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Microorganisms, Volume 7, Issue 4 (April 2019) – 20 articles

Cover Story (view full-size image): Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens that can cause enteric disease and kidney failure in humans. Biofilms contribute to the persistence of STEC in food processing environments. Several factors, including nutrient profile, temperature, physical, and chemical properties of contact surfaces and the genomics of the strain can influence biofilm formation. Identification of the conditions that promote STEC biofilm formation in food processing facilities, is key to developing disinfection and production conditions that reduce the risk of adulteration of food. View this paper.
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14 pages, 2393 KiB  
Article
Sex-Specific Asymmetrical Attack Rates in Combined Sexual-Vectorial Transmission Epidemics
by Ana Carolina W. G. de Barros, Kaline G. Santos, Eduardo Massad and Flávio Codeço Coelho
Microorganisms 2019, 7(4), 112; https://doi.org/10.3390/microorganisms7040112 - 25 Apr 2019
Cited by 1 | Viewed by 4144
Abstract
In 2015–2016, South America went through the largest Zika epidemic in recorded history. One important aspect of this epidemic was the importance of sexual transmission in combination with the usual vectorial transmission, with asymmetrical transmissibilities between sexual partners depending on the type of [...] Read more.
In 2015–2016, South America went through the largest Zika epidemic in recorded history. One important aspect of this epidemic was the importance of sexual transmission in combination with the usual vectorial transmission, with asymmetrical transmissibilities between sexual partners depending on the type of sexual contact; this asymmetry manifested itself in data as an increased risk to women. We propose a mathematical model for the transmission of the Zika virus including sexual transmission via all forms of sexual contact, as well as vector transmission, assuming a constant availability of mosquitoes. From this model, we derive an expression for R 0 , which is used to study and analyze the relative contributions of the male to female sexual transmission route vis-à-vis vectorial transmission. We also perform Bayesian inference of the model’s parameters using data from the 2016 Zika epidemic in Rio de Janeiro. Full article
(This article belongs to the Special Issue Emerging Vector Borne Infections: A Novel Threat for Global Health)
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2 pages, 577 KiB  
Erratum
Erratum: Mpanga, I.K.; et al. The Form of N Supply Determines Plant Growth Promotion by P-Solubilizing Microorganisms in Maize. Microorganisms 2019, 7, 38
by Microorganisms Editorial Office
Microorganisms 2019, 7(4), 111; https://doi.org/10.3390/microorganisms7040111 - 25 Apr 2019
Cited by 1 | Viewed by 2158
Abstract
The following changes have been made to the published paper [...] Full article
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12 pages, 2091 KiB  
Article
Plasma Membrane Potential of Candida albicans Measured by Di-4-ANEPPS Fluorescence Depends on Growth Phase and Regulatory Factors
by Jakub Suchodolski and Anna Krasowska
Microorganisms 2019, 7(4), 110; https://doi.org/10.3390/microorganisms7040110 - 24 Apr 2019
Cited by 15 | Viewed by 4293
Abstract
The potential of the plasma membrane (Δψ) regulates the electrochemical potential between the outer and inner sides of cell membranes. The opportunistic fungal pathogen, Candida albicans, regulates the membrane potential in response to environmental conditions, as well as the physiological state of the [...] Read more.
The potential of the plasma membrane (Δψ) regulates the electrochemical potential between the outer and inner sides of cell membranes. The opportunistic fungal pathogen, Candida albicans, regulates the membrane potential in response to environmental conditions, as well as the physiological state of the cell. Here we demonstrate a new method for detection of cell membrane depolarization/permeabilization in C. albicans using the potentiometric zwitterionic dye di-4-ANEPPS. Di-4-ANEPPS measures the changes in the cell Δψ depending on the phases of growth and external factors regulating Δψ, such as potassium or calcium chlorides, amiodarone or DM-11 (inhibitor of H+-ATPase). We also demonstrated that di-4-ANEPPS is a good tool for fast measurement of the influence of amphipathic compounds on Δψ. Full article
(This article belongs to the Special Issue Candida albicans Virulence Factors and Its Pathogenecity)
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10 pages, 1661 KiB  
Article
Inhibition of Nitric Oxide Production, Oxidative Stress Prevention, and Probiotic Activity of Lactic Acid Bacteria Isolated from the Human Vagina and Fermented Food
by Chang-Ho Kang, Seul Hwa Han, Jin-Seong Kim, YongGyeong Kim, Yulah Jeong, Hye Min Park and Nam-Soo Paek
Microorganisms 2019, 7(4), 109; https://doi.org/10.3390/microorganisms7040109 - 23 Apr 2019
Cited by 13 | Viewed by 5246
Abstract
In this study, lactic acid bacteria (LAB) with antioxidative and probiotic activities were isolated from the vaginas of Korean women and from fermented food. Among 34 isolated LAB strains, four strains (MG4221, MG4231, MG4261, and MG4270) exhibited inhibitory activity against nitric oxide production. [...] Read more.
