Microorganisms

14 pages, 1952 KiB

Open AccessArticle

Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes

by Igor B. Rogozin, Andreu Saura, Anastassia Bykova, Vyacheslav Brover and Vyacheslav Yurchenko

Microorganisms 2023, 11(1), 229; https://doi.org/10.3390/microorganisms11010229 - 16 Jan 2023

Cited by 5 | Viewed by 2847

Abstract

The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of [...] Read more.

The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a “sequence space” of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes. Full article

(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)

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14 pages, 2280 KiB

Open AccessArticle

Comparative Proteomics and Genome-Wide Druggability Analyses Prioritized Promising Therapeutic Targets against Drug-Resistant Leishmania tropica

by Sara Aiman, A. Khuzaim Alzahrani, Fawad Ali, Abida, Mohd. Imran, Mehnaz Kamal, Muhammad Usman, Hamdy Khamees Thabet, Chunhua Li and Asifullah Khan

Microorganisms 2023, 11(1), 228; https://doi.org/10.3390/microorganisms11010228 - 16 Jan 2023

Cited by 4 | Viewed by 3036

Abstract

Leishmania tropica is a tropical parasite causing cutaneous leishmaniasis (CL) in humans. Leishmaniasis is a serious public health threat, affecting an estimated 350 million people in 98 countries. The global rise in antileishmanial drug resistance has triggered the need to explore novel therapeutic [...] Read more.

Leishmania tropica is a tropical parasite causing cutaneous leishmaniasis (CL) in humans. Leishmaniasis is a serious public health threat, affecting an estimated 350 million people in 98 countries. The global rise in antileishmanial drug resistance has triggered the need to explore novel therapeutic strategies against this parasite. In the present study, we utilized the recently available multidrug resistant L. tropica strain proteome data repository to identify alternative therapeutic drug targets based on comparative subtractive proteomic and druggability analyses. Additionally, small drug-like compounds were scanned against novel targets based on virtual screening and ADME profiling. The analysis unveiled 496 essential cellular proteins of L. tropica that were nonhomologous to the human proteome set. The druggability analyses prioritized nine parasite-specific druggable proteins essential for the parasite’s basic cellular survival, growth, and virulence. These prioritized proteins were identified to have appropriate binding pockets to anchor small drug-like compounds. Among these, UDPase and PCNA were prioritized as the top-ranked druggable proteins. The pharmacophore-based virtual screening and ADME profiling predicted MolPort-000-730-162 and MolPort-020-232-354 as the top hit drug-like compounds from the Pharmit resource to inhibit L. tropica UDPase and PCNA, respectively. The alternative drug targets and drug-like molecules predicted in the current study lay the groundwork for developing novel antileishmanial therapies. Full article

(This article belongs to the Special Issue Leishmaniasis: Interventions Used to Control Infection)

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39 pages, 366 KiB

Open AccessEditorial

Acknowledgment to the Reviewers of Microorganisms in 2022

by Microorganisms Editorial Office

Microorganisms 2023, 11(1), 227; https://doi.org/10.3390/microorganisms11010227 - 16 Jan 2023

Viewed by 3034

Abstract

High-quality academic publishing is built on rigorous peer review [...] Full article

13 pages, 1704 KiB

Open AccessArticle

Colletotrichum truncatum Causing Anthracnose of Tomato (Solanum lycopersicum L.) in Malaysia

by Saleh Ahmed Shahriar, Asmaul Husna, Terna Tersoo Paul, Most. Nurjahan Khatun Eaty, Md Quamruzzaman, Abu Bakar Siddique, Md Abdur Rahim, Abu Noman Faruq Ahmmed, Jasim Uddain and Shafiquzzaman Siddiquee

Microorganisms 2023, 11(1), 226; https://doi.org/10.3390/microorganisms11010226 - 16 Jan 2023

Cited by 9 | Viewed by 5621

Abstract

Tomato (Solanum lycopersicum L.) is a popular nutritious vegetable crop grown in Malaysia and other parts of the world. However, fungal diseases such as anthracnose pose significant threats to tomato production by reducing the fruit quality and food value of tomato, resulting [...] Read more.

