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Microorganisms
Volume 8
Issue 3
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Microorganisms, Volume 8, Issue 3 (March 2020) – 149 articles

Cover Story (view full-size image): Siboglinidae worms are known to host chemosynthetic endosymbionts in a dedicated trophosome organ. However, little is known about their tube as a potential niche for other microorganisms. In this study, siboglinids sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV, and Anastasya MV) revealed that the tube was colonized by a thick microbial biofilm. This external biofilm of the tubes was mostly composed of cell-aggregations of methanotrophic bacteria, but other morphotypes such as filamentous, prosthecate, spirillum-like and rod-shaped bacteria were also observed. Yet, these microorganisms seem to influence in the structure and composition of the tube. Thus, siboglinids’ tubes remarkably increase the microbial biomass related to the worms and provide an additional microbial niche in deep-sea ecosystems.View this paper.
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18 pages, 1863 KiB  
Review
The Essential Co-Option of Uracil-DNA Glycosylases by Herpesviruses Invites Novel Antiviral Design
by Renos Savva
Microorganisms 2020, 8(3), 461; https://doi.org/10.3390/microorganisms8030461 - 24 Mar 2020
Cited by 5 | Viewed by 3809
Abstract
Vast evolutionary distances separate the known herpesviruses, adapted to colonise specialised cells in predominantly vertebrate hosts. Nevertheless, the distinct herpesvirus families share recognisably related genomic attributes. The taxonomic Family Herpesviridae includes many important human and animal pathogens. Successful antiviral drugs targeting Herpesviridae are [...] Read more.
Vast evolutionary distances separate the known herpesviruses, adapted to colonise specialised cells in predominantly vertebrate hosts. Nevertheless, the distinct herpesvirus families share recognisably related genomic attributes. The taxonomic Family Herpesviridae includes many important human and animal pathogens. Successful antiviral drugs targeting Herpesviridae are available, but the need for reduced toxicity and improved efficacy in critical healthcare interventions invites novel solutions: immunocompromised patients presenting particular challenges. A conserved enzyme required for viral fitness is Ung, a uracil-DNA glycosylase, which is encoded ubiquitously in Herpesviridae genomes and also host cells. Research investigating Ung in Herpesviridae dynamics has uncovered an unexpected combination of viral co-option of host Ung, along with remarkable Subfamily-specific exaptation of the virus-encoded Ung. These enzymes apparently play essential roles, both in the maintenance of viral latency and during initiation of lytic replication. The ubiquitously conserved Ung active site has previously been explored as a therapeutic target. However, exquisite selectivity and better drug-like characteristics might instead be obtained via targeting structural variations within another motif of catalytic importance in Ung. The motif structure is unique within each Subfamily and essential for viral survival. This unique signature in highly conserved Ung constitutes an attractive exploratory target for the development of novel beneficial therapeutics. Full article
(This article belongs to the Special Issue Herpesviruses: Virus-Host Interaction)
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19 pages, 1962 KiB  
Article
First Report on the Prevalence and Subtype Distribution of Blastocystis sp. in Edible Marine Fish and Marine Mammals: A Large Scale-Study Conducted in Atlantic Northeast and on the Coasts of Northern France
by Nausicaa Gantois, Angélique Lamot, Yuwalee Seesao, Colette Creusy, Luen-Luen Li, Sébastien Monchy, Sadia Benamrouz-Vanneste, Jacky Karpouzopoulos, Jean-Luc Bourgain, Célia Rault, Fabien Demaret, Martha Baydoun, Magali Chabé, Emilie Fréalle, Cécile-Marie Aliouat-Denis, Mélanie Gay, Gabriela Certad and Eric Viscogliosi
Microorganisms 2020, 8(3), 460; https://doi.org/10.3390/microorganisms8030460 - 24 Mar 2020
Cited by 20 | Viewed by 2843
Abstract
Blastocystis is frequently identified in humans and animal hosts and exhibits a large genetic diversity with the identification of 17 subtypes (STs). Despite its zoonotic potential, its prevalence and ST distribution in edible marine fish and marine mammals remain unknown. A large-scale survey [...] Read more.
Blastocystis is frequently identified in humans and animal hosts and exhibits a large genetic diversity with the identification of 17 subtypes (STs). Despite its zoonotic potential, its prevalence and ST distribution in edible marine fish and marine mammals remain unknown. A large-scale survey was thus conducted by screening 345 fish caught in Atlantic Northeast and 29 marine mammals stranded on the coasts of northern France for the presence of the parasite using real-time Polymerase Chain Reaction PCR. The prevalence of the parasite was about 3.5% in marine fish. These animals were mostly colonized by poikilotherm-derived isolates not identified in humans and corresponding to potential new STs, indicating that fish are natural hosts of Blastocystis. Marine fishes are also carriers of human STs and represent a likely limited source of zoonotic transmission. 13.8% of the marine mammals tested were colonized and 6 different STs were identified including 3 potential new STs. The risk of zoonotic transmission through marine mammals is insignificant due to the lack of repeated contact with humans. The present survey represents the first data regarding the prevalence and ST distribution of Blastocystis in marine fish and marine mammals and provides new insights into its genetic diversity, host range and transmission. Full article
(This article belongs to the Section Parasitology)
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12 pages, 1646 KiB  
Article
Unraveling the Fungal Community Associated with Leaf Spot on Crataegus sp.
by Sonia Salazar-Cerezo, María de la Cruz Meneses-Sánchez, Rebeca D. Martínez-Contreras and Nancy Martínez-Montiel
Microorganisms 2020, 8(3), 459; https://doi.org/10.3390/microorganisms8030459 - 24 Mar 2020
Cited by 2 | Viewed by 2684
Abstract
Crataegus sp. is a tree that grows in temperate zones with worldwide distribution and is commonly known in Mexico as tejocote. The use of products derived from Crataegus in traditional medicine, food, and cosmetics has increased over the last few years and the [...] Read more.
Crataegus sp. is a tree that grows in temperate zones with worldwide distribution and is commonly known in Mexico as tejocote. The use of products derived from Crataegus in traditional medicine, food, and cosmetics has increased over the last few years and the relevance of this plant has also grown. Here, we report a disease that was observed in tejocote plants that grew both in the wild and in greenhouses in Puebla (Mexico). The disease was characterized by necrotic spots on the leaf ranging from brown to reddish tones that were accompanied by structures on the back of the leaf. Furthermore, we investigated the fungal genera associated with infected leaves in wild tejocote plants, from which we recovered Alternaria sp., Aureobasidium sp., Dreschlera sp., Fusarium sp., Paecilomyces sp. and Ulocladium sp. genera. Inoculation on healthy Crataegus sp. plants with isolate UAP140 showed similar symptoms as observed in nature, while inoculation with UAP127 resulted in the development of necrotic lesions in the leaf. The identity of these isolates was further studied through the phylogenetic analysis of the ribosomal DNA internal transcribed spacer (ITS) region, where isolate UAP140 showed the highest identity with Fusarium equiseti and isolate UAP127 was similar to Alternaria arborescens. To our knowledge, this is the first report of a characteristic disease developed in Crataegus sp. plants in Mexico where the fungal community associated to the lesion was analyzed. Further studies would be necessary to determine the ecological and environmental implications of the microbiome on the appearance and development of the disease. Full article
(This article belongs to the Section Environmental Microbiology)
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21 pages, 5058 KiB  
Article
Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016–2017) in Valencia (Spain)
by Cristina Santiso-Bellón, Walter Randazzo, Alba Pérez-Cataluña, Susana Vila-Vicent, Roberto Gozalbo-Rovira, Carlos Muñoz, Javier Buesa, Gloria Sanchez and Jesús Rodríguez Díaz
Microorganisms 2020, 8(3), 458; https://doi.org/10.3390/microorganisms8030458 - 24 Mar 2020
Cited by 35 | Viewed by 4448
Abstract
The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period [...] Read more.