In this study, lactic acid bacteria (LAB) with antioxidative and probiotic activities were isolated from the vaginas of Korean women and from fermented food. Among 34 isolated LAB strains, four strains (MG4221, MG4231, MG4261, and MG4270) exhibited inhibitory activity against nitric oxide production. The MG4221 and MG4270 strains were identified as Lactobacillus plantarum, and MG4231 and MG4261 were identified as Lactobacillus fermentum. These strains were able to tolerate pepsin and pancreatin, which is required for probiotic potential. The antioxidant effects of culture filtrates obtained from selected strains included 2,2-diphenyl-1-picryl-hydrazyl (DPPH) radical scavenging capacity. Most of the culture filtrates had effective DPPH scavenging activity.In conclusion, the selected strains have significant activities and are potentially applicable to the development of functional foods. These strains might also contribute to the prevention and control of several diseases associated with oxidative stress, when used as functional probiotics. Full article
(This article belongs to the Special Issue Probiotics: From Quality Assessment to Microbial Ecology)
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8 pages, 1517 KiB  
Article
The Anti-Rotaviral Activity of Low Molecular Weight and Non-Proteinaceous Substance from Bifidobacterium longum BORI Cell Extract
by Yeo Ok Han, Yunju Jeong, Hyun Ju You, Seockmo Ku, Geun Eog Ji and Myeong Soo Park
Microorganisms 2019, 7(4), 108; https://doi.org/10.3390/microorganisms7040108 - 23 Apr 2019
Cited by 7 | Viewed by 3300
Abstract
Rotavirus infection is the most common diarrheal disease worldwide in children under five years of age, and it often results in death. In recent years, research on the relationship between rotavirus and probiotics has shown that probiotics are effective against diarrhea. A clinical [...] Read more.
Rotavirus infection is the most common diarrheal disease worldwide in children under five years of age, and it often results in death. In recent years, research on the relationship between rotavirus and probiotics has shown that probiotics are effective against diarrhea. A clinical trial has reported that Bifidobacterium longum BORI reduced diarrhea induced by rotavirus. The present work investigated the anti-rotaviral effect of B. longum BORI by cytopathic effect observation and real time cell analyses. Our study found that B. longum BORI showed strong anti-rotaviral effect when incubated with MA104 cells prior to viral infection, suggesting that the probiotic does in fact interfere with the interaction of viruses and host cells. It is believed that the efficacy is due to low-molecular weight and non-protein components derived from B. longum BORI. This discovery can help broaden the industrial application of B. longum BORI, which has been proven to be a safe and effective probiotic. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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13 pages, 1834 KiB  
Article
Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake
by Alvaro S. Villalobos, Jutta Wiese, Johannes F. Imhoff, Cristina Dorador, Alexander Keller and Ute Hentschel
Microorganisms 2019, 7(4), 107; https://doi.org/10.3390/microorganisms7040107 - 23 Apr 2019
Cited by 4 | Viewed by 3547
Abstract
Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number [...] Read more.
Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165T linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165T is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165T. These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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17 pages, 2589 KiB  
Article
Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA
by Meghan L. Rodela, Shereen Sabet, Allison Peterson and Jesse G. Dillon
Microorganisms 2019, 7(4), 106; https://doi.org/10.3390/microorganisms7040106 - 19 Apr 2019
Cited by 9 | Viewed by 3671
Abstract
Phages greatly influence the ecology and evolution of their bacterial hosts; however, compared to hosts, a relatively low number of phages, especially halophilic phages, have been studied. This study describes a comparative investigation of physicochemical tolerance between a strain of the halophilic bacterium, [...] Read more.