Tomato (Solanum lycopersicum L.) is a popular nutritious vegetable crop grown in Malaysia and other parts of the world. However, fungal diseases such as anthracnose pose significant threats to tomato production by reducing the fruit quality and food value of tomato, resulting in lower market prices of the crop globally. In the present study, the etiology of tomato anthracnose was investigated in commercial tomato farms in Sabah, Malaysia. A total of 22 fungal isolates were obtained from anthracnosed tomato fruits and identified as Colletotrichum species, using morphological characteristics. The phylogenetic relationships of multiple gene sequence alignments such as internal transcribed spacer (ITS), β-tubulin (tub2), glyceraldehyde 3-phosphate dehydrogenase (gapdh), actin (act), and calmodulin (cal), were adopted to accurately identify the Colletotrichum species as C. truncatum. The results of pathogenicity tests revealed that all C. truncatum isolates caused anthracnose disease symptoms on inoculated tomato fruits. To our knowledge, the present study is the first report of tomato anthracnose caused by C. truncatum in Malaysia. The findings of this study will be helpful in disease monitoring, and the development of strategies for effective control of anthracnose on tomato fruits. Full article

(This article belongs to the Special Issue Molecular Interactions between Plant Pathogens and Crops)

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23 pages, 3282 KiB

Open AccessArticle

Flavonoid Derivatives as New Potent Inhibitors of Cysteine Proteases: An Important Step toward the Design of New Compounds for the Treatment of Leishmaniasis

by Estela Mariana Guimarães Lourenço, Juliana Fortes Di Iório, Fernanda da Silva, Felipe Leonardo Bley Fialho, Melquisedeque Mateus Monteiro, Adilson Beatriz, Renata Trentin Perdomo, Euzébio Guimarães Barbosa, Jean Pierre Oses, Carla Cardozo Pinto de Arruda, Wagner Alves de Souza Júdice, Jamal Rafique and Dênis Pires de Lima

Microorganisms 2023, 11(1), 225; https://doi.org/10.3390/microorganisms11010225 - 16 Jan 2023

Cited by 3 | Viewed by 3229

Abstract

Leishmaniasis is a neglected tropical disease, affecting more than 350 million people globally. However, there is currently no vaccine available against human leishmaniasis, and current treatment is hampered by high cost, side-effects, and painful administration routes. It has become a United Nations goal [...] Read more.

Leishmaniasis is a neglected tropical disease, affecting more than 350 million people globally. However, there is currently no vaccine available against human leishmaniasis, and current treatment is hampered by high cost, side-effects, and painful administration routes. It has become a United Nations goal to end leishmaniasis epidemics by 2030, and multitarget drug strategy emerges as a promising alternative. Among the multitarget compounds, flavonoids are a renowned class of natural products, and a structurally diverse library can be prepared through organic synthesis, which can be tested for biological effectiveness. In this study, we synthesised 17 flavonoid analogues using a scalable, easy-to-reproduce, and inexpensive method. All synthesised compounds presented an impressive inhibition capacity against rCPB2.8, rCPB3, and rH84Y enzymes, which are highly expressed in the amastigote stage, the target form of the parasite. Compounds 3c, f12a, and f12b were found to be effective against all isoforms. Furthermore, their intermolecular interactions were also investigated through a molecular modelling study. These compounds were highly potent against the parasite and demonstrated low cytotoxic action against mammalian cells. These results are pioneering, representing an advance in the investigation of the mechanisms behind the antileishmanial action of flavonoid derivatives. Moreover, compounds have been shown to be promising leads for the design of other cysteine protease inhibitors for the treatment of leishmaniasis diseases. Full article

(This article belongs to the Special Issue Epidemiology of Vector Born Diseases 2.0)

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22 pages, 4134 KiB

Open AccessReview

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

by Magdalena Ptaszek, Loredana Canfora, Massimo Pugliese, Flavia Pinzari, Giovanna Gilardi, Paweł Trzciński and Eligio Malusà

Microorganisms 2023, 11(1), 224; https://doi.org/10.3390/microorganisms11010224 - 16 Jan 2023

Cited by 9 | Viewed by 4362

Abstract

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have [...] Read more.