The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period (September 2016 to September 2017). Norovirus and rotavirus were detected and quantified by RT-qPCR, genotyped by semi-nested RT-PCR and further characterized by sequencing and phylogenetic analyses. Noroviruses and rotaviruses were widely distributed in sewage samples (69.6% for norovirus GI, 76.0% norovirus GII, and 71.7% rotaviruses) and viral loads varied from 4.33 to 5.75 log PCRU/L for norovirus GI, 4.69 to 6.95 log PCRU/L for norovirus GII, and 4.08 to 6.92 log PCRU/L for rotavirus. Overall, 87.5% (28/32) of GI noroviruses could not be genotyped, 6.25% (2/32) of the samples contained GI.2 genotype, and another 6.25% (2/32) were positive for GI.4 genotype. The most common genotype of GII noroviruses was GII.2 (40%, 14/35), followed by GII.6 (8.6%, 3/35) and GII.17 (5.7%, 2/35) while the remaining GII strains could not be typed (45.7%, 16/35). Rotavirus VP4 genotype P[8] was the only one found in 19 out of 33 rotavirus-positive samples (57.7%). G2 was the most prevalent rotavirus VP7 genotype (15.2%, 5/33) followed by G3, G9, and G12, with two positive samples for each genotype (6.1%, 2/33). In one sample both G1 and G2 genotypes were detected simultaneously (3%). The results presented here show that the surveillance of noroviruses and rotaviruses in sewage is useful for the study of their transmission in the population and their molecular epidemiology. Full article
(This article belongs to the Special Issue Enteric Virus Detection: Recent Developments and Application in Food and Waters)
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7 pages, 216 KiB  
Article
Multicenter Evaluation of the C6 Lyme ELISA Kit for the Diagnosis of Lyme Disease
by Silvia Zannoli, Michela Fantini, Simona Semprini, Barbara Marchini, Barbara Ceccarelli, Monica Sparacino, Pasqua Schiavone, Anna Belgrano, Maurizio Ruscio, Martina Gobbetti, Maira Nicoletti, Eva Robatscher, Elisabetta Pagani and Vittorio Sambri
Microorganisms 2020, 8(3), 457; https://doi.org/10.3390/microorganisms8030457 - 24 Mar 2020
Cited by 1 | Viewed by 2500
Abstract
Lyme disease (LD), caused by infection with Borrelia burgdorferi, is the most common tick-borne infection in many regions of Eurasia. Antibody detection is the most frequently used laboratory test, favoring a two-step serodiagnostic algorithm; immunoenzymatic detection of antibodies to C6 has been [...] Read more.
Lyme disease (LD), caused by infection with Borrelia burgdorferi, is the most common tick-borne infection in many regions of Eurasia. Antibody detection is the most frequently used laboratory test, favoring a two-step serodiagnostic algorithm; immunoenzymatic detection of antibodies to C6 has been shown to perform similarly to a standard two-step workflow. The aim of this study was the performance evaluation of the C6 Lyme ELISA kit compared to a standard two-step algorithm in three laboratories located in the northeastern region of Italy which cater to areas with different LD epidemiology. A total of 804 samples were tested, of which 695 gave concordant results between C6 testing and routine workflow (564 negative, 131 positive). Wherever available, clinical presentation and additional laboratory tests were analyzed to solve discrepancies. The C6 based method showed a good concordance with the standard two-step algorithm (Cohen’s κ = 0.619), however, the distribution of discrepancies seems to point towards a slightly lower specificity of C6 testing, which is supported by literature and could impact on patient management. The C6 ELISA, therefore, is not an ideal stand-alone test; however, if integrated into a two-step algorithm, it might play a part in achieving a sensitive, specific laboratory diagnosis of LD. Full article
(This article belongs to the Special Issue Advance in Tick-Borne Diseases Research)
18 pages, 3343 KiB  
Article
Fungal Microbiota of Sea Buckthorn Berries at Two Ripening Stages and Volatile Profiling of Potential Biocontrol Yeasts
by Juliana Lukša, Iglė Vepštaitė-Monstavičė, Violeta Apšegaitė, Laima Blažytė-Čereškienė, Ramunė Stanevičienė, Živilė Strazdaitė-Žielienė, Bazilė Ravoitytė, Dominykas Aleknavičius, Vincas Būda, Raimondas Mozūraitis and Elena Servienė
Microorganisms 2020, 8(3), 456; https://doi.org/10.3390/microorganisms8030456 - 23 Mar 2020
Cited by 11 | Viewed by 3758 | Correction
Abstract
Sea buckthorn, Hippophae rhamnoides L., has considerable potential for landscape reclamation, food, medicinal, and cosmetics industries. In this study, we analyzed fungal microorganism populations associated with carposphere of sea buckthorn harvested in Lithuania. An amplicon metagenomic approach based on the ITS2 region [...] Read more.
Sea buckthorn, Hippophae rhamnoides L., has considerable potential for landscape reclamation, food, medicinal, and cosmetics industries. In this study, we analyzed fungal microorganism populations associated with carposphere of sea buckthorn harvested in Lithuania. An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to reveal the ripening-affected fungal community alterations on sea buckthorn berries. According to alpha and beta diversity analyses, depending on the ripening stage, sea buckthorn displayed significantly different fungal communities. Unripe berries were shown to be prevalent by Aureobasidium, Taphrina, and Cladosporium, while ripe berries were dominated by Aureobasidium and Metschnikowia. The selected yeast strains from unripe and mature berries were applied for volatile organic compounds identification by gas chromatography and mass spectrometry techniques. It was demonstrated that the patterns of volatiles of four yeast species tested were distinct from each other. The current study for the first time revealed the alterations of fungal microorganism communities colonizing the surface of sea buckthorn berries at different ripening stages. The novel information on specific volatile profiles of cultivable sea buckthorn-associated yeasts with a potential role in biocontrol is important for the development of the strategies for plant cultivation and disease management, as well as for the improvement of the quality and preservation of the postharvest berries. Management of the fungal microorganisms present on the surface of berries might be a powerful instrument for control of phytopathogenic and potentially antagonistic microorganisms affecting development and quality of the berries. Full article
(This article belongs to the Special Issue Applying Metaorganism Studies to the Fruit Microbiome: A New Frontier)
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13 pages, 1680 KiB  
Article
Activity of Cinnamaldehyde on Quorum Sensing and Biofilm Susceptibility to Antibiotics in Pseudomonas aeruginosa
by Sanjida Halim Topa, Enzo A. Palombo, Peter Kingshott and Linda L. Blackall
Microorganisms 2020, 8(3), 455; https://doi.org/10.3390/microorganisms8030455 - 23 Mar 2020
Cited by 38 | Viewed by 4476
Abstract
Quorum sensing (QS) plays an important role during infection for the opportunistic human pathogen Pseudomonas aeruginosa. Quorum sensing inhibition (QSI) can disrupt this initial event of infection without killing bacterial cells, and thus QS inhibitors have been suggested as novel approaches for [...] Read more.