Phages greatly influence the ecology and evolution of their bacterial hosts; however, compared to hosts, a relatively low number of phages, especially halophilic phages, have been studied. This study describes a comparative investigation of physicochemical tolerance between a strain of the halophilic bacterium, Salicola, isolated from the Cargill Saltworks (Newark, CA, USA) and its associated phage. The host grew in media between pH 6–8.5, had a salinity growth optimum of 20% total salts (ranging from 10%–30%) and an upper temperature growth limit of 48 °C. The host utilized 61 of 190 substrates tested using BIOLOG Phenotype MicroArrays. The CGφ29 phage, one of only four reported Salicola phages, is a DNA virus of the Siphoviridae family. Overall, the phage tolerated a broader range of environmental conditions than its host (salinity 0–30% total salts; pH 3–9; upper thermal limit 80 °C) and is the most thermotolerant halophilic phage ever reported. This study is the most comprehensive investigation to date of a Salicola host–phage pair and provides novel insights into extreme environmental tolerances among bacteriophages. Full article
(This article belongs to the Section Environmental Microbiology)
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16 pages, 2592 KiB  
Article
Reproduction of Large-Scale Bioreactor Conditions on Microfluidic Chips
by Phuong Ho, Christoph Westerwalbesloh, Eugen Kaganovitch, Alexander Grünberger, Peter Neubauer, Dietrich Kohlheyer and Eric von Lieres
Microorganisms 2019, 7(4), 105; https://doi.org/10.3390/microorganisms7040105 - 19 Apr 2019
Cited by 27 | Viewed by 5770
Abstract
Microbial cells in industrial large-scale bioreactors are exposed to fluctuating conditions, e.g., nutrient concentration, dissolved oxygen, temperature, and pH. These inhomogeneities can influence the cell physiology and metabolism, e.g., decelerate cell growth and product formation. Microfluidic systems offer new opportunities to study such [...] Read more.
Microbial cells in industrial large-scale bioreactors are exposed to fluctuating conditions, e.g., nutrient concentration, dissolved oxygen, temperature, and pH. These inhomogeneities can influence the cell physiology and metabolism, e.g., decelerate cell growth and product formation. Microfluidic systems offer new opportunities to study such effects in great detail by examining responses to varying environmental conditions at single-cell level. However, the possibility to reproduce large-scale bioreactor conditions in microscale cultivation systems has not yet been systematically investigated. Hence, we apply computational fluid dynamics (CFD) simulations to analyze and compare three commonly used microfluidic single-cell trapping and cultivation devices that are based on (i) mother machines (MM), (ii) monolayer growth chambers (MGC), and (iii) negative dielectrophoresis (nDEP). Several representative time-variant nutrient concentration profiles are applied at the chip entry. Responses to these input signals within the studied microfluidic devices are comparatively evaluated at the positions of the cultivated cells. The results are comprehensively presented in a Bode diagram that illustrates the degree of signal damping depending on the frequency of change in the inlet concentration. As a key finding, the MM can accurately reproduce signal changes that occur within 1 s or slower, which are typical for the environmental conditions observed by single cells in large-scale bioreactors, while faster changes are levelled out. In contrast, the nDEP and MGC are found to level out signal changes occurring within 10 s or faster, which can be critical for the proposed application. Full article
(This article belongs to the Special Issue Microbial Cultivation and Analysis in Microsystems)
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20 pages, 647 KiB  
Review
Probiotics: If It Does Not Help It Does Not Do Any Harm. Really?
by Aaron Lerner, Yehuda Shoenfeld and Torsten Matthias
Microorganisms 2019, 7(4), 104; https://doi.org/10.3390/microorganisms7040104 - 11 Apr 2019
Cited by 74 | Viewed by 16163
Abstract
Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions [...] Read more.
Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions expressed criticism on their claimed effects and safety. The present review describes the dark side of the probiotics, in terms of problematic research design, incomplete reporting, lack of transparency, and under-reported safety. Highlighted are the potential virulent factors and the mode of action in the intestinal lumen, risking the physiological microbiome equilibrium. Finally, regulatory topics are discussed to lighten the heterogeneous guidelines applied worldwide. The shift in the scientific world towards a better understanding of the human microbiome, before consumption of the probiotic cargo, is highly endorsed. It is hoped that better knowledge will extend the probiotic repertoire, re-confirm efficacy or safety, establish their efficacy and substantiate their beneficial effects. Full article
(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)
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13 pages, 836 KiB  
Review
Functional Genomics of Aspergillus oryzae: Strategies and Progress
by Bin He, Yayi Tu, Chunmiao Jiang, Zhe Zhang, Yongkai Li and Bin Zeng
Microorganisms 2019, 7(4), 103; https://doi.org/10.3390/microorganisms7040103 - 10 Apr 2019
Cited by 32 | Viewed by 8230
Abstract
Aspergillus oryzae has been used for the production of traditional fermentation and has promising potential to produce primary and secondary metabolites. Due to the tough cell walls and high drug resistance of A. oryzae, functional genomic characterization studies are relatively limited. The [...] Read more.
