Microorganisms

18 pages, 3365 KB

Open AccessArticle

Colonization of Germ-Free Piglets with Commensal Lactobacillus amylovorus, Lactobacillus mucosae, and Probiotic E. coli Nissle 1917 and Their Interference with Salmonella Typhimurium

by Igor Splichal, Sharon M. Donovan, Zdislava Splichalova, Vera Neuzil Bunesova, Eva Vlkova, Vera Jenistova, Jiri Killer, Roman Svejstil, Eva Skrivanova and Alla Splichalova

Microorganisms 2019, 7(8), 273; https://doi.org/10.3390/microorganisms7080273 - 20 Aug 2019

Cited by 17 | Viewed by 5613

Abstract

Non-typhoid Salmonellae are worldwide spread food-borne pathogens that cause diarrhea in humans and animals. Their multi-drug resistances require alternative ways to combat this enteric pathogen. Mono-colonization of a gnotobiotic piglet gastrointestinal tract with commensal lactobacilli Lactobacillus amylovorus and Lactobacillus mucosae and with probiotic [...] Read more.

Non-typhoid Salmonellae are worldwide spread food-borne pathogens that cause diarrhea in humans and animals. Their multi-drug resistances require alternative ways to combat this enteric pathogen. Mono-colonization of a gnotobiotic piglet gastrointestinal tract with commensal lactobacilli Lactobacillus amylovorus and Lactobacillus mucosae and with probiotic E. coli Nissle 1917 and their interference with S. Typhimurium infection was compared. The impact of bacteria and possible protection against infection with Salmonella were evaluated by clinical signs, bacterial translocation, intestinal histology, mRNA expression of villin, claudin-1, claudin-2, and occludin in the ileum and colon, and local intestinal and systemic levels of inflammatory cytokines IL-8, TNF-α, and IL-10. Both lactobacilli colonized the gastrointestinal tract in approximately 100× lower density compare to E. coli Nissle and S. Typhimurium. Neither L. amylovorus nor L. mucosae suppressed the inflammatory reaction caused by the 24 h infection with S. Typhimurium. In contrast, probiotic E. coli Nissle 1917 was able to suppress clinical signs, histopathological changes, the transcriptions of the proteins, and the inductions of the inflammatory cytokines. Future studies are needed to determine whether prebiotic support of the growth of lactobacilli and multistrain lactobacilli inoculum could show higher protective effects. Full article

(This article belongs to the Special Issue Host-Gut Microbiota Interactions)

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19 pages, 1473 KB

Open AccessArticle

Characterization of Non-O157 Escherichia coli from Cattle Faecal Samples in the North-West Province of South Africa

by Emmanuel W. Bumunang, Tim A. McAllister, Rahat Zaheer, Rodrigo Ortega Polo, Kim Stanford, Robin King, Yan D. Niu and Collins N. Ateba

Microorganisms 2019, 7(8), 272; https://doi.org/10.3390/microorganisms7080272 - 20 Aug 2019

Cited by 42 | Viewed by 5541

Abstract

Escherichia coli are commensal bacteria in the gastrointestinal tract of mammals, but some strains have acquired Shiga-toxins and can cause enterohemorrhagic diarrhoea and kidney failure in humans. Shiga-toxigenic E. coli (STEC) strains such as E. coli O157:H7 and some non-O157 strains also contain [...] Read more.

Escherichia coli are commensal bacteria in the gastrointestinal tract of mammals, but some strains have acquired Shiga-toxins and can cause enterohemorrhagic diarrhoea and kidney failure in humans. Shiga-toxigenic E. coli (STEC) strains such as E. coli O157:H7 and some non-O157 strains also contain other virulence traits, some of which contribute to their ability to form biofilms. This study characterized non-O157 E. coli from South African cattle faecal samples for their virulence potential, antimicrobial resistance (AMR), biofilm-forming ability, and genetic relatedness using culture-based methods, pulsed-field gel electrophoresis (PFGE), and whole genome sequencing (WGS). Of 80 isolates screened, 77.5% (62/80) possessed Shiga-toxins genes. Of 18 antimicrobials tested, phenotypic resistance was detected against seven antimicrobials. Resistance ranged from 1.3% (1/80) for ampicillin-sulbactam to 20% (16/80) for tetracycline. Antimicrobial resistance genes were infrequently detected except for tetA, which was found in 31.3% (25/80) and tetB detected in 11.3% (9/80) of isolates. Eight biofilm-forming associated genes were detected in STEC isolates (n = 62) and two non-STEC strains. Prevalence of biofilm genes ranged from 31.3% (20/64) for ehaA^β passenger to 100% for curli structural subunit (csgA) and curli regulators (csgA and crl). Of the 64 STEC and multi-drug resistant isolates, 70.3% (45/64) and 37.5% (24/64) formed strong biofilms on polystyrene at 22 and 37 °C, respectively. Of 59 isolates screened by PFGE, 37 showed unique patterns and the remaining isolates were grouped into five clusters with a ≥90% relatedness. In silico serotyping following WGS on a subset of 24 non-O157 STEC isolates predicted 20 serotypes comprising three novel serotypes, indicating their diversity as potential pathogens. These findings show that North West South African cattle harbour genetically diverse, virulent, antimicrobial-resistant and biofilm-forming non-O157 E. coli. Biofilm-forming ability may increase the likelihood of persistence of these pathogens in the environment and facilitate their dissemination, increasing the risk of cross contamination or establishment of infections in hosts. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)

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17 pages, 1200 KB

Open AccessReview

The Role of Gut Microbiota in Intestinal Inflammation with Respect to Diet and Extrinsic Stressors

by Stefani Lobionda, Panida Sittipo, Hyog Young Kwon and Yun Kyung Lee

Microorganisms 2019, 7(8), 271; https://doi.org/10.3390/microorganisms7080271 - 19 Aug 2019

Cited by 263 | Viewed by 19298

Abstract

The gut microbiota maintains a symbiotic relationship with the host and regulates several important functions including host metabolism, immunity, and intestinal barrier function. Intestinal inflammation and inflammatory bowel disease (IBD) are commonly associated with dysbiosis of the gut microbiota. Alterations in the gut [...] Read more.