Quorum sensing (QS) plays an important role during infection for the opportunistic human pathogen Pseudomonas aeruginosa. Quorum sensing inhibition (QSI) can disrupt this initial event of infection without killing bacterial cells, and thus QS inhibitors have been suggested as novel approaches for anti-infective therapy. Cinnamaldehyde (CAD) is a P. aeruginosa biofilm inhibitor and disperser of preformed biofilms. In this study, the combined use of CAD and colistin (COL) revealed a synergistic activity, but this was not the case for CAD combined with carbenicillin, tobramycin (TOB), or erythromycin in checkerboard assays for P. aeruginosa. CAD demonstrated QSI activity by repression of the expression of lasB, rhlA and pqsA in GFP reporter assays. Approximately 70% reduction in GFP production was observed with the highest CAD concentration tested in all the QS reporter strains. TOB also showed strong QSI when combined with CAD in reporter assays. Combination treatments revealed an additive activity of CAD with COL and TOB in biofilm inhibition (75.2% and 83.9%, respectively) and preformed biofilm dispersion (~90% for both) when compared to the individual treatments. Therefore, a proposed method to mitigate P. aeruginosa infection is a combination therapy of CAD with COL or CAD with TOB as alternatives to current individual drug therapies. Full article
(This article belongs to the Special Issue Natural Antimicrobial Compounds)
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20 pages, 1796 KiB  
Article
Formate Utilization by the Crenarchaeon Desulfurococcus amylolyticus
by Ipek Ergal, Barbara Reischl, Benedikt Hasibar, Lokeshwaran Manoharan, Aaron Zipperle, Günther Bochmann, Werner Fuchs and Simon K.-M. R. Rittmann
Microorganisms 2020, 8(3), 454; https://doi.org/10.3390/microorganisms8030454 - 23 Mar 2020
Cited by 3 | Viewed by 4629
Abstract
Formate is one of the key compounds of the microbial carbon and/or energy metabolism. It owes a significant contribution to various anaerobic syntrophic associations, and may become one of the energy storage compounds of modern energy biotechnology. Microbial growth on formate was demonstrated [...] Read more.
Formate is one of the key compounds of the microbial carbon and/or energy metabolism. It owes a significant contribution to various anaerobic syntrophic associations, and may become one of the energy storage compounds of modern energy biotechnology. Microbial growth on formate was demonstrated for different bacteria and archaea, but not yet for species of the archaeal phylum Crenarchaeota. Here, we show that Desulfurococcus amylolyticus DSM 16532, an anaerobic and hyperthermophilic Crenarchaeon, metabolises formate without the production of molecular hydrogen. Growth, substrate uptake, and production kinetics on formate, glucose, and glucose/formate mixtures exhibited similar specific growth rates and similar final cell densities. A whole cell conversion experiment on formate revealed that D. amylolyticus converts formate into carbon dioxide, acetate, citrate, and ethanol. Using bioinformatic analysis, we examined whether one of the currently known and postulated formate utilisation pathways could be operative in D. amylolyticus. This analysis indicated the possibility that D. amylolyticus uses formaldehyde producing enzymes for the assimilation of formate. Therefore, we propose that formate might be assimilated into biomass through formaldehyde dehydrogenase and the oxidative pentose phosphate pathway. These findings shed new light on the metabolic versatility of the archaeal phylum Crenarchaeota. Full article
(This article belongs to the Section Environmental Microbiology)
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18 pages, 1688 KiB  
Article
Lipid Production from Sugarcane Top Hydrolysate and Crude Glycerol with Rhodosporidiobolus fluvialis Using a Two-Stage Batch-Cultivation Strategy with Separate Optimization of Each Stage
by Jeerapan Boonyarit, Pirapan Polburee, Bongkot Khaenda, Zongbao K. Zhao and Savitree Limtong
Microorganisms 2020, 8(3), 453; https://doi.org/10.3390/microorganisms8030453 - 23 Mar 2020
Cited by 7 | Viewed by 2581
Abstract
Lipids from oleaginous microorganisms, including oleaginous yeasts, are recognized as feedstock for biodiesel production. A production process development of these organisms is necessary to bring lipid feedstock production up to the industrial scale. This study aimed to enhance lipid production of low-cost substrates, [...] Read more.
Lipids from oleaginous microorganisms, including oleaginous yeasts, are recognized as feedstock for biodiesel production. A production process development of these organisms is necessary to bring lipid feedstock production up to the industrial scale. This study aimed to enhance lipid production of low-cost substrates, namely sugarcane top and biodiesel-derived crude glycerol, by using a two-stage cultivation process with Rhodosporidiobolus fluvialis DMKU-SP314. In the first stage, sugarcane top hydrolysate was used for cell propagation, and in the second stage, cells were suspended in a crude glycerol solution for lipid production. Optimization for high cell mass production in the first stage, and for high lipid production in the second stage, were performed separately using a one-factor-at-a-time methodology together with response surface methodology. Under optimum conditions in the first stage (sugarcane top hydrolysate broth containing; 43.18 g/L total reducing sugars, 2.58 g/L soy bean powder, 0.94 g/L (NH4)2SO4, 0.39 g/L KH2PO4 and 2.5 g/L MgSO4 7H2O, pH 6, 200 rpm, 28 °C and 48 h) and second stage (81.54 g/L crude glycerol, pH 5, 180 rpm, 27 °C and 196 h), a high lipid concentration of 15.85 g/L, a high cell mass of 21.07 g/L and a high lipid content of 73.04% dry cell mass were obtained. Full article
(This article belongs to the Section Microbial Biotechnology)
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11 pages, 1467 KiB  
Review
Bridging the Gap: A Role for Campylobacter jejuni Biofilms
by Greg Tram, Christopher J. Day and Victoria Korolik
Microorganisms 2020, 8(3), 452; https://doi.org/10.3390/microorganisms8030452 - 23 Mar 2020
Cited by 20 | Viewed by 4259
Abstract
Campylobacter jejuni is the leading cause of bacterial gastroenteritis in the developed world. Cases of Campylobacteriosis are common, as the organism is an avian commensal and is passed on to humans through contaminated poultry meat, water, and food preparation areas. Although typically a [...] Read more.
Campylobacter jejuni is the leading cause of bacterial gastroenteritis in the developed world. Cases of Campylobacteriosis are common, as the organism is an avian commensal and is passed on to humans through contaminated poultry meat, water, and food preparation areas. Although typically a fastidious organism, C. jejuni can survive outside the avian intestinal tract until it is able to reach a human host. It has long been considered that biofilms play a key role in transmission of this pathogen. The aim of this review is to examine factors that trigger biofilm formation in C. jejuni. A range of environmental elements have been shown to initiate biofilm formation, which are then affected by a suite of intrinsic factors. We also aim to further investigate the role that biofilms may play in the life cycle of this organism. Full article
(This article belongs to the Special Issue Foodborne Pathogen Campylobacter)
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15 pages, 2942 KiB  
Article
Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans
by Lihua Gao, Zhengfu Zhou, Xiaonan Chen, Wei Zhang, Min Lin and Ming Chen
Microorganisms 2020, 8(3), 451; https://doi.org/10.3390/microorganisms8030451 - 23 Mar 2020
Cited by 16 | Viewed by 4781
Abstract
Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. [...] Read more.
Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans. Full article
(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)
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10 pages, 468 KiB  
Article
Liver Transudate, a Potential Alternative to Detect Anti-Hepatitis E Virus Antibodies in Pigs and Wild Boars (Sus scrofa)
by Alejandro Navarro, Carmen Bárcena, Pilar Pozo, Alberto Díez-Guerrier, Irene Martínez, Coral Polo, Clara Duque, David Rodríguez-Lázaro, Joaquín Goyache and Nerea García
Microorganisms 2020, 8(3), 450; https://doi.org/10.3390/microorganisms8030450 - 23 Mar 2020
Cited by 5 | Viewed by 2562
Abstract
In recent years, cases of hepatitis E virus (HEV) infection have increased in Europe in association with the consumption of contaminated food, mainly from pork products but also from wild boars. The animal’s serum is usually tested for the presence of anti-HEV antibodies [...] Read more.
In recent years, cases of hepatitis E virus (HEV) infection have increased in Europe in association with the consumption of contaminated food, mainly from pork products but also from wild boars. The animal’s serum is usually tested for the presence of anti-HEV antibodies and viral RNA but, in many cases such as during hunting, an adequate serum sample cannot be obtained. In the present study, liver transudate was evaluated as an alternative matrix to serum for HEV detection. A total of 125 sera and liver transudates were tested by enzyme-linked immunosorbent assay at different dilutions (1:2, 1:10, 1:20), while 58 samples of serum and liver transudate were checked for the presence of HEV RNA by RT-qPCR. Anti- HEV antibodies were detected by ELISA in 68.0% of the serum samples, and in 61.6% of the undiluted transudate, and in 70.4%, 56.8%, and 44.8% of 1:2, 1:10, or 1:20 diluted transudate, respectively. The best results were obtained for the liver transudate at 1:10 dilution, based on the Kappa statistic (0.630) and intraclass correlation coefficient (0.841). HEV RNA was detected by RT-qPCR in 22.4% of the serum samples and 6.9% of the transudate samples, all samples used for RT-qPCR were positive by ELISA. Our results indicate that liver transudate may be an alternative matrix to serum for the detection of anti-HEV antibodies. Full article
(This article belongs to the Special Issue Hepatitis E Virus, an Emergent Foodborne Pathogen? Public Health Implications)
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18 pages, 972 KiB  
Review
Citrus Postharvest Green Mold: Recent Advances in Fungal Pathogenicity and Fruit Resistance
by Yulin Cheng, Yunlong Lin, Haohao Cao and Zhengguo Li
Microorganisms 2020, 8(3), 449; https://doi.org/10.3390/microorganisms8030449 - 23 Mar 2020
Cited by 50 | Viewed by 5869
Abstract
As the major postharvest disease of citrus fruit, postharvest green mold is caused by the necrotrophic fungus Penicillium digitatum (Pd), which leads to huge economic losses worldwide. Fungicides are still the main method currently used to control postharvest green mold in [...] Read more.
As the major postharvest disease of citrus fruit, postharvest green mold is caused by the necrotrophic fungus Penicillium digitatum (Pd), which leads to huge economic losses worldwide. Fungicides are still the main method currently used to control postharvest green mold in citrus fruit storage. Investigating molecular mechanisms of plant–pathogen interactions, including pathogenicity and plant resistance, is crucial for developing novel and safer strategies for effectively controlling plant diseases. Despite fruit–pathogen interactions remaining relatively unexplored compared with well-studied leaf–pathogen interactions, progress has occurred in the citrus fruit–Pd interaction in recent years, mainly due to their genome sequencing and establishment or optimization of their genetic transformation systems. Recent advances in Pd pathogenicity on citrus fruit and fruit resistance against Pd infection are summarized in this review. Full article
(This article belongs to the Special Issue Plant Microbial Interactions)
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28 pages, 3630 KiB  
Article
Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum
by Emelia H. Adator, Matthew Walker, Claudia Narvaez-Bravo, Rahat Zaheer, Noriko Goji, Shaun R. Cook, Lisa Tymensen, Sherry J. Hannon, Deirdre Church, Calvin W. Booker, Kingsley Amoako, Celine A. Nadon, Ron Read and Tim A. McAllister
Microorganisms 2020, 8(3), 448; https://doi.org/10.3390/microorganisms8030448 - 22 Mar 2020
Cited by 18 | Viewed by 4621
Abstract
Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase [...] Read more.
Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; blaEC, blaTEM-1, blaSHV, blaOXA, blaCTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32), blaCTX-M-1, blaCTX-M-14, blaOXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while blaTEM-150, blaSHV-11–12, dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Livestock)
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15 pages, 2708 KiB  
Article
Identification and in vitro Characterization of a Novel Phage Endolysin that Targets Gram-Negative Bacteria
by Jaewoo Bai, Sangmi Lee and Sangryeol Ryu
Microorganisms 2020, 8(3), 447; https://doi.org/10.3390/microorganisms8030447 - 21 Mar 2020
Cited by 14 | Viewed by 4120
Abstract
Most double-stranded (ds) DNA phages utilize holin proteins to secrete endolysin for host peptidoglycan lysis. In contrast, several holin-independent endolysins with secretion sequences or signal-arrest-release (SAR) sequences are secreted via the Sec pathway. In this study, we characterized a novel lysis protein (M4Lys) [...] Read more.
Most double-stranded (ds) DNA phages utilize holin proteins to secrete endolysin for host peptidoglycan lysis. In contrast, several holin-independent endolysins with secretion sequences or signal-arrest-release (SAR) sequences are secreted via the Sec pathway. In this study, we characterized a novel lysis protein (M4Lys) encoded by the dsDNA phage BSPM4, whose lysis function is not dependent on either holin or the Sec pathway in vitro. In silico analysis of M4Lys revealed that it contains a putative virion protein domain and an unusual C-terminal transmembrane domain (TMD). Turbidity reduction assays and liquid chromatography-mass spectrometry using purified peptidoglycan showed that the virion protein domain of M4Lys has peptidoglycan lysis activity. In vitro overproduction of M4Lys in Escherichia coli revealed that M4Lys alone caused rapid cell lysis. Treatment of E. coli with a Sec inhibitor did not inhibit the lysis activity of M4Lys, indicating that the Sec pathway is not involved in M4Lys-mediated cell lysis. Truncation of the TMD eliminated the cell lysis phenomenon, while production of the TMD alone did not induce the cell lysis. All these findings demonstrate that M4Lys is a novel endolysin that has a unique mosaic structure distinct from other canonical endolysins and the TMD plays a critical role in M4Lys-mediated in vitro cell lysis. Full article
(This article belongs to the Section Food Microbiology)
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12 pages, 1350 KiB  
Review
Do Foliar Endophytes Matter in Litter Decomposition?
by Emily R. Wolfe and Daniel J. Ballhorn
Microorganisms 2020, 8(3), 446; https://doi.org/10.3390/microorganisms8030446 - 21 Mar 2020
Cited by 27 | Viewed by 4969
Abstract
Litter decomposition rates are affected by a variety of abiotic and biotic factors, including the presence of fungal endophytes in host plant tissues. This review broadly analyzes the findings of 67 studies on the roles of foliar endophytes in litter decomposition, and their [...] Read more.