Aspergillus oryzae has been used for the production of traditional fermentation and has promising potential to produce primary and secondary metabolites. Due to the tough cell walls and high drug resistance of A. oryzae, functional genomic characterization studies are relatively limited. The exploitation of selection markers and genetic transformation methods are critical for improving A. oryzae fermentative strains. In this review, we describe the genome sequencing of various A. oryzae strains. Recently developed selection markers and transformation strategies are also described in detail, and the advantages and disadvantages of transformation methods are presented. Lastly, we introduce the recent progress on highlighted topics in A. oryzae functional genomics including conidiation, protein secretion and expression, and secondary metabolites, which will be beneficial for improving the application of A. oryzae to industrial production. Full article
(This article belongs to the Section Food Microbiology)
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19 pages, 2217 KiB  
Article
New R-Based Methodology to Optimize the Identification of Root Endophytes against Heterobasidion parviporum
by Linda Rigerte, Kathrin Blumenstein and Eeva Terhonen
Microorganisms 2019, 7(4), 102; https://doi.org/10.3390/microorganisms7040102 - 6 Apr 2019
Cited by 6 | Viewed by 4970
Abstract
Many root fungal endophytes inhabiting forest trees have potential impact on the health and disease progression of certain tree species. Hence, the screening of root endophytes for their biocontrol abilities is relevant for their potential to protect their hosts against invaders. The aim [...] Read more.
Many root fungal endophytes inhabiting forest trees have potential impact on the health and disease progression of certain tree species. Hence, the screening of root endophytes for their biocontrol abilities is relevant for their potential to protect their hosts against invaders. The aim of this research is to screen for the potential inhibitory effects of selected conifer root endophytes during interaction, in vitro, with the root rot pathogen, Heterobasidion parviporum. Here, we introduce a guideline that facilitates the use of root fungal endophytes as biocontrol agents. We isolated fungal root endophytes from eight different conifers. These root fungal endophytes were evaluated for their antagonism against the root rot pathogen, H. parviporum, by means of paired-culture antagonism assays. We determined the antagonism of the isolated root fungal endophytes to elucidate potential biocontrol applications. For the analysis, a software package in R was developed. Endophyte candidates with antagonistic potential were identified. Full article
(This article belongs to the Special Issue Ecology and Genomics of Forest Fungi and Their Interactions)
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15 pages, 1426 KiB  
Article
Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria
by Sabina Zoledowska, Luana Presta, Marco Fondi, Francesca Decorosi, Luciana Giovannetti, Alessio Mengoni and Ewa Lojkowska
Microorganisms 2019, 7(4), 101; https://doi.org/10.3390/microorganisms7040101 - 5 Apr 2019
Cited by 11 | Viewed by 4608
Abstract
Understanding plant–microbe interactions is crucial for improving plants’ productivity and protection. Constraint-based metabolic modeling is one of the possible ways to investigate the bacterial adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. We reconstructed [...] Read more.
Understanding plant–microbe interactions is crucial for improving plants’ productivity and protection. Constraint-based metabolic modeling is one of the possible ways to investigate the bacterial adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. We reconstructed a raw metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193 with the use of KBase. The model was curated by using inParanoind and phenotypic data generated with the use of the OmniLog system. Metabolic modeling was performed through COBRApy Toolbox v. 0.10.1. The curated metabolic model of P. parmentieri SCC3193 is highly reliable, as in silico obtained results overlapped up to 91% with experimental data on carbon utilization phenotypes. By mean of flux balance analysis (FBA), we predicted the metabolic adaptation of P. parmentieri SCC3193 to two different ecological niches, relevant for the persistence and plant colonization by this bacterium: soil and the rhizosphere. We performed in silico gene deletions to predict the set of essential core genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen. Full article
(This article belongs to the Special Issue Macro and Microorganism Interactions)
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18 pages, 2440 KiB  
Article
Lysis Profiles of Salmonella Phages on Salmonella Isolates from Various Sources and Efficiency of a Phage Cocktail against S. Enteritidis and S. Typhimurium
by Kantiya Petsong, Soottawat Benjakul, Soraya Chaturongakul, Andrea I. Moreno Switt and Kitiya Vongkamjan
Microorganisms 2019, 7(4), 100; https://doi.org/10.3390/microorganisms7040100 - 5 Apr 2019
Cited by 38 | Viewed by 5483
Abstract
Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium are major foodborne pathogens of concern worldwide. Bacteriophage applications have gained more interest for biocontrol in foods. This study isolated 36 Salmonella phages from several animal farms in Thailand and tested them on 47 [...] Read more.
Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium are major foodborne pathogens of concern worldwide. Bacteriophage applications have gained more interest for biocontrol in foods. This study isolated 36 Salmonella phages from several animal farms in Thailand and tested them on 47 Salmonella strains from several sources, including farms, seafood processing plant and humans in Thailand and USA. Phages were classified into three major groups. The estimated phage genome size showed the range from 50 ± 2 to 200 ± 2 kb. An effective phage cocktail consisting of three phages was developed. Approximately 4 log CFU/mL of S. Enteritidis and S. Typhimurium could be reduced. These phages revealed a burst size of up to 97.7 on S. Enteritidis and 173.7 PFU/cell on S. Typhimurium. Our phage cocktail could decrease S. Enteritidis on chicken meat and sunflower sprouts by 0.66 log CFU/cm2 and 1.27 log CFU/g, respectively. S. Typhimurium on chicken meat and sunflower sprouts were decreased by 1.73 log CFU/cm2 and 1.17 log CFU/g, respectively. Overall, animal farms in Thailand provided high abundance and diversity of Salmonella phages with the lysis ability on Salmonella hosts from various environments and continents. A developed phage cocktail suggests a potential biocontrol against Salmonella in fresh foods. Full article
(This article belongs to the Special Issue Biocontrol of Food Borne Pathogens)
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13 pages, 2550 KiB  
Article
Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior
by Takahiro Segawa, Satoshi Fukuchi, Dylan Bodington, Sayaka Tsuchida, Pierre Philippe Mbehang Nguema, Hiroshi Mori and Kazunari Ushida
Microorganisms 2019, 7(4), 99; https://doi.org/10.3390/microorganisms7040099 - 4 Apr 2019
Cited by 5 | Viewed by 3484
Abstract
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility [...] Read more.
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species. Full article
(This article belongs to the Special Issue Wildlife Microbiology)
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8 pages, 1750 KiB  
Article
The Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains
by Yen-Yi Liu, Ji-Wei Lin and Chih-Chieh Chen
Microorganisms 2019, 7(4), 98; https://doi.org/10.3390/microorganisms7040098 - 3 Apr 2019
Cited by 3 | Viewed by 3411
Abstract
Extended multi-locus sequence typing (eMLST) methods have become popular in the field of genomic epidemiology. Before eMLST methods can be applied in epidemiological investigations, the selection of a suitable scheme is critical. The core genome scheme (cgMLST) has become the most popular eMLST [...] Read more.
Extended multi-locus sequence typing (eMLST) methods have become popular in the field of genomic epidemiology. Before eMLST methods can be applied in epidemiological investigations, the selection of a suitable scheme is critical. The core genome scheme (cgMLST) has become the most popular eMLST approach for strain typing in the epidemiological domain. In addition to strain typing, many public health researchers and clinical microbiologists wish to investigate which genes cause genetic differences between compared strains. Therefore, a tool that can be used to extract canonical genes with an eMLST scheme would be particularly useful. In this study, we present cano-eMLST, a well-designed program that applies a feature-selection methodology to create a canonical locus combination with discriminatory power by traversing a genetic relatedness tree based on a user-selected scheme. The cano-eMLST program is provided mainly to help infectious disease laboratory researchers identify potential factors related to bacterial pathogenesis. The core program (tree-traversing approach) of cano-eMLST is implemented in Perl and Python. All the necessary dependencies and environmental settings are provided in the encapsulated version (VirtualBox or VMware) and self-installation version (all use source code and libraries). Full article
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29 pages, 796 KiB  
Review
Food Supplements to Mitigate Detrimental Effects of Pelvic Radiotherapy
by Charlotte Segers, Mieke Verslegers, Sarah Baatout, Natalie Leys, Sarah Lebeer and Felice Mastroleo
Microorganisms 2019, 7(4), 97; https://doi.org/10.3390/microorganisms7040097 - 3 Apr 2019
Cited by 19 | Viewed by 6423
Abstract
Pelvic radiotherapy has been frequently reported to cause acute and late onset gastrointestinal (GI) toxicities associated with significant morbidity and mortality. Although the underlying mechanisms of pelvic radiation-induced GI toxicity are poorly understood, they are known to involve a complex interplay between all [...] Read more.