The gut microbiota maintains a symbiotic relationship with the host and regulates several important functions including host metabolism, immunity, and intestinal barrier function. Intestinal inflammation and inflammatory bowel disease (IBD) are commonly associated with dysbiosis of the gut microbiota. Alterations in the gut microbiota and associated changes in metabolites as well as disruptions in the intestinal barrier are evidence of the relationship between the gut microbiota and intestinal inflammation. Recent studies have found that many factors may alter the gut microbiota, with the effects of diet being commonly-studied. Extrinsic stressors, including environmental stressors, antibiotic exposure, sleep disturbance, physical activity, and psychological stress, may also play important roles in altering the composition of the gut microbiota. Herein, we discuss the roles of the gut microbiota in intestinal inflammation in relation to diet and other extrinsic stressors. Full article

(This article belongs to the Special Issue Feature Papers in Gut Microbiota)

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24 pages, 409 KB

Open AccessReview

Novel Antibiotics for Multidrug-Resistant Gram-Positive Microorganisms

by Despoina Koulenti, Elena Xu, Isaac Yin Sum Mok, Andrew Song, Drosos E. Karageorgopoulos, Apostolos Armaganidis, Jeffrey Lipman and Sotirios Tsiodras

Microorganisms 2019, 7(8), 270; https://doi.org/10.3390/microorganisms7080270 - 18 Aug 2019

Cited by 78 | Viewed by 10311

Abstract

Increasing multidrug-resistance to Gram-positive pathogens, particularly to staphylococci, enterococci and streptococci, is a major problem, resulting in significant morbidity, mortality and healthcare costs. In recent years, only a small number of novel antibiotics effective against Gram-positive bacteria has been approved. This review will [...] Read more.

Increasing multidrug-resistance to Gram-positive pathogens, particularly to staphylococci, enterococci and streptococci, is a major problem, resulting in significant morbidity, mortality and healthcare costs. In recent years, only a small number of novel antibiotics effective against Gram-positive bacteria has been approved. This review will discuss the current evidence for novel branded antibiotics that are highly effective in the treatment of multidrug-resistant infections by Gram-positive pathogens, namely ceftobiprole, ceftaroline, telavancin, oritavancin, dalbavancin, tedizolid, besifloxacin, delafloxacin, ozenoxacin, and omadacycline. The mechanism of action, pharmacokinetics, microbiological spectrum, efficacy and safety profile will be concisely presented. As for any emerging antibiotic agent, resistance is likely to develop against these highly effective antibiotics. Only through appropriate dosing, utilization and careful resistance development monitoring will these novel antibiotics continue to treat Gram-positive pathogens in the future. Full article

(This article belongs to the Special Issue Multidrug-Resistant Pathogens)

32 pages, 4059 KB

Open AccessReview

Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era

by Rahul Mahadev Shelake, Dibyajyoti Pramanik and Jae-Yean Kim

Microorganisms 2019, 7(8), 269; https://doi.org/10.3390/microorganisms7080269 - 17 Aug 2019

Cited by 107 | Viewed by 23336

Abstract

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant–microbe (PM) interactions are either beneficial or harmful. The [...] Read more.

Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant–microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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19 pages, 1878 KB

Open AccessArticle

Administration of a Postbiotic Causes Immunomodulatory Responses in Broiler Gut and Reduces Disease Pathogenesis Following Challenge

by Casey N. Johnson, Michael H. Kogut, Kenneth Genovese, Haiqi He, Steve Kazemi and Ryan J. Arsenault

Microorganisms 2019, 7(8), 268; https://doi.org/10.3390/microorganisms7080268 - 17 Aug 2019

Cited by 83 | Viewed by 6377

Abstract

With the reemergence of poultry diseases such as necrotic enteritis following the restriction of in-feed antibiotics, the search for antibiotic alternatives has become critically important. Postbiotics are non-viable bacterial products or metabolic byproducts from probiotic microorganisms that have positive effects on the host [...] Read more.

With the reemergence of poultry diseases such as necrotic enteritis following the restriction of in-feed antibiotics, the search for antibiotic alternatives has become critically important. Postbiotics are non-viable bacterial products or metabolic byproducts from probiotic microorganisms that have positive effects on the host or microbiota. These are a promising alternative to antibiotics. Here, we describe the mechanism of action of a postbiotic in the context of a Clostridium perfringens (C. perfringens) challenge model. By using performance measurements and a peptide array kinome analysis, we describe the kinotypes and signal transduction changes elicited by the postbiotic with and without C. perfringens challenge. The postbiotic improves lesion scores, C. perfringens counts and mortality compared to challenge groups without the postbiotic, and it improves weight gain in the most severely challenged birds. The postbiotic predominantly affects the innate immune response and appears immunomodulatory. In the context of infection, it reduces the proinflammatory responses and generates a homeostatic-like response. This postbiotic is a viable alternative to antibiotics to improve poultry health in the context of C. perfringens pathogen challenge. Full article

(This article belongs to the Special Issue Gut Health in Poultry Production)

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17 pages, 2098 KB

Open AccessArticle

Production of Hydrophobic Zein-Based Films Bioinspired by The Lotus Leaf Surface: Characterization and Bioactive Properties

by Ângelo Luís, Fernanda Domingues and Ana Ramos

Microorganisms 2019, 7(8), 267; https://doi.org/10.3390/microorganisms7080267 - 16 Aug 2019

Cited by 44 | Viewed by 7549

Abstract

Hydrophobic zein-based functional films incorporating licorice essential oil were successfully developed as new alternative materials for food packaging. The lotus-leaf negative template was obtained using polydimethylsiloxane (PDMS). The complex surface patterns of the lotus leaves were transferred onto the surface of the zein-based [...] Read more.

Hydrophobic zein-based functional films incorporating licorice essential oil were successfully developed as new alternative materials for food packaging. The lotus-leaf negative template was obtained using polydimethylsiloxane (PDMS). The complex surface patterns of the lotus leaves were transferred onto the surface of the zein-based films with high fidelity (positive replica), which validates the proposed proof-of-concept. The films were prepared by casting method and fully characterized by Scanning Electron Microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR) and Differential Scanning Calorimetry (DSC). The grammage, thickness, contact angle, mechanical, optical and barrier properties of the films were measured, together with the evaluation of their biodegradability, antioxidant and antibacterial activities against common foodborne pathogens (Enterococcus faecalis and Listeria monocytogenes). The zein-based films with the incorporation of licorice essential oil presented the typical rugosities of the lotus leaf making the surfaces very hydrophobic (water contact angle of 112.50°). In addition to having antioxidant and antibacterial properties, the films also shown to be biodegradable, making them a strong alternative to the traditional plastics used in food packaging. Full article

(This article belongs to the Special Issue Natural Alternatives against Bacterial Foodborne Pathogens)

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18 pages, 4878 KB

Open AccessArticle

Pediococcus pentosaceus xy46 Can Absorb Zearalenone and Alleviate its Toxicity to the Reproductive Systems of Male Mice

by Shuhua Yang, Ping Gong, Jianwen Pan, Nan Wang, Jingjing Tong, Mingyang Wang, Miao Long, Peng Li and Jianbin He

Microorganisms 2019, 7(8), 266; https://doi.org/10.3390/microorganisms7080266 - 16 Aug 2019

Cited by 22 | Viewed by 4186

Abstract

Zearalenone (ZEA) contamination is a very serious problem around the world as it can induce reproductive disorders in animals and affect the health of humans. Therefore, reducing the damage it causes to humans and animals is a current focus of research. In this [...] Read more.