Litter decomposition rates are affected by a variety of abiotic and biotic factors, including the presence of fungal endophytes in host plant tissues. This review broadly analyzes the findings of 67 studies on the roles of foliar endophytes in litter decomposition, and their effects on decomposition rates. From 29 studies and 1 review, we compiled a comprehensive table of 710 leaf-associated fungal taxa, including the type of tissue these taxa were associated with and isolated from, whether they were reported as endo- or epiphytic, and whether they had reported saprophytic abilities. Aquatic (i.e., in-stream) decomposition studies of endophyte-affected litter were significantly under-represented in the search results (p < 0.0001). Indicator species analyses revealed that different groups of fungal endophytes were significantly associated with cool or tropical climates, as well as specific plant host genera (p < 0.05). Finally, we argue that host plant and endophyte interactions can significantly influence litter decomposition rates and should be considered when interpreting results from both terrestrial and in-stream litter decomposition experiments. Full article
(This article belongs to the Special Issue Fungal Endophytes and Their Interactions with Plants)
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11 pages, 1839 KiB  
Article
Evaluation of Cyprinid Herpesvirus 2 Latency and Reactivation in Carassius gibel
by Wenjun Chai, Lin Qi, Yujun Zhang, Mingming Hong, Ling Jin, Lijuan Li and Junfa Yuan
Microorganisms 2020, 8(3), 445; https://doi.org/10.3390/microorganisms8030445 - 21 Mar 2020
Cited by 13 | Viewed by 2555
Abstract
Cyprinid herpesvirus 2 (CyHV-2, species Cyprinid herpesvirus 2) causes severe mortality in ornamental goldfish, crucian carp (Carassius auratus), and gibel carp (Carassius gibelio). It has been shown that the genomic DNA of CyHV-2 could be detected in subclinical [...] Read more.
Cyprinid herpesvirus 2 (CyHV-2, species Cyprinid herpesvirus 2) causes severe mortality in ornamental goldfish, crucian carp (Carassius auratus), and gibel carp (Carassius gibelio). It has been shown that the genomic DNA of CyHV-2 could be detected in subclinical fish, which implied that CyHV-2 could establish persistent infection. In this study, the latency of CyHV-2 was investigated in the survival fish after primary infection. CyHV-2 genomic DNA was detected in multiple tissues of acute infection samples; however, detection of CyHV-2 DNA was significantly reduced in fish recovered from the primary infection on day 300 postinfection. No active viral gene transcription, such as DNA polymerase and ORF99, was detected in recovered fish. Following temperature stress, an increase of CyHV-2 DNA copy numbers and gene transcription were observed in tissues examined, which suggests that CyHV-2 was reactivated under stress. In addition, a cell line (GCBLat1) derived from the brain tissue from CyHV-2-exposed fish harbored CyHV-2 genome but did not produce infectious virions under normal culture conditions. However, CyHV-2 replication and viral gene transcription occurred when GCBLat1 cells were treated with trichostatin A (TSA) or phorbol 12-myristate 13-acetate (TPA). It suggests CyHV-2 can remain latent in vitro and can reactivate under stress condition. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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12 pages, 1518 KiB  
Article
Prevalence, Antimicrobial Resistance, Virulence Genes and Genetic Diversity of Salmonella Isolated from Retail Duck Meat in Southern China
by Zhengquan Chen, Jie Bai, Shaojun Wang, Xibin Zhang, Zeqiang Zhan, Haiyan Shen, Hongxia Zhang, Junping Wen, Yuan Gao, Ming Liao and Jianmin Zhang
Microorganisms 2020, 8(3), 444; https://doi.org/10.3390/microorganisms8030444 - 21 Mar 2020
Cited by 32 | Viewed by 3393
Abstract
Salmonella is an important cause of foodborne diseases. This study was undertaken to investigate the prevalence, serotype distribution, antimicrobial resistance, virulence genes, and genetic diversity of Salmonella isolates recovered from fresh duck meat obtained from retail markets in Southern China. In total, 365 [...] Read more.
Salmonella is an important cause of foodborne diseases. This study was undertaken to investigate the prevalence, serotype distribution, antimicrobial resistance, virulence genes, and genetic diversity of Salmonella isolates recovered from fresh duck meat obtained from retail markets in Southern China. In total, 365 samples of fresh duck meat were collected from retail markets in six different cities of Guangdong Province between May 2017 and April 2019. High levels of Salmonella contamination were detected in duck meat (151/365, 41.4%). Twenty-six different Salmonella serotypes were identified: S. Corvallis (n = 25, 16.6%), S. Kentucky (n = 22, 14.6%) and S. Agona (n = 20, 13.3%) were the most prevalent serotypes. All isolates were resistant to at least one antibiotic and 133 (88.1%) isolates exhibited multidrug resistance (MDR). Most (86.1%) Salmonella isolates carried seven classes of virulence-associated genes. This study showed the diversity of Salmonella serotypes and genotypes and the high prevalence of MDR isolates carrying multiple virulence-associated genes among isolates from duck meat obtained from retail markets in Southern China. Isolates from different districts had similar pulsed-field gel electrophoresis (PFGE) patterns indicating that circulating foodborne Salmonella constitutes a potential public health issue across different districts. Full article
(This article belongs to the Section Food Microbiology)
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19 pages, 11196 KiB  
Article
Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions
by Manoj Kaushal, Rony Swennen and George Mahuku
Microorganisms 2020, 8(3), 443; https://doi.org/10.3390/microorganisms8030443 - 20 Mar 2020
Cited by 33 | Viewed by 9432
Abstract
We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, [...] Read more.
We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa. Full article
(This article belongs to the Special Issue Plant Microbial Interactions)
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22 pages, 334 KiB  
Article
Potential PGPR Properties of Cellulolytic, Nitrogen-Fixing, Phosphate-Solubilizing Bacteria in Rehabilitated Tropical Forest Soil
by Amelia Tang, Ahmed Osumanu Haruna, Nik Muhamad Ab. Majid and Mohamadu Boyie Jalloh
Microorganisms 2020, 8(3), 442; https://doi.org/10.3390/microorganisms8030442 - 20 Mar 2020
Cited by 52 | Viewed by 7065
Abstract
In the midst of the major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are being established to avoid the further deterioration of forest lands. In this context, cellulolytic, nitrogen-fixing (N-fixing), phosphate-solubilizing bacteria are very important functional groups in regulating the [...] Read more.