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers’ point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing. Full article

(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)

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11 pages, 1432 KiB

Open AccessArticle

Low Interferon-γ Levels in Cord and Peripheral Blood of Pregnant Women Infected with SARS-CoV-2

by Michele Cennamo, Evelina La Civita, Laura Sarno, Gianluigi Carbone, Sarah Di Somma, Serena Cabaro, Jacopo Troisi, Angelo Sirico, Francesco Paolo Improda, Maurizio Guida, Daniela Terracciano and Giuseppe Portella

Microorganisms 2023, 11(1), 223; https://doi.org/10.3390/microorganisms11010223 - 16 Jan 2023

Cited by 5 | Viewed by 2662

Abstract

COVID-19 is characterized by the immune system’s overreaction resulting in a ‘cytokine storm’, consisting in a massive release of cytokine into the bloodstream, leading to local and systemic inflammatory response. This clinical picture is further complicated in case of infection of patients with [...] Read more.

COVID-19 is characterized by the immune system’s overreaction resulting in a ‘cytokine storm’, consisting in a massive release of cytokine into the bloodstream, leading to local and systemic inflammatory response. This clinical picture is further complicated in case of infection of patients with a peculiar immunological status, such as pregnancy. In this paper, we focused on Interferon-γ, which plays a pivotal immunomodulatory role in normal pregnancy and fetal development, as well as in defense against pathogens. In this study, we compared the levels of Interferon-γ and the Interferon autoantibodies of the peripheral and cord blood of pregnant women with confirmed mild COVID-19 and healthy pregnant women. The Interferon-γ was significantly lower both in the peripheral and cord blood of SARS-CoV-2-positive mothers, suggesting that infection can affect the fetal microenvironment even without severe maternal symptoms. In conclusion, further studies are needed to clarify whether lower levels of Interferon-γ due to SARS-CoV-2 infection affect the development or infection susceptibility of infants born to SARS-CoV-2-infected mothers. Full article

(This article belongs to the Special Issue SARS-CoV-2 Systemic Effects: New Clues)

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25 pages, 3773 KiB

Open AccessArticle

Interesting Halophilic Sulphur-Oxidising Bacteria with Bioleaching Potential: Implications for Pollutant Mobilisation from Mine Waste

by Chiamaka Belsonia Opara, Nor Kamariah, Jeroen Spooren, Katrin Pollmann and Sabine Kutschke

Microorganisms 2023, 11(1), 222; https://doi.org/10.3390/microorganisms11010222 - 15 Jan 2023

Cited by 6 | Viewed by 2485

Abstract

For many years, research on the microbial-dissolution of metals from ores or waste materials mainly focussed on the study of acidophilic organisms. However, most acidophilic bioleaching microorganisms have limited tolerance to high chloride concentrations, thereby requiring fresh water for bioleaching operations. There is [...] Read more.