Zearalenone (ZEA) contamination is a very serious problem around the world as it can induce reproductive disorders in animals and affect the health of humans. Therefore, reducing the damage it causes to humans and animals is a current focus of research. In this study, we assess the removing capacity of Pediococcus pentosaceus xy46 towards ZEA and investigate the mechanism responsible for its action, thus confirming if it can alleviate ZEA toxicity to the reproductive systems of male mice. Our results show that the rate at which the strain removes ZEA is as high as 89.2% in 48 h when the concentration of ZEA is 4 μg/mL in the liquid medium. Heat and acid treatment significantly enhanced the ability of the bacteria to remove ZEA. The animal experiments results show that the oral administration of xy46 to mice (0.2 mL daily at a concentration of 10⁹ CFU/mL for 28 days) significantly reduces the degree of testicular pathomorphological changes and apoptosis induced by ZEA when the mice are intragastric administration with 40 mg/kg ZEA daily for 28 days. Moreover, oral administration of xy46 enhances the decrease in the testosterone level and improves the oxidative stress injury induced by ZEA. Furthermore, oral administration of xy46 reverts the expression of these genes and proteins in the testicular tissues of the mice involved in the blood–testis barrier and apoptosis (e.g., Vim, caspase 12, Cldn11, N-cad, Bax, and Bcl-2). However, xy46 cannot significantly revert in some of these evaluated parameters, especially in sperm quantity and quality when the mice were given 70 mg/kg ZEA daily for 28 days. In conclusion, our results suggest that the strain Pediococcus pentosaceus xy46 can efficiently remove ZEA from the liquid medium, the mechanism responsible for its action is absorption, and it can alleviate the toxicity of ZEA to the reproductive systems of male mice when the mice are given 40 mg/kg ZEA daily, However, it cannot completely alleviate the reproductive toxicity of higher dosage of zearalenone through its ability to adsorb ZEA. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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16 pages, 2503 KB

Open AccessArticle

Biodiesel-Derived Glycerol Obtained from Renewable Biomass—A Suitable Substrate for the Growth of Candida zeylanoides Yeast Strain ATCC 20367

by Laura Mitrea, Floricuța Ranga, Florinela Fetea, Francisc Vasile Dulf, Alexandru Rusu, Monica Trif and Dan Cristian Vodnar

Microorganisms 2019, 7(8), 265; https://doi.org/10.3390/microorganisms7080265 - 16 Aug 2019

Cited by 31 | Viewed by 5984

Abstract

Used kitchen oil represents a feasible and renewable biomass to produce green biofuels such as biodiesel. Biodiesel production generates large amounts of by-products such as the crude glycerol fraction, which can be further used biotechnologically as a valuable nutrient for many microorganisms. In [...] Read more.

Used kitchen oil represents a feasible and renewable biomass to produce green biofuels such as biodiesel. Biodiesel production generates large amounts of by-products such as the crude glycerol fraction, which can be further used biotechnologically as a valuable nutrient for many microorganisms. In this study, we transesterified used kitchen oil with methanol and sodium hydroxide in order to obtain biodiesel and crude glycerol fractions. The crude glycerol fraction consisting of 30% glycerol was integrated into a bioreactor cultivation process as a nutrient source for the growth of Candida zeylanoides ATCC 20367. Cell viability and biomass production were similar to those obtained with batch cultivations on pure glycerol or glucose as the main nutrient substrates. However, the biosynthesis of organic acids (e.g., citric and succinic) was significantly different compared to pure glycerol and glucose used as main carbon sources. Full article

(This article belongs to the Section Microbial Biotechnology)

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11 pages, 1487 KB

Open AccessArticle

Unveiling of Concealed Processes for the Degradation of Pharmaceutical Compounds by Neopestalotiopsis sp.

by Bo Ram Kang, Min Sung Kim and Tae Kwon Lee

Microorganisms 2019, 7(8), 264; https://doi.org/10.3390/microorganisms7080264 - 16 Aug 2019

Cited by 10 | Viewed by 3900

Abstract

The presence of pharmaceutical products has raised emerging biorisks in aquatic environments. Fungi have been considered in sustainable approaches for the degradation of pharmaceutical compounds from aquatic environments. Soft rot fungi of the Ascomycota phylum are the most widely distributed among fungi, but [...] Read more.

The presence of pharmaceutical products has raised emerging biorisks in aquatic environments. Fungi have been considered in sustainable approaches for the degradation of pharmaceutical compounds from aquatic environments. Soft rot fungi of the Ascomycota phylum are the most widely distributed among fungi, but their ability to biodegrade pharmaceuticals has not been studied as much as that of white rot fungi of the Basidiomycota phylum. Herein, we evaluated the capacity of the soft rot fungus Neopestalotiopsis sp. B2B to degrade pharmaceuticals under treatment of woody and nonwoody lignocellulosic biomasses. Nonwoody rice straw induced laccase activity fivefold compared with that in YSM medium containing polysaccharide. But B2B preferentially degraded polysaccharide over lignin regions in woody sources, leading to high concentrations of sugar. Hence, intermediate products from saccharification may inhibit laccase activity and thereby halt the biodegradation of pharmaceutical compounds. These results provide fundamental insights into the unique characteristics of pharmaceutical degradation by soft rot fungus Neopestalotiopsis sp. in the presence of preferred substrates during delignification. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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9 pages, 1092 KB

Open AccessArticle

Transcriptional Terminators Allow Leak-Free Chromosomal Integration of Genetic Constructs in Cyanobacteria

by Ciarán L. Kelly, George M. Taylor, Aistė Šatkutė, Linda Dekker and John T. Heap

Microorganisms 2019, 7(8), 263; https://doi.org/10.3390/microorganisms7080263 - 16 Aug 2019

Cited by 25 | Viewed by 4707

Abstract

Cyanobacteria are promising candidates for sustainable bioproduction of chemicals from sunlight and carbon dioxide. However, the genetics and metabolism of cyanobacteria are less well understood than those of model heterotrophic organisms, and the suite of well-characterised cyanobacterial genetic tools and parts is less [...] Read more.

Cyanobacteria are promising candidates for sustainable bioproduction of chemicals from sunlight and carbon dioxide. However, the genetics and metabolism of cyanobacteria are less well understood than those of model heterotrophic organisms, and the suite of well-characterised cyanobacterial genetic tools and parts is less mature and complete. Transcriptional terminators use specific RNA structures to halt transcription and are routinely used in both natural and recombinant contexts to achieve independent control of gene expression and to ‘insulate’ genes and operons from one another. Insulating gene expression can be particularly important when heterologous or synthetic genetic constructs are inserted at genomic locations where transcriptional read-through from chromosomal promoters occurs, resulting in poor control of expression of the introduced genes. To date, few terminators have been described and characterised in cyanobacteria. In this work, nineteen heterologous, synthetic or putative native Rho-independent (intrinsic) terminators were tested in the model freshwater cyanobacterium, Synechocystis sp. PCC 6803, from which eleven strong terminators were identified. A subset of these strong terminators was then used to successfully insulate a chromosomally–integrated, rhamnose-inducible rhaBAD expression system from hypothesised ‘read-through’ from a neighbouring chromosomal promoter, resulting in greatly improved inducible control. The addition of validated strong terminators to the cyanobacterial toolkit will allow improved independent control of introduced genes. Full article

(This article belongs to the Special Issue The Emerging Role of Cyanobacteria in Green Biotechnology)

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12 pages, 1256 KB

Open AccessCommunication

Large Plasmid Complement Resolved: Complete Genome Sequencing of Lactobacillus plantarum MF1298, a Candidate Probiotic Strain Associated with Unfavorable Effect

by Anette McLeod, Annette Fagerlund, Ida Rud and Lars Axelsson

Microorganisms 2019, 7(8), 262; https://doi.org/10.3390/microorganisms7080262 - 14 Aug 2019

Cited by 16 | Viewed by 7014

Abstract

Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. L. plantarum strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. L. plantarum strain MF1298 was considered a candidate probiotic, demonstrating [...] Read more.

Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. L. plantarum strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. L. plantarum strain MF1298 was considered a candidate probiotic, demonstrating in vitro probiotic properties and the ability to survive passage through the human intestinal tract. However, the strain showed an unfavorable effect on symptoms in subjects with irritable bowel syndrome in a clinical trial. The properties and the genome of this strain are thus of general interest. Obtaining the complete genome of strain MF1298 proved difficult due to its large plasmid complement. Here, we exploit a combination of sequencing approaches to obtain the complete chromosome and plasmid assemblies of MF1298. The Oxford Nanopore Technologies MinION long-read sequencer was particularly useful in resolving the unusually large number of plasmids in the strain, 14 in total. The complete genome sequence of 3,576,440 basepairs contains 3272 protein-encoding genes, of which 315 are located on plasmids. Few unique regions were found in comparison with other L. plantarum genomes. Notably, however, one of the plasmids contains genes related to vitamin B12 (cobalamin) turnover and genes encoding bacterial reverse transcriptases, features not previously reported for L. plantarum. The extensive plasmid information will be important for future studies with this strain. Full article

(This article belongs to the Special Issue Safety Aspects of Lactic Acid Bacteria)

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10 pages, 1435 KB

Open AccessArticle

Assessing Transcriptional Responses to Light by the Dinoflagellate Symbiodinium

by Bahareh Zaheri, Steve Dagenais-Bellefeuille, Bo Song and David Morse

Microorganisms 2019, 7(8), 261; https://doi.org/10.3390/microorganisms7080261 - 14 Aug 2019

Cited by 9 | Viewed by 4191

Abstract

The control of transcription is poorly understood in dinoflagellates, a group of protists whose permanently condensed chromosomes are formed without histones. Furthermore, while transcriptomes contain a number of proteins annotated as transcription factors, the majority of these are cold shock domain proteins which [...] Read more.

The control of transcription is poorly understood in dinoflagellates, a group of protists whose permanently condensed chromosomes are formed without histones. Furthermore, while transcriptomes contain a number of proteins annotated as transcription factors, the majority of these are cold shock domain proteins which are also known to bind RNA, meaning the number of true transcription factors is unknown. Here we have assessed the transcriptional response to light in the photosynthetic species Symbiodinium kawagutii. We find that three genes previously reported to respond to light using qPCR do not show differential expression using northern blots or RNA-Seq. Interestingly, global transcript profiling by RNA-Seq at LD 0 (dawn) and LD 12 (dusk) found only seven light-regulated genes (FDR = 0.1). qPCR using three randomly selected genes out of the seven was only able to validate differential expression of two. We conclude that there is likely to be less light regulation of gene expression in dinoflagellates than previously thought and suggest that transcriptional responses to other stimuli should also be more thoroughly evaluated in this class of organisms. Full article

(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)

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8 pages, 644 KB

Open AccessOpinion

Should We Not Further Study the Impact of Microbial Activity on Snow and Polar Atmospheric Chemistry?

by Florent Domine

Microorganisms 2019, 7(8), 260; https://doi.org/10.3390/microorganisms7080260 - 14 Aug 2019

Cited by 7 | Viewed by 4013

Abstract

Since 1999, atmospheric and snow chemists have shown that snow is a very active photochemical reactor that releases reactive gaseous species to the atmosphere including nitrogen oxides, hydrocarbons, aldehydes, halocarbons, carboxylic acids and mercury. Snow photochemistry therefore affects the formation of ozone, a [...] Read more.

Since 1999, atmospheric and snow chemists have shown that snow is a very active photochemical reactor that releases reactive gaseous species to the atmosphere including nitrogen oxides, hydrocarbons, aldehydes, halocarbons, carboxylic acids and mercury. Snow photochemistry therefore affects the formation of ozone, a potent greenhouse gas, and of aerosols, which affect the radiative budget of the planet and, therefore, its climate. In parallel, microbiologists have investigated microbes in snow, identified and quantified species, and sometimes discussed their nutrient supplies and metabolism, implicitly acknowledging that microbes could modify snow chemical composition. However, it is only in the past 10 years that a small number of studies have revealed that microbial activity in cold snow (< 0 °C, in the absence of significant amounts of liquid water) could lead to the release of nitrogen oxides, halocarbons, and mercury into the atmosphere. I argue here that microbes may have a significant effect on snow and atmospheric composition, especially during the polar night when photochemistry is shut off. Collaborative studies between microbiologists and snow and atmospheric chemists are needed to investigate this little-explored field. Full article

(This article belongs to the Special Issue Ice and Snow Microbiology)

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11 pages, 1557 KB

Open AccessArticle

Anatomic Characterization of the Ocular Surface Microbiome in Children

by Kara M. Cavuoto, Anat Galor and Santanu Banerjee

Microorganisms 2019, 7(8), 259; https://doi.org/10.3390/microorganisms7080259 - 14 Aug 2019

Cited by 30 | Viewed by 4080

Abstract

The microbiome is important in the evolution of the immune system in children; however, information is lacking regarding the composition of the pediatric ocular microbiome and its surrounding structures. A prospective, cross-sectional study of the ocular microbiome was conducted in children <18 years [...] Read more.

