal that over the evolutionary history of these organisms, large scale chromosomal rearrangements have occurred. Factors within the genomes, such as repetitive sequences and prophage, are believed to have contributed to these observations. However, the timescale in which rearrangements occur is not clear, nor whether it might be expected for them to happen in the laboratory. In this study, N. gonorrhoeae was repeatedly passaged in the laboratory and assessed for large scale chromosomal rearrangements. Using gonococcal strain NCCP11945, for which there is a complete genome sequence, cultures were passaged for eight weeks in the laboratory. The resulting genomic DNA was assessed using Pulsed Field Gel Electrophoresis, comparing the results to the predicted results from the genome sequence data. Three cultures generated Pulsed Field Gel Electrophoresis patterns that varied from the genomic data and were further investigated for potential chromosomal rearrangements. Full article
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Open AccessArticle Defining Multidrug Resistance of Gram-Negative Bacteria in the Dutch–German Border Region—Impact of National Guidelines
Microorganisms 2018, 6(1), 11; doi:10.3390/microorganisms6010011
Received: 29 December 2017 / Revised: 23 January 2018 / Accepted: 25 January 2018 / Published: 26 January 2018
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Abstract
Preventing the spread of multidrug-resistant Gram-negative bacteria (MDRGNB) is a public health priority. However, the definition of MDRGNB applied for planning infection prevention measures such as barrier precautions differs depending on national guidelines. This is particularly relevant in the Dutch–German border region, where
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Preventing the spread of multidrug-resistant Gram-negative bacteria (MDRGNB) is a public health priority. However, the definition of MDRGNB applied for planning infection prevention measures such as barrier precautions differs depending on national guidelines. This is particularly relevant in the Dutch–German border region, where patients are transferred between healthcare facilities located in the two different countries, because clinicians and infection control personnel must understand antibiograms indicating MDRGNB from both sides of the border and using both national guidelines. This retrospective study aimed to compare antibiograms of Gram-negative bacteria and classify them using the Dutch and German national standards for MDRGNB definition. A total of 31,787 antibiograms from six Dutch and four German hospitals were classified. Overall, 73.7% were no MDRGNB according to both guidelines. According to the Dutch and German guideline, 7772/31,787 (24.5%) and 4586/31,787 (12.9%) were MDRGNB, respectively (p < 0.0001). Major divergent classifications were observed for extended-spectrum β-lactamase (ESBL) -producing Enterobacteriaceae, non-carbapenemase-producing carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. The observed differences show that medical staff must carefully check previous diagnostic findings when patients are transferred across the Dutch–German border, as it cannot be assumed that MDRGNB requiring special hygiene precautions are marked in the transferred antibiograms in accordance with both national guidelines. Full article
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Open AccessArticle Responses of an Agricultural Soil Microbiome to Flooding with Seawater after Managed Coastal Realignment
Microorganisms 2018, 6(1), 12; doi:10.3390/microorganisms6010012
Received: 7 December 2017 / Revised: 12 January 2018 / Accepted: 18 January 2018 / Published: 26 January 2018
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Abstract
Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with
[...] Read more.
Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with seawater. How flooding with seawater impacts soil microbiomes and the biogeochemical cycling of elements is poorly understood. To address this, we conducted a microcosm experiment using soil cores collected at the nature restoration project site Gyldensteen Strand (Denmark), which were flooded with seawater and monitored over six months. Throughout the experiment, biogeochemical analyses, microbial community fingerprinting and the quantification of marker genes documented clear shifts in microbiome composition and activity. The flooding with seawater initially resulted in accelerated heterotrophic activity that entailed high ammonium production and net removal of nitrogen from the system, also demonstrated by a concurrent increase in the abundances of marker genes for ammonium oxidation and denitrification. Due to the depletion of labile soil organic matter, microbial activity decreased after approximately four months. The event of flooding caused the largest shifts in microbiome composition with the availability of labile organic matter subsequently being the most important driver for the succession in microbiome composition in soils flooded with seawater. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessArticle Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM
Microorganisms 2018, 6(1), 13; doi:10.3390/microorganisms6010013
Received: 20 November 2017 / Revised: 25 January 2018 / Accepted: 5 February 2018 / Published: 8 February 2018
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Abstract
Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent
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Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10−12 to 5.9 × 10−10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R2 = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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Open AccessArticle Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community
Microorganisms 2018, 6(1), 14; doi:10.3390/microorganisms6010014
Received: 20 November 2017 / Revised: 23 January 2018 / Accepted: 8 February 2018 / Published: 11 February 2018
Cited by 1 | PDF Full-text (2368 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and
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Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed a 16S rDNA taxonomic bacterial profiling of the rhizosphere and endorhizosphere of two high-yield rice cultivars—Pionero 2010 FL and DANAC SD20A—extensively grown in Venezuela in 2014. Fifteen putative bacterial endophytes were then isolated from surface-sterilized roots and further studied in vitro and in planta. We have then performed inoculation of rice seedlings with a simplified community composed by 10 of the isolates and we have tracked them in the course of 30 days in greenhouse cultivation. The results obtained suggest that a set was able to significantly colonize together the rice endorhizospheres, indicating possible cooperation and the ability to form a stable multispecies community. This approach can be useful in the development of microbial solutions for a more sustainable rice production. Full article
(This article belongs to the Special Issue Symbiotic Plant-Bacterial Endospheric Interactions)
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Open AccessCommunication Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters
Microorganisms 2018, 6(1), 15; doi:10.3390/microorganisms6010015
Received: 8 December 2017 / Revised: 1 February 2018 / Accepted: 12 February 2018 / Published: 14 February 2018
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Abstract
Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do
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Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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Open AccessArticle Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
Microorganisms 2018, 6(1), 16; doi:10.3390/microorganisms6010016
Received: 2 January 2018 / Revised: 14 February 2018 / Accepted: 17 February 2018 / Published: 23 February 2018
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Abstract
Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM
[...] Read more.
Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations. Full article
(This article belongs to the Special Issue Microorganisms for Environmental and Industrial Applications)
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Open AccessArticle Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows
Microorganisms 2018, 6(1), 17; doi:10.3390/microorganisms6010017
Received: 22 December 2017 / Revised: 21 February 2018 / Accepted: 23 February 2018 / Published: 24 February 2018
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Abstract
The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate
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The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6–50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcus flavefaciens and Fibrobacter succinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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Open AccessArticle World-Wide Variation in Incidence of Staphylococcus aureus Associated Ventilator-Associated Pneumonia: A Meta-Regression
Microorganisms 2018, 6(1), 18; doi:10.3390/microorganisms6010018
Received: 19 January 2018 / Revised: 13 February 2018 / Accepted: 25 February 2018 / Published: 27 February 2018
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Abstract
Staphylococcus aureus (S. aureus) is a common Ventilator-Associated Pneumonia (VAP) isolate. The objective here is to define the extent and possible reasons for geographic variation in the incidences of S. aureus-associated VAP, MRSA-VAP and overall VAP. A meta-regression model of
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Staphylococcus aureus (S. aureus) is a common Ventilator-Associated Pneumonia (VAP) isolate. The objective here is to define the extent and possible reasons for geographic variation in the incidences of S. aureus-associated VAP, MRSA-VAP and overall VAP. A meta-regression model of S. aureus-associated VAP incidence per 1000 Mechanical Ventilation Days (MVD) was undertaken using random effects methods among publications obtained from a search of the English language literature. This model incorporated group level factors such as admission to a trauma ICU, year of publication and use of bronchoscopic sampling towards VAP diagnosis. The search identified 133 publications from seven worldwide regions published over three decades. The summary S. aureus-associated VAP incidence was 4.5 (3.9–5.3) per 1000 MVD. The highest S. aureus-associated VAP incidence is amongst reports from the Mediterranean (mean; 95% confidence interval; 6.1; 4.1–8.5) versus that from Asian ICUs (2.1; 1.5–3.0). The incidence of S. aureus-associated VAP varies by up to three-fold (for the lowest versus highest incidence) among seven geographic regions worldwide, whereas the incidence of VAP varies by less than two-fold. Admission to a trauma unit is the most important group level correlate for S. aureus-associated VAP. Full article
(This article belongs to the Special Issue Staphylococcus aureus Infection and Antimicrobial Resistance)
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Open AccessArticle Differential Transcriptional Activation of Genes Encoding Soluble Methane Monooxygenase in a Facultative Versus an Obligate Methanotroph
Microorganisms 2018, 6(1), 20; doi:10.3390/microorganisms6010020
Received: 8 February 2018 / Revised: 28 February 2018 / Accepted: 1 March 2018 / Published: 6 March 2018
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Abstract
Methanotrophs are a specialized group of bacteria that can utilize methane (CH4) as a sole energy source. A key enzyme responsible for methane oxidation is methane monooxygenase (MMO), of either a soluble, cytoplasmic type (sMMO), or a particulate, membrane-bound type (pMMO).