For many years, research on the microbial-dissolution of metals from ores or waste materials mainly focussed on the study of acidophilic organisms. However, most acidophilic bioleaching microorganisms have limited tolerance to high chloride concentrations, thereby requiring fresh water for bioleaching operations. There is a growing interest in the use of seawater for leaching purposes, especially in regions with less access to fresh water. Consequently, there is a need to find halophilic organisms with bioleaching potentials. This study investigated the bioleaching potentials of four moderately halophilic sulphur-oxidising bacteria: Thiomicrospira cyclica, Thiohalobacter thiocyanaticus, Thioclava electrotropha and Thioclava pacifica. Results revealed T. electrotropha and T. pacifica as the most promising for bioleaching. Pure cultures of the two Thioclava strains liberated about 30% Co, and between 8–17% Cu, Pb, Zn, K, Cd, and Mn from a mine waste rock sample from the Neves Corvo mine, Portugal. Microwave roasting of the waste rock at 400 and 500 °C improved the bioleaching efficiency of T. electrotropha for Pb (13.7 to 45.7%), Ag (5.3 to 36%) and In (0 to 27.4%). Mineralogical analysis of the bioleached residues using SEM/MLA-GXMAP showed no major difference in the mineral compositions before or after bioleaching by the Thioclava spp. Generally, the bioleaching rates of the Thioclava spp. are quite low compared to that of the conventional acidophilic bioleaching bacteria. Nevertheless, their ability to liberate potential pollutants (metal(loid)s) into solution from mine waste raises environmental concerns. This is due to their relevance in the biogeochemistry of mine waste dumps, as similar neutrophile halophilic sulphur-oxidising organisms (e.g., Halothiobacillus spp.) have been isolated from mine wastes. On the other hand, the use of competent halophilic microorganisms could be the future of bioleaching due to their high tolerance to Cl^- ions and their potential to catalyse mineral dissolution in seawater media, instead of fresh water. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 655 KiB

Open AccessReview

HIV and Drug-Resistant Subtypes

by Bianca Maria Nastri, Pasquale Pagliano, Carla Zannella, Veronica Folliero, Alfonso Masullo, Luca Rinaldi, Massimiliano Galdiero and Gianluigi Franci

Microorganisms 2023, 11(1), 221; https://doi.org/10.3390/microorganisms11010221 - 15 Jan 2023

Cited by 23 | Viewed by 4614

Abstract

Acquired Immunodeficiency Syndrome (AIDS) is a human viral infectious disease caused by the positive-sense single-stranded (ss) RNA Human Immunodeficiency Virus (HIV) (Retroviridae family, Ortervirales order). HIV-1 can be distinguished into various worldwide spread groups and subtypes. HIV-2 also causes human immunodeficiency, which develops [...] Read more.

Acquired Immunodeficiency Syndrome (AIDS) is a human viral infectious disease caused by the positive-sense single-stranded (ss) RNA Human Immunodeficiency Virus (HIV) (Retroviridae family, Ortervirales order). HIV-1 can be distinguished into various worldwide spread groups and subtypes. HIV-2 also causes human immunodeficiency, which develops slowly and tends to be less aggressive. HIV-2 only partially homologates to HIV-1 despite the similar derivation. Antiretroviral therapy (ART) is the treatment approved to control HIV infection, based on multiple antiretroviral drugs that belong to different classes: (i) NNRTIs, (ii) NRTIs, (iii) PIs, (iv) INSTIs, and (v) entry inhibitors. These drugs, acting on different stages of the HIV life cycle, decrease the patient’s total burden of HIV, maintain the function of the immune system, and prevent opportunistic infections. The appearance of several strains resistant to these drugs, however, represents a problem today that needs to be addressed as best as we can. New outbreaks of strains show a widespread geographic distribution and a highly variable mortality rate, even affecting treated patients significantly. Therefore, novel treatment approaches should be explored. The present review discusses updated information on HIV-1– and HIV-2–resistant strains, including details on different mutations responsible for drug resistance. Full article

(This article belongs to the Section Virology)

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17 pages, 2374 KiB

Open AccessArticle

Biodegradation of Iprodione and Chlorpyrifos Using an Immobilized Bacterial Consortium in a Packed-Bed Bioreactor

by Marcela Levío-Raimán, Cristian Bornhardt and M. Cristina Diez

Microorganisms 2023, 11(1), 220; https://doi.org/10.3390/microorganisms11010220 - 15 Jan 2023

Cited by 6 | Viewed by 2155

Abstract

This work provides the basis for implementing a continuous treatment system using a bacterial consortium for wastewater containing a pesticide mixture of iprodione (IPR) and chlorpyrifos (CHL). Two bacterial strains (Achromobacter spanius C1 and Pseudomonas rhodesiae C4) isolated from the biomixture of [...] Read more.