The microbiome is important in the evolution of the immune system in children; however, information is lacking regarding the composition of the pediatric ocular microbiome and its surrounding structures. A prospective, cross-sectional study of the ocular microbiome was conducted in children <18 years old. Samples from the inferior conjunctival fornix of both eyes, eyelid margin, and periocular skin underwent DNA amplification and 16S sequencing using Illumina MiSeq 250. The microbiome was analyzed using Qiime. Statistical analysis was performed using a two-sided Student’s t-test, diversity indices, and principal coordinate analysis. A total of 15 children were enrolled. The ocular surface microbiome was predominantly composed of Proteobacteria, whereas Bacteroidetes dominated the eyelid margin, and Firmicutes dominated the periocular skin. Despite these variations, no statistically significant compositional differences were found with Bray-Curtis analysis. The conjunctiva had the lowest Shannon diversity index with a value of 2.3, which was significantly lower than those of the eyelid margin (3.4, p = 0.01) and the periocular skin (3.5, p = 0.001). However, the evenness of the species using Faith’s phylogenetic diversity index was similar at all sites. Overall, the ocular surface microbiome is dominated by Proteobacteria in children. The niche is similar to the surrounding structures in terms of composition, but has a lower number and relative abundance of species. Full article

(This article belongs to the Special Issue Insights Into The Molecular Pathogenesis of Ocular Infections)

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13 pages, 1931 KB

Open AccessArticle

Evaluation of Physiological Effects Induced by Manuka Honey Upon Staphylococcus aureus and Escherichia coli

by Patricia Combarros-Fuertes, Leticia M. Estevinho, Rita Teixeira-Santos, Acácio G. Rodrigues, Cidália Pina-Vaz, Jose M. Fresno and M. Eugenia Tornadijo

Microorganisms 2019, 7(8), 258; https://doi.org/10.3390/microorganisms7080258 - 13 Aug 2019

Cited by 20 | Viewed by 6046

Abstract

Several studies have explored the antimicrobial properties of manuka honey (MkH). However, the data available regarding antibacterial action mechanisms are scarcer. The aim of this study was to scrutinize and characterize primary effects of manuka honey (MkH) upon the physiological status of Staphylococcus [...] Read more.

Several studies have explored the antimicrobial properties of manuka honey (MkH). However, the data available regarding antibacterial action mechanisms are scarcer. The aim of this study was to scrutinize and characterize primary effects of manuka honey (MkH) upon the physiological status of Staphylococcus aureus and Escherichia coli (as Gram-positive and Gram-negative bacteria models, respectively), using flow cytometry (FC) to reveal its antibacterial action mechanisms. Effects of MkH on membrane potential, membrane integrity and metabolic activity were assessed using different fluorochromes in a 180 min time course assay. Time-kill experiments were carried out under the same conditions. Additionally, MkH effect on efflux pumps was also studied in an E. coli strain with an over-expression of several efflux pumps. Exposure of bacteria to MkH resulted in physiological changes related to membrane potential and membrane integrity; these effects displayed slight differences among bacteria. MkH induced a remarkable metabolic disruption as primary physiological effect upon S. aureus and was able to block efflux pump activity in a dose-dependent fashion in the E. coli strain. Full article

(This article belongs to the Special Issue Recent Advances in Applied Microbiology)

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9 pages, 867 KB

Open AccessArticle

Dietary Non-Drug Feed Additive as an Alternative for Antibiotic Growth Promoters for Broilers During a Necrotic Enteritis Challenge

by Ali Calik, Islam I. Omara, Mallory B. White, Nicholas P. Evans, T. Peter Karnezos and Rami A. Dalloul

Microorganisms 2019, 7(8), 257; https://doi.org/10.3390/microorganisms7080257 - 13 Aug 2019

Cited by 29 | Viewed by 4932

Abstract

Necrotic enteritis, caused by Clostridium perfringens, is an enteric disease that leads to poor performance and increased mortality, resulting in significant economic losses in poultry production. This study evaluated the effects of a proprietary prebiotic, probiotic, and plant extract blend on performance of [...] Read more.

Necrotic enteritis, caused by Clostridium perfringens, is an enteric disease that leads to poor performance and increased mortality, resulting in significant economic losses in poultry production. This study evaluated the effects of a proprietary prebiotic, probiotic, and plant extract blend on performance of broilers during coccidiosis challenge leading to necrotic enteritis (NE). In total, 744 Cobb500 male broilers were randomly allocated to 3 treatments (8 replicates, 31 birds/pen) including, the negative control (NC) fed a basal diet; the positive control (PC) fed a basal diet with Virginiamycin; and the additive group fed basal diet with a blend of prebiotic, probiotic, and plant extract (BSN). A unique, naturally occurring NE model developed to mimic field conditions was implemented to challenge the birds. This model consists of spraying a concentrated commercial coccidiosis vaccine on litter and feed upon bird placement, which, in conjunction with the presence of C. perfringens spores in the environment, leads to the development of a NE outbreak one week post vaccine application. At the onset of NE on d7, three birds/pen were selected for scoring NE lesions. Body weight gain (BWG), feed intake (FI), and feed conversion ratio (FCR) were recorded on days 7, 14, 28, and 42. Carcass composition was assessed by dual energy X-ray absorptiometry (DXA) analysis on day 42. Dietary supplementation of BSN significantly (p < 0.05) improved FCR during starter and grower periods. Dietary treatments had no effect on NE lesions in the small intestine. DXA analysis revealed slightly higher lean content in BSN birds compared to NC. These results showed that dietary supplementation of the BSN blend significantly improved broilers performance during the early NE challenge phase, as well as in the grower period. Full article

(This article belongs to the Special Issue Feature Papers in Gut Microbiota)

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16 pages, 3936 KB

Open AccessArticle

The Algal Symbiont Modifies the Transcriptome of the Scleractinian Coral Euphyllia paradivisa during Heat Stress

by Dalit Meron, Keren Maor-Landaw, Eviatar Weizman, Hiba Waldman Ben-Asher, Gal Eyal, Ehud Banin, Yossi Loya and Oren Levy

Microorganisms 2019, 7(8), 256; https://doi.org/10.3390/microorganisms7080256 - 12 Aug 2019

Cited by 12 | Viewed by 6623

Abstract

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship—coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa [...] Read more.

The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship—coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphyllia paradivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of “symbiosis differentially expressed genes” and “coral heat-stress genes” in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E. paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions)

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16 pages, 606 KB

Open AccessReview

Adjuvant Strategies for More Effective Tuberculosis Vaccine Immunity

by Erica Stewart, James A Triccas and Nikolai Petrovsky

Microorganisms 2019, 7(8), 255; https://doi.org/10.3390/microorganisms7080255 - 12 Aug 2019

Cited by 33 | Viewed by 8540 | Correction

Abstract

Tuberculosis (TB) caused by Mycobacterium tuberculosis infection is responsible for the most deaths by a single infectious agent worldwide, with 1.6 million deaths in 2017 alone. The World Health Organization, through its “End TB” strategy, aims to reduce TB deaths by 95% by [...] Read more.