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Methanotrophs are a specialized group of bacteria that can utilize methane (CH4) as a sole energy source. A key enzyme responsible for methane oxidation is methane monooxygenase (MMO), of either a soluble, cytoplasmic type (sMMO), or a particulate, membrane-bound type (pMMO). Methylocella silvestris BL2 and Methyloferula stellata AR4 are closely related methanotroph species that oxidize methane via sMMO only. However, Methyloferula stellata is an obligate methanotroph, while Methylocella silvestris is a facultative methanotroph able to grow on several multicarbon substrates in addition to methane. We constructed transcriptional fusions of the mmo promoters of Methyloferula stellata and Methylocella silvestris to a promoterless gfp in order to compare their transcriptional regulation in response to different growth substrates, in the genetic background of both organisms. The following patterns were observed: (1) The mmo promoter of the facultative methanotroph Methylocella silvestris was either transcriptionally downregulated or repressed by any growth substrate other than methane in the genetic background of Methylocella silvetris; (2) Growth on methane alone upregulated the mmo promoter of Methylocella silvetris in its native background but not in the obligate methanotroph Methyloferula stellata; (3) The mmo promoter of Methyloferula stellata was constitutive in both organisms regardless of the growth substrate, but with much lower promoter activity than the mmo promoter of Methylocella silvetris. These results support a conclusion that a different mode of transcriptional regulation of sMMO contributes to the facultative lifestyle of Methylocella silvetris compared to the obligate methanotroph Methyloferula stellata. Full article
(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle Fungal Disease Prevention in Seedlings of Rice (Oryza sativa) and Other Grasses by Growth-Promoting Seed-Associated Endophytic Bacteria from Invasive Phragmites australis
Microorganisms 2018, 6(1), 21; doi:10.3390/microorganisms6010021
Received: 26 January 2018 / Revised: 28 February 2018 / Accepted: 2 March 2018 / Published: 8 March 2018
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Abstract
Non-cultivated plants carry microbial endophytes that may be used to enhance development and disease resistance of crop species where growth-promoting and protective microbes may have been lost. During seedling establishment, seedlings may be infected by several fungal pathogens that are seed or soil
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Non-cultivated plants carry microbial endophytes that may be used to enhance development and disease resistance of crop species where growth-promoting and protective microbes may have been lost. During seedling establishment, seedlings may be infected by several fungal pathogens that are seed or soil borne. Several species of Fusarium, Pythium and other water moulds cause seed rots during germination. Fusarium blights of seedlings are also very common and significantly affect seedling development. In the present study we screened nine endophytic bacteria isolated from the seeds of invasive Phragmites australis by inoculating onto rice, Bermuda grass (Cynodon dactylon), or annual bluegrass (Poa annua) seeds to evaluate plant growth promotion and protection from disease caused by Fusarium oxysporum. We found that three bacteria belonging to genus Pseudomonas spp. (SLB4-P. fluorescens, SLB6-Pseudomonas sp. and SY1-Pseudomonas sp.) promoted seedling development, including enhancement of root and shoot growth, and stimulation of root hair formation. These bacteria were also found to increase phosphate solubilization in in vitro experiments. Pseudomonas sp. (SY1) significantly protected grass seedlings from Fusarium infection. In co-culture experiments, strain SY1 strongly inhibited fungal pathogens with 85.71% growth inhibition of F. oxysporum, 