In the midst of the major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are being established to avoid the further deterioration of forest lands. In this context, cellulolytic, nitrogen-fixing (N-fixing), phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soils. As is the case for other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and can improve their growth. This study was conducted to isolate, identify, and characterize selected PGP properties of these three functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. The bacteria were isolated based on their colonial growth on respective functional media, identified using both molecular and selected biochemical properties, and were assessed for their functional quantitative activities as well as PGP properties based on seed germination tests and indole-3-acetic acid (IAA) production. Out of the 15 identified bacterial isolates that exhibited beneficial phenotypic traits, a third belong to the genus Burkholderia and a fifth to Stenotrophomonas sp., with both genera consisting of members from two different functional groups. The results of the experiments confirm the multiple PGP traits of some selected bacterial isolates based on their respective high functional activities, root and shoot lengths, and seedling vigor improvements when bacterized on mung bean seeds, as well as significant IAA production. The results of this study suggest that these functional bacterial strains could potentially be included in bio-fertilizer formulations for crop growth on acid soils. Full article
(This article belongs to the Section Environmental Microbiology)
18 pages, 2554 KiB  
Article
Taxonomic Characterization and Secondary Metabolite Analysis of NEAU-wh3-1: An Embleya Strain with Antitumor and Antibacterial Activity
by Han Wang, Tianyu Sun, Wenshuai Song, Xiaowei Guo, Peng Cao, Xi Xu, Yue Shen and Junwei Zhao
Microorganisms 2020, 8(3), 441; https://doi.org/10.3390/microorganisms8030441 - 20 Mar 2020
Cited by 4 | Viewed by 2660
Abstract
Cancer is a serious threat to human health. With the increasing resistance to known drugs, it is still urgent to find new drugs or pro-drugs with anti-tumor effects. Natural products produced by microorganisms have played an important role in the history of drug [...] Read more.
Cancer is a serious threat to human health. With the increasing resistance to known drugs, it is still urgent to find new drugs or pro-drugs with anti-tumor effects. Natural products produced by microorganisms have played an important role in the history of drug discovery, particularly in the anticancer and anti-infective areas. The plant rhizosphere ecosystem is a rich resource for the discovery of actinomycetes with potential applications in pharmaceutical science, especially Streptomyces. We screened Streptomyces-like strains from the rhizosphere soil of wheat (Triticum aestivum L.) in Hebei province, China, and thirty-nine strains were obtained. Among them, the extracts of 14 isolates inhibited the growth of colon tumor cell line HCT-116. Strain NEAU-wh-3-1 exhibited better inhibitory activity, and its active ingredients were further studied. Then, 16S rRNA gene sequence similarity studies showed that strain NEAU-wh3-1 with high sequence similarities to Embleya scabrispora DSM 41855T (99.65%), Embleya hyalina MB891-A1T (99.45%), and Streptomyces lasii 5H-CA11T (98.62%). Moreover, multilocus sequence analysis based on the five other house-keeping genes (atpD, gyrB, rpoB, recA, and trpB) and polyphasic taxonomic approach comprising chemotaxonomic, phylogenetic, morphological, and physiological characterization indicated that the isolate should be assigned to the genus Embleya and was different from its closely related strains, therefore, it is proposed that strain NEAU-wh3-1 may be classified as representatives of a novel species of the genus Embleya. Furthermore, active substances in the fermentation broth of strain NEAU-wh-3-1 were isolated by bioassay-guided analysis and identified by nuclear magnetic resonance (NMR) and mass spectrometry (MS) analyses. Consequently, one new Zincophorin analogue together with seven known compounds was detected. The new compound showed highest antitumor activity against three human cell lines with the 50% inhibition (IC50) values of 8.8–11.6 μg/mL and good antibacterial activity against four pathogenic bacteria, the other known compounds also exhibit certain biological activity. Full article
(This article belongs to the Special Issue Actinobacteria and Myxobacteria—Important Resources for Novel Antibiotics 2.0)
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8 pages, 901 KiB  
Brief Report
Seroprevalence in Bats and Detection of Borrelia burgdorferi in Bat Ectoparasites
by Arinjay Banerjee, Kaushal Baid, Taylor Byron, Alyssa Yip, Caleb Ryan, Prasobh Raveendran Thampy, Hugh Broders, Paul Faure and Karen Mossman
Microorganisms 2020, 8(3), 440; https://doi.org/10.3390/microorganisms8030440 - 20 Mar 2020
Cited by 6 | Viewed by 3899
Abstract
The role of bats in the enzootic cycle of Lyme disease and relapsing fever-causing bacteria is a matter of speculation. In Canada, Borrelia burgdorferi sensu stricto (ss) is the genospecies that is responsible for most cases of Lyme disease in humans. In this [...] Read more.
The role of bats in the enzootic cycle of Lyme disease and relapsing fever-causing bacteria is a matter of speculation. In Canada, Borrelia burgdorferi sensu stricto (ss) is the genospecies that is responsible for most cases of Lyme disease in humans. In this study, we determined if big brown bats, Eptesicus fuscus, have been exposed to spirochetes from the genus Borrelia. We collected serum from 31 bats and tested them for the presence of anti-Borrelia burgdorferi antibodies using a commercial enzyme-linked immunosorbent assay (ELISA). We detected cross-reactive antibodies to Borrelia spp. in 14 of 31 bats. We confirmed the ELISA data using a commercial immunoblot assay. Pooled sera from ELISA-positive bats also cross-reacted with Borrelia antigens coated on the immunoblot strips, whereas pooled sera from ELISA-negative bats did not bind to Borrelia spp. antigens. Furthermore, to identify if bat ectoparasites, such as mites, can carry Borrelia spp., we analyzed DNA from 142 bat ectoparasites that were collected between 2003 and 2019. We detected DNA for the Borrelia burgdorferi flaB gene in one bat mite, Spinturnix americanus. The low detection rate of Borrelia burgdorferi DNA in bat ectoparasites suggests that bats are not reservoirs of this bacterium. Data from this study also raises intriguing questions about Borrelia infections in bats, including the role of humoral immunity and the ability of bats to be infected with Borrelia burgdorferi. This study can lead to more sampling efforts and controlled laboratory studies to identify if bats can be infected with Borrelia burgdorferi and the role of bat ectoparasites, such as S. americanus, in the transmission of this spirochete. Furthermore, we outlined reagents that can be used to adapt ELISA kits and immunoblot strips for use with bat sera. Full article
(This article belongs to the Special Issue Bats in Infectiology Research—Novel Tools and New Findings)
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15 pages, 571 KiB  
Article
Lactobacillus paracasei A13 and High-Pressure Homogenization Stress Response
by Lorenzo Siroli, Giacomo Braschi, Samantha Rossi, Davide Gottardi, Francesca Patrignani and Rosalba Lanciotti
Microorganisms 2020, 8(3), 439; https://doi.org/10.3390/microorganisms8030439 - 20 Mar 2020
Cited by 18 | Viewed by 2801
Abstract
Sub-lethal high-pressure homogenization treatments applied to Lactobacillus paracasei A13 demonstrated to be a useful strategy to enhance technological and functional properties without detrimental effects on the viability of this strain. Modification of membrane fatty acid composition is reported to be the main regulatory [...] Read more.