Tuberculosis (TB) caused by Mycobacterium tuberculosis infection is responsible for the most deaths by a single infectious agent worldwide, with 1.6 million deaths in 2017 alone. The World Health Organization, through its “End TB” strategy, aims to reduce TB deaths by 95% by 2035. In order to reach this goal, a more effective vaccine than the Bacillus Calmette-Guerin (BCG) vaccine currently in use is needed. Subunit TB vaccines are ideal candidates, because they can be used as booster vaccinations for individuals who have already received BCG and would also be safer for use in immunocompromised individuals in whom BCG is contraindicated. However, subunit TB vaccines will almost certainly require formulation with a potent adjuvant. As the correlates of vaccine protection against TB are currently unclear, there are a variety of adjuvants currently being used in TB vaccines in preclinical and clinical development. This review describes the various adjuvants in use in TB vaccines, their effectiveness, and their proposed mechanisms of action. Notably, adjuvants with less inflammatory and reactogenic profiles that can be administered safely via mucosal routes, may have the biggest impact on future directions in TB vaccine design. Full article

(This article belongs to the Special Issue Virulence Identification and Analysis from Pathogenic Mycobacteria of Humans and Animals)

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22 pages, 3611 KB

Open AccessArticle

Piacentinu Ennese PDO Cheese as Reservoir of Promising Probiotic Bacteria

by Alessandra Pino, Nunziatina Russo, Koenraad Van Hoorde, Maria De Angelis, Giuseppe Sferrazzo, Cinzia Lucia Randazzo and Cinzia Caggia

Microorganisms 2019, 7(8), 254; https://doi.org/10.3390/microorganisms7080254 - 12 Aug 2019

Cited by 34 | Viewed by 5101

Abstract

Piacentinu Ennese is a protected designation of origin (PDO) cheese produced in the surrounding area of Enna (Sicily, Italy), using raw ewe’s milk without the addition of any starter cultures. In the present study, the Lactobacillus population of Piacentinu Ennese PDO cheese was [...] Read more.

Piacentinu Ennese is a protected designation of origin (PDO) cheese produced in the surrounding area of Enna (Sicily, Italy), using raw ewe’s milk without the addition of any starter cultures. In the present study, the Lactobacillus population of Piacentinu Ennese PDO cheese was in vitro screened in order to select promising probiotic strains to be further used in humans. One hundred and sixty-nine lactic acid bacteria (LAB) were isolated from 90 days ripened cheeses and identified by Rep-PCR genomic fingerprinting, using the (GTG)₅-primer, and by MALDI-TOF MS. One hundred and thirteen (113) isolates belonging to QPS-list species were characterized for both safety and functional properties. All tested isolates were considered safe because none showed either gelatinase, DNase, mucinase, or hemolytic activity. Tolerance to lysozyme, bile salts, and acidic conditions, along with ability to survive under simulated gastrointestinal digestion, were observed. In addition, based on antimicrobial activity against pathogens, cell surface characteristics, Caco-2 adhesion abilities, and anti-inflammatory potential, it was possible to confirm the strain-dependent functional aptitude, suggesting that Piacentinu Ennese PDO cheese may be considered a precious source of probiotic candidates. Full article

(This article belongs to the Special Issue Artisanal Foods: Challenges for Microbiological Control and Safety)

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18 pages, 4630 KB

Open AccessArticle

Biocontrol of Aspergillus flavus in Ensiled Sorghum by Water Kefir Microorganisms

by Mariana Gonda, Gabriela Garmendia, Caterina Rufo, Ángela León Peláez, Michael Wisniewski, Samir Droby and Silvana Vero

Microorganisms 2019, 7(8), 253; https://doi.org/10.3390/microorganisms7080253 - 10 Aug 2019

Cited by 27 | Viewed by 4911

Abstract

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 [...] Read more.

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 °C. A. flavus growth was quantified by qPCR after incubation. Mold growth was inhibited in the presence of water kefir while no inhibition was observed when filter-sterilized water kefir was applied, demonstrating the relevant role of the microorganisms in the kefir water in the biocontrol process. Fungal and bacterial diversity in treated sorghum mini-silos was analyzed by high-throughput sequencing. Firmicutes was the predominant bacterial phyla and Lactobacillus represented the most abundant genus, while Ascomycota was the predominant fungal phyla with Saccharomyces and Pichia as the major genera. Bacterial and yeast counts before and after incubation indicated that the microbial community obtained from WK was able to grow in the sorghum mini-silos in the presence of A. flavus. Results of the present work indicate that the use of a mixed inoculum of microorganisms present in WK may represent an alternative management practice to avoid the growth of A. flavus in ensiled sorghum grains and the concomitant contamination with aflatoxins. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

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18 pages, 3073 KB

Open AccessArticle

Wastewater Biofilm Photosynthesis in Photobioreactors

by Antonella Guzzon, Francesca Di Pippo and Roberta Congestri

Microorganisms 2019, 7(8), 252; https://doi.org/10.3390/microorganisms7080252 - 10 Aug 2019

Cited by 22 | Viewed by 4930

Abstract

Photosynthetic performance of algal-bacterial biofilms from an Italian wastewater treatment plant was studied in a flow-lane photobioreactor at different irradiances, temperatures, and flow regime to evaluate the effects of these environmental parameters on biofilms’ functioning, in view of application of these communities in [...] Read more.

Photosynthetic performance of algal-bacterial biofilms from an Italian wastewater treatment plant was studied in a flow-lane photobioreactor at different irradiances, temperatures, and flow regime to evaluate the effects of these environmental parameters on biofilms’ functioning, in view of application of these communities in wastewater biological treatment. Pulse amplitude modulated fluorescence was used to estimate the effective quantum yield of PSII (ΔF/F_m’) of the light-acclimated biofilms and to perform rapid light curves (RLCs) for the determination of the photosynthetic parameters (rel.ETR_max, α, I_k). Chl a, ash free dry weight (AFDW), and dry weight (DW) were measured to assess phototrophic and whole biofilm biomass development over time. From the analysis of photosynthetic parameter variation with light intensity, temperature and flow rate, it was possible to identify the set of experimental values favoring biofilm photosynthetic activity. Biomass increased over time, especially at the highest irradiances, where substrata were fastly colonized and mature biofilms developed at all temperatures and flow conditions tested. Full article

(This article belongs to the Special Issue Microbiological Wastewater Treatment)

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18 pages, 3265 KB

Open AccessArticle

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects

by Stefano Raimondi, Lucia Righini, Francesco Candeliere, Eliana Musmeci, Francesca Bonvicini, Giovanna Gentilomi, Marjanca Starčič Erjavec, Alberto Amaretti and Maddalena Rossi

Microorganisms 2019, 7(8), 251; https://doi.org/10.3390/microorganisms7080251 - 10 Aug 2019

Cited by 40 | Viewed by 7072

Abstract

Escherichia coli may innocuously colonize the intestine of healthy subjects or may instigate infections in the gut or in other districts. This study investigated intestinal E. coli isolated from 20 healthy adults. Fifty-one strains were genotyped by molecular fingerprinting and analyzed for genetic [...] Read more.