86.33% growth inhibition of Curvularia sp. and 82.14% growth inhibition of Alternaria sp. Seedlings previously treated with bacteria were found much less infected by F. oxysporum in comparison to non-treated controls. On microscopic observation we found that bacteria appeared to degrade fungal mycelia actively. Metabolite products of strain SY1 in agar were also found to inhibit fungal growth on nutrient media. Pseudomonas sp. (SY1) was found to produce antifungal volatiles. Polymerase chain reaction (PCR) amplification using specific primers for pyrrolnitirin synthesis and HCN (hydrogen cyanide) production suggested presence of genes for both compounds in the genome of SY1. HCN was detected in cultures of SY1. We conclude that microbes from non-cultivated plants may provide disease protection and promote growth of crop plants. Full article
(This article belongs to the Special Issue Symbiotic Plant-Bacterial Endospheric Interactions)
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Open AccessArticle Effects of Elevated Hydrostatic Pressure against Mesophilic Background Microflora and Habituated Salmonella Serovars in Orange Juice
Microorganisms 2018, 6(1), 23; doi:10.3390/microorganisms6010023
Received: 17 January 2018 / Revised: 25 February 2018 / Accepted: 6 March 2018 / Published: 9 March 2018
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Abstract
With recent improvements in the commercial feasibility of high pressure pasteurization units, the technology is gaining rapid acceptability across various sectors of food manufacturing, thus requiring extensive validation studies for effective adoption. Various times (1 min to 10 min) and intensity levels (0
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With recent improvements in the commercial feasibility of high pressure pasteurization units, the technology is gaining rapid acceptability across various sectors of food manufacturing, thus requiring extensive validation studies for effective adoption. Various times (1 min to 10 min) and intensity levels (0 MPa to 380 MPa) of elevated hydrostatic pressure were investigated for decontamination of mesophilic background microflora and inoculated Salmonella in orange juice. Results were analyzed by GLM procedure of SAS using Tukey- and Dunnett-adjusted ANOVA, additionally the Kmax and D-values were calculated using best-fitted (maximum R2) model obtained by GInaFit software. At 380 MPa, for treatments of 1 min to 10 min, D-value of 1.35, and inactivation Kmax of 3.34 were observed for Salmonella serovars. D-values were 5.90 and 14.68 for treatments of 241 MPa and 103 MPa, respectively. Up to 1.01 and >7.22 log CFU/mL reductions (p < 0.05) of habituated Salmonella serovars at planktonic stages were achieved using application of pressure at 380 MPa for 1 min and 10 min, respectively. Mesophilic background microflora counts were reduced (p < 0.05) by 1.68 to 5.29 log CFU/mL after treatment at 380 MPa for 1 min and 10 min, respectively. Treatments below two minutes were less efficacious (p ≥ 0.05) against the pathogen and background microflora, in vast majority of time and pressure combinations. Full article
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Open AccessArticle Description of New and Amended Clades of the Genus Photobacterium
Microorganisms 2018, 6(1), 24; doi:10.3390/microorganisms6010024
Received: 15 January 2018 / Revised: 5 March 2018 / Accepted: 7 March 2018 / Published: 12 March 2018
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Abstract
Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in