Sub-lethal high-pressure homogenization treatments applied to Lactobacillus paracasei A13 demonstrated to be a useful strategy to enhance technological and functional properties without detrimental effects on the viability of this strain. Modification of membrane fatty acid composition is reported to be the main regulatory mechanisms adopted by probiotic lactobacilli to counteract high-pressure stress. This work is aimed to clarify and understand the relationship between the modification of membrane fatty acid composition and the expression of genes involved in fatty acid biosynthesis in Lactobacillus paracasei A13, before and after the application of different sub-lethal hyperbaric treatments. Our results showed that Lactobacillus paracasei A13 activated a series of reactions aimed to control and stabilize membrane fluidity in response to high-pressure homogenization treatments. In fact, the production of cyclic fatty acids was counterbalanced by the unsaturation and elongation of fatty acids. The gene expression data indicate an up-regulation of the genes accA, accC, fabD, fabH and fabZ after high-pressure homogenization treatment at 150 and 200 MPa, and of fabK and fabZ after a treatment at 200 MPa suggesting this regulation of the genes involved in fatty acids biosynthesis as an immediate response mechanism adopted by Lactobacillus paracasei A13 to high-pressure homogenization treatments to balance the membrane fluidity. Although further studies should be performed to clarify the modulation of phospholipids and glycoproteins biosynthesis since they play a crucial role in the functional properties of the probiotic strains, this study represents an important step towards understanding the response mechanisms of Lactobacillus paracasei A13 to sub-lethal high-pressure homogenization treatments. Full article
(This article belongs to the Section Food Microbiology)
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19 pages, 2685 KiB  
Article
The Interplay between Mucosal Microbiota Composition and Host Gene-Expression is Linked with Infliximab Response in Inflammatory Bowel Diseases
by Nikolas Dovrolis, George Michalopoulos, George E. Theodoropoulos, Kostantinos Arvanitidis, George Kolios, Leonardo A. Sechi, Aristidis G. Eliopoulos and Maria Gazouli
Microorganisms 2020, 8(3), 438; https://doi.org/10.3390/microorganisms8030438 - 20 Mar 2020
Cited by 45 | Viewed by 3878
Abstract
Even though anti-TNF therapy significantly improves the rates of remission in inflammatory bowel disease (IBD) patients, there is a noticeable subgroup of patients who do not respond to treatment. Dysbiosis emerges as a key factor in IBD pathogenesis. The aim of the present [...] Read more.
Even though anti-TNF therapy significantly improves the rates of remission in inflammatory bowel disease (IBD) patients, there is a noticeable subgroup of patients who do not respond to treatment. Dysbiosis emerges as a key factor in IBD pathogenesis. The aim of the present study is to profile changes in the gut microbiome and transcriptome before and after administration of the anti-TNF agent Infliximab (IFX) and investigate their potential to predict patient response to IFX at baseline. Mucosal biopsy samples from 20 IBD patients and nine healthy controls (HC) were examined for differences in microbiota composition (16S rRNA gene sequencing) and mucosal gene expression (RT-qPCR) at baseline and upon completion of IFX treatment, accordingly, via an in silico pipeline. Significant differences in microbiota composition were found between the IBD and HC groups. Several bacterial genera, which were found only in IBD patients and not HC, had their populations dramatically reduced after anti-TNF treatment regardless of response. Alpha and beta diversity metrics showed significant differences between our study groups. Correlation analysis revealed six microbial genera associated with differential expression of inflammation-associated genes in IFX treatment responders at baseline. This study shows that IFX treatment has a notable impact on both the gut microbial composition and the inflamed tissue transcriptome in IBD patients. Importantly, our results identify enterotypes that correlate with transcriptome changes and help differentiate IFX responders versus non-responders at baseline, suggesting that, in combination, these signatures can be an effective tool to predict anti-TNF response. Full article
(This article belongs to the Special Issue Mycobacteria Infections and Autoimmune Diseases)
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19 pages, 4737 KiB  
Article
Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b
by Sanzhar Naizabekov and Eun Yeol Lee
Microorganisms 2020, 8(3), 437; https://doi.org/10.3390/microorganisms8030437 - 20 Mar 2020
Cited by 19 | Viewed by 5093
Abstract
Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) [...] Read more.
Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) for methane oxidation. While the source of electrons is known for sMMO, there is less consensus regarding electron donor to pMMO. To investigate this and other questions regarding methane metabolism, the genome-scale metabolic model for M. trichosporium OB3b (model ID: iMsOB3b) was reconstructed. The model accurately predicted oxygen: methane molar uptake ratios and specific growth rates on nitrate-supplemented medium with methane as carbon and energy source. The redox-arm mechanism which links methane oxidation with complex I of electron transport chain has been found to be the most optimal mode of electron transfer. The model was also qualitatively validated on ammonium-supplemented medium indicating its potential to accurately predict methane metabolism in different environmental conditions. Finally, in silico investigations regarding flux distribution in central carbon metabolism of M. trichosporium OB3b were performed. Overall, iMsOB3b can be used as an organism-specific knowledgebase and a platform for hypothesis-driven theoretical investigations of methane metabolism. Full article
(This article belongs to the Special Issue Genome-Scale Modeling of Microorganisms in the Real World)
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14 pages, 2568 KiB  
Article
Application of an O-Linked Glycosylation System in Yersinia enterocolitica Serotype O:9 to Generate a New Candidate Vaccine against Brucella abortus
by Jing Huang, Chao Pan, Peng Sun, Erling Feng, Jun Wu, Li Zhu and Hengliang Wang
Microorganisms 2020, 8(3), 436; https://doi.org/10.3390/microorganisms8030436 - 20 Mar 2020
Cited by 16 | Viewed by 2767
Abstract
Brucellosis is a major zoonotic public health threat worldwide, causing veterinary morbidity and major economic losses in endemic regions. However, no efficacious brucellosis vaccine is yet available, and live attenuated vaccines commonly used in animals can cause human infection. N- and O [...] Read more.
Brucellosis is a major zoonotic public health threat worldwide, causing veterinary morbidity and major economic losses in endemic regions. However, no efficacious brucellosis vaccine is yet available, and live attenuated vaccines commonly used in animals can cause human infection. N- and O-linked glycosylation systems have been successfully developed and exploited for the production of successful bioconjugate vaccines. Here, we applied an O-linked glycosylation system to a low-pathogenicity bacterium, Yersinia enterocolitica serotype O:9 (Y. enterocolitica O:9), which has repeating units of O-antigen polysaccharide (OPS) identical to that of Brucella abortus (B. abortus), to develop a bioconjugate vaccine against Brucella. The glycoprotein we produced was recognized by both anti-B. abortus and anti-Y. enterocolitica O:9 monoclonal antibodies. Three doses of bioconjugate vaccine-elicited B. abortus OPS-specific serum IgG in mice, significantly reducing bacterial loads in the spleen following infection with the B. abortus hypovirulent smooth strain A19. This candidate vaccine mitigated B. abortus infection and prevented severe tissue damage, thereby protecting against lethal challenge with A19. Overall, the results indicated that the bioconjugate vaccine elicited a strong immune response and provided significant protection against brucellosis. The described vaccine preparation strategy is safe and avoids large-scale culture of the highly pathogenic B. abortus. Full article
(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems)
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10 pages, 1687 KiB  
Communication
OXA-48 Carbapenemase in Klebsiella pneumoniae Sequence Type 307 in Ecuador
by José E. Villacís, Jorge A. Reyes, Hugo G. Castelán-Sánchez, Sonia Dávila-Ramos, Miguel Angel Lazo, Ahmad Wali, Luis A. Bodero, Yadira Toapanta, Cristina Naranjo, Lorena Montero, Josefina Campos, Marcelo G. Galas and Mónica C. Gestal
Microorganisms 2020, 8(3), 435; https://doi.org/10.3390/microorganisms8030435 - 19 Mar 2020
Cited by 6 | Viewed by 4055
Abstract
Antibiotic resistance is on the rise, leading to an increase in morbidity and mortality due to infectious diseases. Klebsiella pneumoniae is a Gram-negative bacterium that causes bronchopneumonia, abscesses, urinary tract infection, osteomyelitis, and a wide variety of infections. The ubiquity of this microorganism [...] Read more.