Pelvic radiotherapy has been frequently reported to cause acute and late onset gastrointestinal (GI) toxicities associated with significant morbidity and mortality. Although the underlying mechanisms of pelvic radiation-induced GI toxicity are poorly understood, they are known to involve a complex interplay between all cell types comprising the intestinal wall. Furthermore, increasing evidence states that the human gut microbiome plays a role in the development of radiation-induced health damaging effects. Gut microbial dysbiosis leads to diarrhea and fatigue in half of the patients. As a result, reinforcement of the microbiome has become a hot topic in various medical disciplines. To counteract GI radiotoxicities, apart from traditional pharmacological compounds, adjuvant therapies are being developed including food supplements like vitamins, prebiotics, and probiotics. Despite the easy, cheap, safe, and feasible approach to protect patients against acute radiation-induced toxicity, clinical trials have yielded contradictory results. In this review, a detailed overview is given of the various clinical, intestinal manifestations after pelvic irradiation as well as the role of the gut microbiome herein. Furthermore, whilst discussing possible strategies to prevent these symptoms, food supplements are presented as auspicious, prophylactic, and therapeutic options to mitigate acute pelvic radiation-induced GI injury by exploring their molecular mechanisms of action. Full article
(This article belongs to the Section Gut Microbiota)
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25 pages, 3775 KiB  
Article
Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii
by Senjie Lin, Liying Yu and Huan Zhang
Microorganisms 2019, 7(4), 96; https://doi.org/10.3390/microorganisms7040096 - 2 Apr 2019
Cited by 27 | Viewed by 5416
Abstract
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal [...] Read more.
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses. Full article
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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11 pages, 6151 KiB  
Article
Biofilm Formation by Shiga Toxin-Producing Escherichia coli on Stainless Steel Coupons as Affected by Temperature and Incubation Time
by Zhi Ma, Emmanuel W. Bumunang, Kim Stanford, Xiaomei Bie, Yan D. Niu and Tim A. McAllister
Microorganisms 2019, 7(4), 95; https://doi.org/10.3390/microorganisms7040095 - 31 Mar 2019
Cited by 36 | Viewed by 5690
Abstract
Forming biofilm is a strategy utilized by Shiga toxin-producing Escherichia coli (STEC) to survive and persist in food processing environments. We investigated the biofilm-forming potential of STEC strains from 10 clinically important serogroups on stainless steel at 22 °C or 13 °C after [...] Read more.
Forming biofilm is a strategy utilized by Shiga toxin-producing Escherichia coli (STEC) to survive and persist in food processing environments. We investigated the biofilm-forming potential of STEC strains from 10 clinically important serogroups on stainless steel at 22 °C or 13 °C after 24, 48, and 72 h of incubation. Results from crystal violet staining, plate counts, and scanning electron microscopy (SEM) identified a single isolate from each of the O113, O145, O91, O157, and O121 serogroups that was capable of forming strong or moderate biofilms on stainless steel at 22 °C. However, the biofilm-forming strength of these five strains was reduced when incubation time progressed. Moreover, we found that these strains formed a dense pellicle at the air-liquid interface on stainless steel, which suggests that oxygen was conducive to biofilm formation. At 13 °C, biofilm formation by these strains decreased (P < 0.05), but gradually increased over time. Overall, STEC biofilm formation was most prominent at 22 °C up to 24 h. The findings in this study identify the environmental conditions that may promote STEC biofilm formation in food processing facilities and suggest that the ability of specific strains to form biofilms contributes to their persistence within these environments. Full article
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17 pages, 1879 KiB  
Article
Efficiency of Single Phage Suspensions and Phage Cocktail in the Inactivation of Escherichia coli and Salmonella Typhimurium: An In Vitro Preliminary Study
by Pedro Costa, Carla Pereira, Ana T. P. C. Gomes and Adelaide Almeida
Microorganisms 2019, 7(4), 94; https://doi.org/10.3390/microorganisms7040094 - 31 Mar 2019
Cited by 55 | Viewed by 5146
Abstract
Enterobacteriaceae Escherichia coli and Salmonella enterica serovar Typhimurium strains are among the main pathogens responsible for moderate and serious infections at hospital and community environments, in part because they frequently present resistance to antibiotics. As the treatment of Enterobacteriaceae infections is empiric, using [...] Read more.