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Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of gyrB, gapA, topA, ftsZ and mreB housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the Photobacterium clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus Photobacterium into the following 5 clades: Phosphoreum (comprises P. aquimaris, “P. carnosum,” P. iliopiscarium, P. kishitanii, P. phosphoreum, “P. piscicola” and “P. toruni”); clade Profundum (composed of P. aestuarii, P. alginatilyticum, P. frigidiphilum, P. indicum, P. jeanii, P. lipolyticum, “P. marinum,” and P. profundum); clade Damselae (two subspecies of P. damselae, damselae and piscicida); and two new clades: clade Ganghwense (includes P. aphoticum, P. aquae, P. galatheae, P. ganghwense, P. halotolerans, P. panuliri and P. proteolyticum); and clade Leiognathi (composed by P. angustum, P. leiognathi subsp. leiognathi and “P. leiognathi subsp. mandapamensis”). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only P. aplysiae could not be included in none of the established clade, constituting an orphan clade. Full article
(This article belongs to the Special Issue Marine Vibrios and Photobacteria: Taxonomy, Ecology and Pathogenesis)
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Open AccessArticle Identification of sucA, Encoding β-Fructofuranosidase, in Rhizopus microsporus
Microorganisms 2018, 6(1), 26; doi:10.3390/microorganisms6010026
Received: 22 January 2018 / Revised: 5 March 2018 / Accepted: 13 March 2018 / Published: 13 March 2018
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Abstract
Rhizopus microsporus NBRC 32995 was found to hydrolyze fructooligosaccharides (FOS), as well as sucrose, almost completely into monosaccharides through the production of sufficient amounts of organic acids, indicating that the complete hydrolysis of FOS was caused by the secretion of β-fructofuranosidase from fungal
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Rhizopus microsporus NBRC 32995 was found to hydrolyze fructooligosaccharides (FOS), as well as sucrose, almost completely into monosaccharides through the production of sufficient amounts of organic acids, indicating that the complete hydrolysis of FOS was caused by the secretion of β-fructofuranosidase from fungal cells. Thus, the sucA gene, encoding a β-fructofuranosidase, was amplified by degenerate PCR, and its complete nucleotide sequence was determined. The total length of the sucA gene was 1590 bp, and the SucA protein of R. microsporus NBRC 32995 belonged to clade VIa, which also contains Rhizopus delemar and is closely related to Saccharomycotina, a subdivision of the Ascomycota. Full article
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Open AccessArticle Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought
Microorganisms 2018, 6(1), 27; doi:10.3390/microorganisms6010027
Received: 1 February 2018 / Revised: 3 March 2018 / Accepted: 9 March 2018 / Published: 15 March 2018
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Abstract
Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are
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Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are also nitrogen limited and depend on plant associated diazotrophs as their source of ‘new’ nitrogen. A 4-year study was conducted to investigate the structure and composition of the rhizosphere diazotroph assemblages associated with 5 distinct plant zones in one such salt marsh. A period of greatly restricted tidal inundation and precipitation, as well as two periods of drought (June–July 2004, and May 2007) occurred during the study. DGGE of nifH PCR amplicons from rhizosphere samples, Principal Components Analysis of the resulting banding patterns, and unconstrained ordination analysis of taxonomic data and environmental parameters were conducted. Diazotroph assemblages were organized into 5 distinct groups (R2 = 0.41, p value < 0.001) whose presence varied with the environmental conditions of the marsh. Diazotroph assemblage group detection differed during and after the drought event, indicating that persistent diazotrophs maintained populations that provided reduced supplies of new nitrogen for vegetation during the periods of drought. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessReview Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?