This work provides the basis for implementing a continuous treatment system using a bacterial consortium for wastewater containing a pesticide mixture of iprodione (IPR) and chlorpyrifos (CHL). Two bacterial strains (Achromobacter spanius C1 and Pseudomonas rhodesiae C4) isolated from the biomixture of a biopurification system were able to efficiently remove pesticides IPR and CHL at different concentrations (10 to 100 mg L⁻¹) from the liquid medium as individual strains and free consortium. The half-life time (T_1/2) for IPR and CHL was determined for individual strains and a free bacterial consortium. However, when the free bacterial consortium was used, a lower T_1/2 was obtained, especially for CHL. Based on these results, an immobilized bacterial consortium was formulated with each bacterial strain encapsulated individually in alginate beads. Then, different inoculum concentrations (5, 10, and 15% w/v) of the immobilized consortium were evaluated in batch experiments for IPR and CHL removal. The inoculum concentration of 15% w/v demonstrated the highest pesticide removal. Using this inoculum concentration, the packed-bed bioreactor with an immobilized bacterial consortium was operated in continuous mode at different flow rates (30, 60, and 90 mL h⁻¹) at a pesticide concentration of 50 mg L⁻¹ each. The performance in the bioreactor demonstrated that it is possible to efficiently remove a pesticide mixture of IPR and CHL in a continuous system. The metabolites 3,5-dichloroaniline (3,5-DCA) and 3,5,6-trichloro-2-pyridinol (TCP) were produced, and a slight accumulation of TCP was observed. The bioreactor was influenced by TCP accumulation but was able to recover performance quickly. Finally, after 60 days of operation, the removal efficiency was 96% for IPR and 82% for CHL. The findings of this study demonstrate that it is possible to remove IPR and CHL from pesticide-containing wastewater in a continuous system. Full article

(This article belongs to the Special Issue Microbial Biodegradation of Toxic Pollutants)

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22 pages, 3898 KiB

Open AccessArticle

Microbial Dynamics of a Specialty Italian Raw Ewe’s Milk Cheese Curdled with Extracts from Spontaneous and Cultivated Onopordum tauricum Willd

by Giorgia Rampanti, Luca Belleggia, Federica Cardinali, Vesna Milanović, Andrea Osimani, Cristiana Garofalo, Ilario Ferrocino and Lucia Aquilanti

Microorganisms 2023, 11(1), 219; https://doi.org/10.3390/microorganisms11010219 - 15 Jan 2023

Cited by 7 | Viewed by 2253

Abstract

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe’s milk cheese produced in [...] Read more.

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe’s milk cheese produced in a family run dairy farm located in the Marche region (Central Italy). The microbiota of the three thistle-based milk coagulants and their effect on the microbial dynamics of raw milk cheeses during fermentation and maturation (from day 0 up until day 60) were investigated through a combined approach based on viable counting and Illumina DNA sequencing. In both the control and experimental cheeses, despite the slight differences emerged depending on the coagulant used, Lactococcus lactis and Debaryomyces hansenii were the prevalent species among bacteria and fungi, respectively. Moreover, raw ewe’s milk was the main factor affecting the evolution of both the bacterial and fungal microbiota in all cheeses. The overall similarities between control and experimental cheeses herein analyzed supports the exploitation of Onopordum tauricum Willd. as an alternative milk coagulating agent for production of Caciofiore and, more in general, raw ewe’s milk cheeses. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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15 pages, 1061 KiB

Open AccessReview

TORC1 Signaling in Fungi: From Yeasts to Filamentous Fungi

by Yuhua Wang, Xi Zheng, Guohong Li and Xin Wang

Microorganisms 2023, 11(1), 218; https://doi.org/10.3390/microorganisms11010218 - 15 Jan 2023

Cited by 8 | Viewed by 4020

Abstract

Target of rapamycin complex 1 (TORC1) is an important regulator of various signaling pathways. It can control cell growth and development by integrating multiple signals from amino acids, glucose, phosphate, growth factors, pressure, oxidation, and so on. In recent years, it has been [...] Read more.