Enterobacteriaceae Escherichia coli and Salmonella enterica serovar Typhimurium strains are among the main pathogens responsible for moderate and serious infections at hospital and community environments, in part because they frequently present resistance to antibiotics. As the treatment of Enterobacteriaceae infections is empiric, using the same antibiotics to treat E. coli and Salmonella infections, the same concept can be applied with phages. The use of different phages combined in cocktails, frequently used to circumvent the development of phage-resistant mutants, also allows for the treatment of multiple pathogens, broadening the phages’ action spectrum. As such, the aim of this study was to evaluate the efficiency of a cocktail of two phages (ELY-1, produced on E. coli and phSE-5, produced on S. Typhimurium) to control E. coli and S. Typhimurium. Phages ELY-1 and phSE-5 were effective against E. coli (maximum reductions of 4.5 and 3.8 log CFU/mL, respectively), S. Typhimurium (maximum reductions of 2.2 and 2.6 log CFU/mL, respectively), and the mixture of both bacteria (maximum reductions of 2.2 and 2.0 log CFU/mL, respectively). The cocktail ELY-1/phSE-5 was more effective against S. Typhimurium and the mixture of both bacteria (maximum reduction of 3.2 log CFU/mL for both) than the single phage suspensions and as effective against E. coli as its specific phage ELY-1 (maximum reductions of 4.5 log CFU/mL). The use of both the phage cocktails, as well as the single-phage suspensions, however, did not prevent the occurrence of phage-resistant mutants. Overall, the results indicate that the application of the phages in the form of a cocktail show their potential to be used presumptively, that is, prior to the identification of the pathogens, paving its use to control E. coli or S. Typhimurium. Full article
(This article belongs to the Special Issue Strategies and Weapons to Fight Antimicrobial Resistance)
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14 pages, 1469 KiB  
Article
Impact of Aquaculture Practices on Intestinal Bacterial Profiles of Pacific Whiteleg Shrimp Litopenaeus vannamei
by Angela Landsman, Benoit St-Pierre, Misael Rosales-Leija, Michael Brown and William Gibbons
Microorganisms 2019, 7(4), 93; https://doi.org/10.3390/microorganisms7040093 - 30 Mar 2019
Cited by 36 | Viewed by 6837
Abstract
Considering the crucial role of the gut microbiome in animal health and nutrition, solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth on lower cost feeds, may lie in manipulation of their microbial symbionts. However, achieving this goal will [...] Read more.
Considering the crucial role of the gut microbiome in animal health and nutrition, solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth on lower cost feeds, may lie in manipulation of their microbial symbionts. However, achieving this goal will require a deeper understanding of shrimp microbial communities and how their composition is influenced by diet formulation, environmental conditions, and host factors. In this context, the current study investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei—the most widely aquaculture-farmed shrimp worldwide) reared in indoor aquaculture facilities and outdoor pond systems. While samples showed very consistent intestinal bacterial community profiles within each production system, major differences were uncovered between the two practices. Indeed, bacteria affiliated with Rhodobacteraceae (Proteobacteria) and Actinobacteria were significantly more abundant in indoor samples (84.4% vs. 5.1%; 3.0% vs. 0.06%, respectively), while Vibrionaceae (Proteobacteria), Firmicutes, Fusobacteria and Cyanobacteria were predominant in pond samples (0.03% vs. 44.8%; 0.7% vs. 36.0%; 0.0% vs. 7.9%; 0.001% vs. 1.6%, respectively). Accordingly, the abundance of 11 of the 12 most prominent Operational Taxonomic Units (OTUs) were found to be statistically different between the two production environments. Together, these results indicate that aquaculture practices greatly influence the intestinal bacterial profile of the whiteleg shrimp, and further suggest that bacterial communities of this economically important crustacean could be effectively manipulated using diet composition or environmental conditions. Full article
(This article belongs to the Special Issue Gut Microorganisms of Aquatic Animals)
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