Microorganisms 2018, 6(1), 1; doi:10.3390/microorganisms6010001
Received: 14 November 2017 / Revised: 15 December 2017 / Accepted: 19 December 2017 / Published: 21 December 2017
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Abstract
The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the
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The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail. Full article
(This article belongs to the Special Issue The Functions of the Microbiome in Skin Health and Disease)
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Open AccessReview Inteins: Localized Distribution, Gene Regulation, and Protein Engineering for Biological Applications
Microorganisms 2018, 6(1), 19; doi:10.3390/microorganisms6010019
Received: 12 February 2018 / Revised: 24 February 2018 / Accepted: 25 February 2018 / Published: 28 February 2018
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Abstract
Inteins are self-splicing polypeptides with an ability to excise themselves from flanking host protein regions with remarkable precision; in the process, they ligate flanked host protein fragments. Inteins are distributed sporadically across all three domains of life (bacteria, archaea, and unicellular eukaryotes). However,
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Inteins are self-splicing polypeptides with an ability to excise themselves from flanking host protein regions with remarkable precision; in the process, they ligate flanked host protein fragments. Inteins are distributed sporadically across all three domains of life (bacteria, archaea, and unicellular eukaryotes). However, their apparent localized distribution in DNA replication, repair, and recombination proteins (the 3Rs), particularly in bacteria and archaea, is enigmatic. Our understanding of the localized distribution of inteins in the 3Rs, and their possible regulatory role in such distribution, is still only partial. Nevertheless, understanding the chemistry of post-translational self-splicing of inteins has opened up opportunities for protein chemists to modify, manipulate, and bioengineer proteins. Protein-splicing technology is adapted to a wide range of applications, starting with untagged protein purification, site-specific protein labeling, protein biotinylation, isotope incorporation, peptide cyclization, as an antimicrobial target, and so on. This review is focused on the chemistry of splicing; the localized distribution of inteins, particularly in the 3Rs and their possible role in regulating host protein function; and finally, the use of protein-splicing technology in various protein engineering applications. Full article
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Open AccessReview The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis
Microorganisms 2018, 6(1), 22; doi:10.3390/microorganisms6010022
Received: 5 February 2018 / Revised: 23 February 2018 / Accepted: 5 March 2018 / Published: 9 March 2018
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Abstract
In recent years, the gut microbiota has been considered as a full-fledged actor of the gut–brain axis, making it possible to take a new step in understanding the pathophysiology of both neurological and psychiatric diseases. However, most of the studies have been devoted
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In recent years, the gut microbiota has been considered as a full-fledged actor of the gut–brain axis, making it possible to take a new step in understanding the pathophysiology of both neurological and psychiatric diseases. However, most of the studies have been devoted to gut bacterial microbiota, forgetting the non-negligible fungal flora. In this review, we expose how the role of the fungal component in the microbiota-gut-brain axis is legitimate, through its interactions with both the host, especially with the immune system, and the gut bacteria. We also discuss published data that already attest to a role of the mycobiome in the microbiota-gut-brain axis, and the impact of fungi on clinical and therapeutic research. Full article
(This article belongs to the Special Issue Microbiome Gut Brain Axis)
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Open AccessReview Antibody-Based Agents in the Management of Antibiotic-Resistant Staphylococcus aureus Diseases
Microorganisms 2018, 6(1), 25; doi:10.3390/microorganisms6010025
Received: 13 February 2018 / Revised: 8 March 2018 / Accepted: 11 March 2018 / Published: 13 March 2018
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Abstract
Staphylococcus aureus is a human pathogen that can cause a wide spectrum of diseases, including sepsis, pneumonia, arthritis, and endocarditis. Ineffective treatment of a number of staphylococcal infections with antibiotics is due to the development and spread of antibiotic-resistant strains following decades of
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Staphylococcus aureus is a human pathogen that can cause a wide spectrum of diseases, including sepsis, pneumonia, arthritis, and endocarditis. Ineffective treatment of a number of staphylococcal infections with antibiotics is due to the development and spread of antibiotic-resistant strains following decades of antibiotic usage. This has generated renewed interest within the scientific community in alternative therapeutic agents, such as anti-S. aureus antibodies. Although the role of antibodies in the management of S. aureus diseases is controversial, the success of this pathogen in neutralizing humoral immunity clearly indicates that antibodies offer the host extensive protection. In this review, we report an update on efforts to develop antibody-based agents, particularly monoclonal antibodies, and their therapeutic potential in the passive immunization approach to the treatment and prevention of S. aureus infections. Full article
(This article belongs to the Special Issue Staphylococcus aureus Infection and Antimicrobial Resistance)
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