Target of rapamycin complex 1 (TORC1) is an important regulator of various signaling pathways. It can control cell growth and development by integrating multiple signals from amino acids, glucose, phosphate, growth factors, pressure, oxidation, and so on. In recent years, it has been reported that TORC1 is of great significance in regulating cytotoxicity, morphology, protein synthesis and degradation, nutrient absorption, and metabolism. In this review, we mainly discuss the upstream and downstream signaling pathways of TORC1 to reveal its role in fungi. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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11 pages, 3129 KiB

Open AccessArticle

Evaluation of Serratia marcescens Adherence to Contact Lens Materials

by Reed Pifer, Valerie Harris, Deaja Sanders, Monica Crary and Paul Shannon

Microorganisms 2023, 11(1), 217; https://doi.org/10.3390/microorganisms11010217 - 15 Jan 2023

Cited by 3 | Viewed by 2608

Abstract

Bacterial keratitis is a risk associated with the use of contact lenses for cosmetic purposes or vision correction. In this in vitro experimental study, we examined the ability of the ocular pathogen Serratia marcescens to adhere to monthly or biweekly replacement contact lenses. [...] Read more.

Bacterial keratitis is a risk associated with the use of contact lenses for cosmetic purposes or vision correction. In this in vitro experimental study, we examined the ability of the ocular pathogen Serratia marcescens to adhere to monthly or biweekly replacement contact lenses. We performed quantitative adhesion assays to evaluate the adherence of S. marcescens to seven contact lens materials: comfilcon A, senofilcon A, omafilcon B, fanfilcon A, balafilcon A, senofilcon C, and lehfilcon A. Lehfilcon A is a newly marketed silicon hydrogel contact lens with a surface modification of poly-(2-methacryloyloxyethyl phosphorylcholine) (PMPC). PMPC has previously been demonstrated to be an effective anti-biofouling treatment for numerous surfaces. We observed low S. marcescens adherence to lehfilcon A compared to other materials. We demonstrate the use of the fluorescent dye 5(6)-Carboxytetramethylrhodamine succinimidyl ester to covalently stain live cells prior to material adhesion studies. Full article

(This article belongs to the Section Medical Microbiology)

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15 pages, 2631 KiB

Open AccessArticle

Characterization of Phytopythium Species Involved in the Establishment and Development of Kiwifruit Vine Decline Syndrome

by Simona Prencipe, Giada Schiavon, Marco Rosati, Luca Nari, Leonardo Schena and Davide Spadaro

Microorganisms 2023, 11(1), 216; https://doi.org/10.3390/microorganisms11010216 - 15 Jan 2023

Cited by 7 | Viewed by 3337

Abstract

Since 2012, the kiwifruit vine decline syndrome (KVDS) has progressively compromised Italian kiwifruit orchards. Different abiotic and biotic factors have been associated with the establishment and development of KVDS. During monitoring of orchards affected by KVDS in north-western Italy during 2016–2019, 71 Phytopythium [...] Read more.