Escherichia coli may innocuously colonize the intestine of healthy subjects or may instigate infections in the gut or in other districts. This study investigated intestinal E. coli isolated from 20 healthy adults. Fifty-one strains were genotyped by molecular fingerprinting and analyzed for genetic and phenotypic traits, encompassing the profile of antibiotic resistance, biofilm production, the presence of surface structures (such as curli and cellulose), and their performance as recipients in conjugation experiments. A phylogroup classification and analysis of 34 virulence determinants, together with genes associated to the pks island (polyketide-peptide genotoxin colibactin) and conjugative elements, was performed. Most of the strains belonged to the phylogroups B1 and B2. The different phylogroups were separated in a principal coordinate space, considering both genetic and functional features, but not considering pulsed-field gel electrophoresis. Within the B2 and F strains, 12 shared the pattern of virulence genes with potential uropathogens. Forty-nine strains were sensitive to all the tested antibiotics. Strains similar to the potential pathogens innocuously inhabited the gut of healthy subjects. However, they may potentially act as etiologic agents of extra-intestinal infections and are susceptible to a wide range of antibiotics. Nevertheless, there is still the possibility to control infections with antibiotic therapy. Full article

(This article belongs to the Special Issue Feature Papers in Gut Microbiota)

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28 pages, 3023 KB

Open AccessArticle

Metagenomic Sequencing Identifies Highly Diverse Assemblages of Dinoflagellate Cysts in Sediments from Ships’ Ballast Tanks

by Lixia Shang, Zhangxi Hu, Yunyan Deng, Yuyang Liu, Xinyu Zhai, Zhaoyang Chai, Xiaohan Liu, Zifeng Zhan, Fred C. Dobbs and Ying Zhong Tang

Microorganisms 2019, 7(8), 250; https://doi.org/10.3390/microorganisms7080250 - 9 Aug 2019

Cited by 46 | Viewed by 7384

Abstract

Ships’ ballast tanks have long been known as vectors for the introduction of organisms. We applied next-generation sequencing to detect dinoflagellates (mainly as cysts) in 32 ballast tank sediments collected during 2001–2003 from ships entering the Great Lakes or Chesapeake Bay and subsequently [...] Read more.

Ships’ ballast tanks have long been known as vectors for the introduction of organisms. We applied next-generation sequencing to detect dinoflagellates (mainly as cysts) in 32 ballast tank sediments collected during 2001–2003 from ships entering the Great Lakes or Chesapeake Bay and subsequently archived. Seventy-three dinoflagellates were fully identified to species level by this metagenomic approach and single-cell polymerase chain reaction (PCR)-based sequencing, including 19 toxic species, 36 harmful algal bloom (HAB) forming species, 22 previously unreported as producing cysts, and 55 reported from ballast tank sediments for the first time (including 13 freshwater species), plus 545 operational taxonomic units (OTUs) not fully identified due to a lack of reference sequences, indicating tank sediments are repositories of many previously undocumented taxa. Analyses indicated great heterogeneity of species composition among samples from different sources. Light and scanning electron microscopy and single-cell PCR sequencing supported and confirmed results of the metagenomic approach. This study increases the number of fully identified dinoflagellate species from ballast tank sediments to 142 (>50% increase). From the perspective of ballast water management, the high diversity and spatiotemporal heterogeneity of dinoflagellates in ballast tanks argues for continuing research and stringent adherence to procedures intended to prevent unintended introduction of non-indigenous toxic and HAB-forming species. Full article

(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)

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29 pages, 14661 KB

Open AccessArticle

Screening of the High-Rhizosphere Competent Limoniastrum monopetalum’ Culturable Endophyte Microbiota Allows the Recovery of Multifaceted and Versatile Biocontrol Agents

by Houda Ben Slama, Mohamed Ali Triki, Ali Chenari Bouket, Fedia Ben Mefteh, Faizah N. Alenezi, Lenka Luptakova, Hafsa Cherif-Silini, Armelle Vallat, Tomasz Oszako, Neji Gharsallah and Lassaad Belbahri

Microorganisms 2019, 7(8), 249; https://doi.org/10.3390/microorganisms7080249 - 9 Aug 2019

Cited by 30 | Viewed by 6466

Abstract

Halophyte Limoniastrum monopetalum, an evergreen shrub inhabiting the Mediterranean region, has well-documented phytoremediation potential for metal removal from polluted sites. It is also considered to be a medicinal halophyte with potent activity against plant pathogens. Therefore, L. monopetalum may be a suitable [...] Read more.

Halophyte Limoniastrum monopetalum, an evergreen shrub inhabiting the Mediterranean region, has well-documented phytoremediation potential for metal removal from polluted sites. It is also considered to be a medicinal halophyte with potent activity against plant pathogens. Therefore, L. monopetalum may be a suitable candidate for isolating endophytic microbiota members that provide plant growth promotion (PGP) and resistance to abiotic stresses. Selected for biocontrol abilities, these endophytes may represent multifaceted and versatile biocontrol agents, combining pathogen biocontrol in addition to PGP and plant protection against abiotic stresses. In this study 117 root culturable bacterial endophytes, including Gram-positive (Bacillus and Brevibacillus), Gram-negative (Proteus, Providencia, Serratia, Pantoea, Klebsiella, Enterobacter and Pectobacterium) and actinomycete Nocardiopsis genera have been recovered from L. monopetalum. The collection exhibited high levels of biocontrol abilities against bacterial (Agrobacterium tumefaciens MAT2 and Pectobacterium carotovorum MAT3) and fungal (Alternaria alternata XSZJY-1, Rhizoctonia bataticola MAT1 and Fusarium oxysporum f. sp. radicis lycopersici FORL) pathogens. Several bacteria also showed PGP capacity and resistance to antibiotics and metals. A highly promising candidate Bacillus licheniformis LMRE 36 with high PGP, biocontrol, metal and antibiotic, resistance was subsequently tested in planta (potato and olive trees) for biocontrol of a collection of 14 highly damaging Fusarium species. LMRE 36 proved very effective against the collection in both species and against an emerging Fusarium sp. threatening olive trees culture in nurseries. These findings provide a demonstration of our pyramiding strategy. Our strategy was effective in combining desirable traits in biocontrol agents towards broad-spectrum resistance against pathogens and protection of crops from abiotic stresses. Stacking multiple desirable traits into a single biocontrol agent is achieved by first, careful selection of a host for endophytic microbiota recovery; second, stringent in vitro selection of candidates from the collection; and third, application of the selected biocontrol agents in planta experiments. That pyramiding strategy could be successfully used to mitigate effects of diverse biotic and abiotic stresses on plant growth and productivity. It is anticipated that the strategy will provide a new generation of biocontrol agents by targeting the microbiota of plants in hostile environments. Full article

(This article belongs to the Special Issue Plant Control of Symbiotic Microbe Behavior and Reproduction)

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10 pages, 1356 KB

Open AccessArticle

Genomic Sequence Analysis of the Multidrug-Resistance Region of Avian Salmonella enterica serovar Indiana Strain MHYL

by Yan Lu, Yanjia Wen, Ge Hu, Yuqi Liu, Ross C. Beier and Xiaolin Hou

Microorganisms 2019, 7(8), 248; https://doi.org/10.3390/microorganisms7080248 - 9 Aug 2019

Cited by 5 | Viewed by 4072

Abstract

A series of human and animal diseases that are caused by Salmonella infections pose a serious threat to human health and huge economic losses to the livestock industry. We found antibiotic resistance (AR) genes in the genome of 133 strains of S. Indiana [...] Read more.