Antibiotic resistance is on the rise, leading to an increase in morbidity and mortality due to infectious diseases. Klebsiella pneumoniae is a Gram-negative bacterium that causes bronchopneumonia, abscesses, urinary tract infection, osteomyelitis, and a wide variety of infections. The ubiquity of this microorganism confounds with the great increase in antibiotic resistance and have bred great concern worldwide. K. pneumoniae sequence type (ST) 307 is a widespread emerging clone associated with hospital-acquired infections, although sporadic community infections have also been reported. The aim of our study is to describe the first case of Klebsiella pneumoniae (ST) 307 harboring the blaOXA-48-like gene in Ecuador. We characterized a new plasmid that carry OXA-48 and could be the source of future outbreaks. The strain was recovered from a patient with cancer previously admitted in a Ukrainian hospital, suggesting that this mechanism of resistance could be imported. These findings highlight the importance of programs based on active molecular surveillance for the intercontinental spread of multidrug-resistant microorganisms with emergent carbapenemases. Full article
(This article belongs to the Special Issue Infectious Diseases, New Approaches to Old Problems)
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40 pages, 1853 KiB  
Review
An Overview of Potential Oleaginous Microorganisms and Their Role in Biodiesel and Omega-3 Fatty Acid-Based Industries
by Alok Patel, Dimitra Karageorgou, Emma Rova, Petros Katapodis, Ulrika Rova, Paul Christakopoulos and Leonidas Matsakas
Microorganisms 2020, 8(3), 434; https://doi.org/10.3390/microorganisms8030434 - 19 Mar 2020
Cited by 145 | Viewed by 12961
Abstract
Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from [...] Read more.
Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from short hydrocarbonated chain (C6) to long hydrocarbonated chain (C36), which may be saturated (SFA), monounsaturated (MUFA), or polyunsaturated fatty acids (PUFA), depending on the presence and number of double bonds in hydrocarbonated chains. Depending on the fatty acid profile, the oils obtained from oleaginous microorganisms are utilized as feedstock for either biodiesel production or as nutraceuticals. Mainly microalgae, bacteria, and yeasts are involved in the production of biodiesel, whereas thraustochytrids, fungi, and some of the microalgae are well known to be producers of very long-chain PUFA (omega-3 fatty acids). In this review article, the type of oleaginous microorganisms and their expertise in the field of biodiesel or omega-3 fatty acids, advances in metabolic engineering tools for enhanced lipid accumulation, upstream and downstream processing of lipids, including purification of biodiesel and concentration of omega-3 fatty acids are reviewed. Full article
(This article belongs to the Special Issue Yeast and Fungal Metabolites)
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22 pages, 7207 KiB  
Article
Molecular Ecological Network Complexity Drives Stand Resilience of Soil Bacteria to Mining Disturbances among Typical Damaged Ecosystems in China
by Jing Ma, Yongqiang Lu, Fu Chen, Xiaoxiao Li, Dong Xiao and Hui Wang
Microorganisms 2020, 8(3), 433; https://doi.org/10.3390/microorganisms8030433 - 19 Mar 2020
Cited by 12 | Viewed by 3413
Abstract
Understanding the interactions of soil microbial species and how they responded to disturbances are essential to ecological restoration and resilience in the semihumid and semiarid damaged mining areas. Information on this, however, remains unobvious and deficiently comprehended. In this study, based on the [...] Read more.
Understanding the interactions of soil microbial species and how they responded to disturbances are essential to ecological restoration and resilience in the semihumid and semiarid damaged mining areas. Information on this, however, remains unobvious and deficiently comprehended. In this study, based on the high throughput sequence and molecular ecology network analysis, we have investigated the bacterial distribution in disturbed mining areas across three provinces in China, and constructed molecular ecological networks to reveal the interactions of soil bacterial communities in diverse locations. Bacterial community diversity and composition were classified measurably between semihumid and semiarid damaged mining sites. Additionally, we distinguished key microbial populations across these mining areas, which belonged to Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Moreover, the network modules were significantly associated with some environmental factors (e.g., annual average temperature, electrical conductivity value, and available phosphorus value). The study showed that network interactions were completely different across the different mining areas. The keystone species in different mining areas suggested that selected microbial communities, through natural successional processes, were able to resist the corresponding environment. Moreover, the results of trait-based module significances showed that several environmental factors were significantly correlated with some keystone species, such as OTU_8126 (Acidobacteria), OTU_8175 (Burkholderiales), and OTU_129 (Chloroflexi). Our study also implied that the complex network of microbial interaction might drive the stand resilience of soil bacteria in the semihumid and semiarid disturbed mining areas. Full article
(This article belongs to the Section Environmental Microbiology)
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14 pages, 2120 KiB  
Article
Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo
by Ann-Kathrin Kniggendorf, Regina Nogueira, Somayeh Nasiri Bahmanabad, Andreas Pommerening-Röser and Bernhard Wilhelm Roth
Microorganisms 2020, 8(3), 432; https://doi.org/10.3390/microorganisms8030432 - 19 Mar 2020
Cited by 8 | Viewed by 2487
Abstract
The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth [...] Read more.
The stress response of ammonia-oxidizing bacteria (AOB) to oxygen deprivation limits AOB growth and leads to different nitrification pathways that cause the release of greenhouse gases. Measuring the stress response of AOB has proven to be a challenge due to the low growth rates of stressed AOB, making the sample volumes required to monitor the internal stress response of AOB prohibitive to repeated analysis. In a proof-of-concept study, confocal Raman microscopy with excitation resonant to the heme c moiety of cytochrome c was used to compare the cytochrome c content and activity of stressed and unstressed Nitrosomonas europaea (Nm 50), Nitrosomonas eutropha (Nm 57), Nitrosospira briensis (Nsp 10), and Nitrosospira sp. (Nsp 02) in vivo. Each analysis required no more than 1000 individual cells per sampling; thus, the monitoring of cultures with low cell concentrations was possible. The identified spectral marker delivered reproducible results within the signal-to-noise ratio of the underlying Raman spectra. Cytochrome c content was found to be elevated in oxygen-deprived and previously oxygen-deprived samples. In addition, cells with predominantly ferrous cytochrome c content were found in deprived Nitrosomonas eutropha and Nitrosospira samples, which may be indicative of ongoing electron storage at the time of measurement. Full article
(This article belongs to the Special Issue Ecology, Diversity and Functions of Ammonia-Oxidizing Bacteria)
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