Since 2012, the kiwifruit vine decline syndrome (KVDS) has progressively compromised Italian kiwifruit orchards. Different abiotic and biotic factors have been associated with the establishment and development of KVDS. During monitoring of orchards affected by KVDS in north-western Italy during 2016–2019, 71 Phytopythium spp. were isolated. Based on maximum likelihood concatenated phylogeny on the ITS1-5.8S-ITS2 region of the rDNA, large subunit rDNA, and cytochrome oxidase I, isolates were identified as P. vexans (52), P. litorale (10), P. chamaehyphon (7) and P. helicoides (2). Phytopythium litorale and P. helicoides are reported for the first time as agents of KVDS in Italy. To demonstrate pathogenicity and fulfil Koch’s postulates, representative isolates of P. vexans, P. litorale, P. chamaehyphon and P. helicoides were inoculated in potted plants. In these trials, waterlogging was applied to stress plant with a temporary anoxia and to favour the production of infective zoospores by the oomycetes. In experiments in vitro, the four species showed the highest growth at 25–30 °C, depending on the media used. P. helicoides was able to grow also at 40 °C. The four species were able to grow in vitro at a pH ranging from 5.0 to 8.0, showing that pH had less effect on growth than temperature. The present study suggests a strong role of different species of Phytopythium in the establishment and development of KVDS. Phytopythium spp. could be favoured by the average increase in soil temperatures during summer, associated with global warming. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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16 pages, 2827 KiB

Open AccessArticle

Application of Cloning-Free Genome Engineering to Escherichia coli

by Lucia Romeo, Antonia Esposito, Alberto Bernacchi, Daniele Colazzo, Alberto Vassallo, Marco Zaccaroni, Renato Fani and Sara Del Duca

Microorganisms 2023, 11(1), 215; https://doi.org/10.3390/microorganisms11010215 - 15 Jan 2023

Cited by 1 | Viewed by 2539

Abstract

The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to [...] Read more.

The propagation of foreign DNA in Escherichia coli is central to molecular biology. Recent advances have dramatically expanded the ability to engineer (bacterial) cells; however, most of these techniques remain time-consuming. The aim of the present work was to explore the possibility to use the cloning-free genome editing (CFGE) approach, proposed by Döhlemann and coworkers (2016), for E. coli genetics, and to deepen the knowledge about the homologous recombination mechanism. The E. coli auxotrophic mutant strains FB182 (hisF892) and FB181 (hisI903) were transformed with the circularized wild-type E. coli (i) hisF gene and hisF gene fragments of decreasing length, and (ii) hisIE gene, respectively. His⁺ clones were selected based on their ability to grow in the absence of histidine, and their hisF/hisIE gene sequences were characterized. CFGE method allowed the recombination of wild-type his genes (or fragments of them) within the mutated chromosomal copy, with a different recombination frequency based on the fragment length, and the generation of clones with a variable number of in tandem his genes copies. Data obtained pave the way to further evolutionary studies concerning the homologous recombination mechanism and the fate of in tandem duplicated genes. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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14 pages, 2183 KiB

Open AccessArticle

RyhB Paralogs Downregulate the Expressions of Multiple Survival-Associated Genes and Attenuate the Survival of Salmonella Enteritidis in the Chicken Macrophage HD11

by Xia Meng, Mengping He, Binjie Chen, Pengpeng Xia, Jinqiu Wang, Chunhong Zhu, Heng Wang and Guoqiang Zhu

Microorganisms 2023, 11(1), 214; https://doi.org/10.3390/microorganisms11010214 - 15 Jan 2023

Cited by 2 | Viewed by 2628

Abstract

RyhB-1 and RyhB-2 are small non-coding RNAs in Salmonella that act as regulators of iron homeostasis by sensing the environmental iron concentration. Expressions of RyhB paralogs from Salmonella Typhimurium are increased within microphages. RyhB paralogs restrain the growth of S. Typhimurium in RAW264.7 [...] Read more.