A series of human and animal diseases that are caused by Salmonella infections pose a serious threat to human health and huge economic losses to the livestock industry. We found antibiotic resistance (AR) genes in the genome of 133 strains of S. Indiana from a poultry production site in Shandong Province, China. Salmonella enterica subsp. enterica serovar Indiana strain MHYL had multidrug-resistance (MDR) genes on its genome. Southern blot analysis was used to locate genes on the genomic DNA. High-throughput sequencing technology was used to determine the gene sequence of the MHYL genome. Areas containing MDR genes were mapped based on the results of gene annotation. The AR genes bla_TEM, strA, tetA, and aac(6′)-Ib-cr were found on the MHYL genome. The resistance genes were located in two separate MDR regions, RR1 and RR2, containing type I integrons, and Tn7 transposons and multiple IS26 complex transposons with transposable functions. Portions of the MDR regions were determined to be highly homologous to the structure of plasmid pAKU_1 in S. enterica serovar Paratyphi A (accession number: AM412236), SGI11 in S. enterica serovar Typhimurium (accession number: KM023773), and plasmid pS414 in S. Indiana (accession No.: KC237285). Full article

(This article belongs to the Special Issue Foodborne Pathogen Distribution, Ecology, Inactivation and Methods of Differentiation)

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20 pages, 6408 KB

Open AccessArticle

Taxonomic Distribution of Cytochrome P450 Monooxygenases (CYPs) among the Budding Yeasts (Sub-Phylum Saccharomycotina)

by Tomas Linder

Microorganisms 2019, 7(8), 247; https://doi.org/10.3390/microorganisms7080247 - 8 Aug 2019

Cited by 11 | Viewed by 7139

Abstract

Cytochrome P450 monooxygenases (CYPs) are ubiquitous throughout the tree of life and play diverse roles in metabolism including the synthesis of secondary metabolites as well as the degradation of recalcitrant organic substrates. The genomes of budding yeasts (phylum Ascomycota, sub-phylum Saccharomycotina) [...] Read more.

Cytochrome P450 monooxygenases (CYPs) are ubiquitous throughout the tree of life and play diverse roles in metabolism including the synthesis of secondary metabolites as well as the degradation of recalcitrant organic substrates. The genomes of budding yeasts (phylum Ascomycota, sub-phylum Saccharomycotina) typically contain fewer families of CYPs than filamentous fungi. There are currently five CYP families among budding yeasts with known function while at least another six CYP families with unknown function (“orphan CYPs”) have been described. The current study surveyed the genomes of 372 species of budding yeasts for CYP-encoding genes in order to determine the taxonomic distribution of individual CYP families across the sub-phylum as well as to identify novel CYP families. Families CYP51 and CYP61 (represented by the ergosterol biosynthetic genes ERG11 and ERG5, respectively) were essentially ubiquitous among the budding yeasts while families CYP52 (alkane/fatty acid hydroxylases), CYP56 (N-formyl-l-tyrosine oxidase) displayed several instances of gene loss at the genus or family level. Phylogenetic analysis suggested that the three orphan families CYP5217, CYP5223 and CYP5252 diverged from a common ancestor gene following the origin of the budding yeast sub-phylum. The genomic survey also identified eight CYP families that had not previously been reported in budding yeasts. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

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22 pages, 2687 KB

Open AccessArticle

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

by Zahid Hassan, Munawar Sultana, Sirajul I. Khan, Martin Braster, Wilfred F.M. Röling and Hans V. Westerhoff

Microorganisms 2019, 7(8), 246; https://doi.org/10.3390/microorganisms7080246 - 8 Aug 2019

Cited by 10 | Viewed by 4668

Abstract

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we [...] Read more.

Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. SY) and heterotrophic arsenite-oxidizing strains. The enriched cultures also contained aioA phylotypes not detected in the previous survey of uncultivated samples from the same wells. Anaerobic enrichments disclosed a wider diversity of arsenite oxidizing aioA phylotypes than did aerobic enrichments. The cultivatable chemolithoautotrophic and heterotrophic arsenite oxidizers are of great interest for future in or ex-situ arsenic bioremediation technologies for the detoxification of drinking water by oxidizing arsenite to arsenate that should then precipitates with iron oxides. The microbial activities required for such a technology seem present, amplifiable, diverse and hence robust. Full article

(This article belongs to the Special Issue Subsurface Geomicrobiology)

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19 pages, 1503 KB

Open AccessReview

The Biochemistry and Evolution of the Dinoflagellate Nucleus

by Sebastian G. Gornik, Ian Hu, Imen Lassadi and Ross F. Waller

Microorganisms 2019, 7(8), 245; https://doi.org/10.3390/microorganisms7080245 - 8 Aug 2019

Cited by 37 | Viewed by 9875

Abstract

Dinoflagellates are known to possess a highly aberrant nucleus—the so-called dinokaryon—that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps [...] Read more.

Dinoflagellates are known to possess a highly aberrant nucleus—the so-called dinokaryon—that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones—the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon. Full article

(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)

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14 pages, 4500 KB

Open AccessArticle

Encapsulated Bdellovibrio Powder as a Potential Bio-Disinfectant against Whiteleg Shrimp-Pathogenic Vibrios

by Haipeng Cao, Huicong Wang, Jingjing Yu, Jian An and Jun Chen

Microorganisms 2019, 7(8), 244; https://doi.org/10.3390/microorganisms7080244 - 7 Aug 2019

Cited by 29 | Viewed by 5270

Abstract

Liquid preparations of bdellovibrios are currently commercialized as water quality improvers to control bacterial pathogens in whiteleg shrimp Penaeus vannamei. However, the efficacy of these liquid preparations is significantly impaired due to a dramatic loss of viable cells during long-term room temperature [...] Read more.

Liquid preparations of bdellovibrios are currently commercialized as water quality improvers to control bacterial pathogens in whiteleg shrimp Penaeus vannamei. However, the efficacy of these liquid preparations is significantly impaired due to a dramatic loss of viable cells during long-term room temperature storage. Thus, new formulations of bdellovibrios are greatly needed for high-stablility room-temperature storage. In the present study, the encapsulated powder of Bdellovibrio sp. strain F16 was prepared using spray drying with 20 g L⁻¹ gelatin as the coating material under a spray flow of 750 L h⁻¹, a feed rate of 12 mL min⁻¹, and an air inlet temperature of 140 °C. It was found to have a cell density of 5.4 × 10⁷ PFU g⁻¹ and to have spherical microparticles with a wrinkled surface and a diameter of 3 μm to 12 μm. In addition, the encapsulated Bdellovibrio powder presented good storage stability with its cell density still remaining at 3.5 × 10⁷ PFU g⁻¹ after 120 days of room-temperature storage; it was safe for freshwater-farmed whiteleg shrimp with an LD₅₀ over 1200 mg L⁻¹, and it exhibited significant antibacterial and protective effects at 0.8 mg L⁻¹ against shrimp-pathogenic vibrios. To our knowledge, this is the first report on a promising Bdellovibrio powder against shrimp vibrios with high stable room-temperature storage. Full article

(This article belongs to the Special Issue Recent Advances in Applied Microbiology)

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