RyhB-1 and RyhB-2 are small non-coding RNAs in Salmonella that act as regulators of iron homeostasis by sensing the environmental iron concentration. Expressions of RyhB paralogs from Salmonella Typhimurium are increased within microphages. RyhB paralogs restrain the growth of S. Typhimurium in RAW264.7 macrophages by modulating the expression of Salmonella pathogenicity island 1 (SPI-1) genes sicA and rtsB. However, little is known about the regulatory role of RyhBs and their virulence-associated targets in Salmonella Enteritidis. We studied candidate targets of RyhB paralogs via RNA-Seq in conditions of iron limitation and hypoxia. RyhB paralogs were expressed when the S. Enteritidis strain CMCC(B)50336 (SE50336) interacted with the chicken macrophage line HD11. We analyzed gene expression associated with Salmonella survival and replication in macrophages in wild-type strain SE50336 and the RyhB deletion mutants after co-incubation with HD11 and screened out targets regulated by RyhBs. The expressions of both RyhB-1 and RyhB-2 were increased after co-incubation with HD11 for 8 h and several survival-associated genes within macrophages, such as ssaI, sseA, pagC, sodC, mgtC, yaeB, pocR, and hns, were upregulated in the ryhB-1 deletion mutant. Specifically, ssaI, the type-three secretion system 2 (T3SS-2) effector encoded by SPI-2, which promoted the survival of Salmonella in macrophages, was upregulated more than 3-fold in the ryhB-1 deletion mutant. We confirmed that both RyhB-1 and RyhB-2 downregulated the expression of ssaI to repress its mRNA translation by directly interacting with its coding sequence (CDS) region via an incomplete complementary base-pairing mechanism. The SPI-2 gene sseA was indirectly modulated by RyhB-1. The survival assays in macrophages showed that the ability of intracellular survival of ryhB-1 and/or ryhB-2 deletion mutants in HD11 was higher than that of the wild-type strain. These results indicate that RyhB paralogs downregulate survival-related virulence factors and attenuate the survival of S. Enteritidis inside chicken macrophage HD11. Full article

(This article belongs to the Special Issue Type III Secretion Systems in Human/Animal Pathogenic Bacteria 2.0)

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18 pages, 1657 KiB

Open AccessArticle

Susceptibility and Virulence of Enterobacteriaceae Isolated from Urinary Tract Infections in Benin

by Funkè F. Assouma, Haziz Sina, Tomabu Adjobimey, Agossou Damien Pacôme Noumavo, Akim Socohou, Bawa Boya, Ange D. Dossou, Lauriane Akpovo, Basile Boni Saka Konmy, Jacques F. Mavoungou, Adolphe Adjanohoun and Lamine Baba-Moussa

Microorganisms 2023, 11(1), 213; https://doi.org/10.3390/microorganisms11010213 - 14 Jan 2023

Cited by 9 | Viewed by 4192

Abstract

Enterobacteriaceae represent one of the main families of Gram-negative bacilli responsible for serious urinary tract infections (UTIs). The present study aimed to define the resistance profile and the virulence of Enterobacteriaceae strains isolated in urinary tract infections in Benin. A total of 390 [...] Read more.

Enterobacteriaceae represent one of the main families of Gram-negative bacilli responsible for serious urinary tract infections (UTIs). The present study aimed to define the resistance profile and the virulence of Enterobacteriaceae strains isolated in urinary tract infections in Benin. A total of 390 urine samples were collected from patients with UTIs, and Enterobacteriaceae strains were isolated according to standard microbiology methods. The API 20E gallery was used for biochemical identification. All the isolated strains were subjected to antimicrobial susceptibility testing using the disc diffusion method. Extended-spectrum beta-lactamase (ESBL) production was investigated using a double-disc synergy test (DDST), and biofilm production was quantified using the microplate method. Multiplex PCR was used to detect uro-virulence genes, namely: PapG, IronB, Sfa, iucD, Hly, FocG, Sat, FyuA and Cnf, using commercially designed primers. More than 26% (103/390) of our samples were contaminated by Enterobacteriaceae strains at different levels. Thus, E. coli (31.07%, 32/103), Serratia marcescens (11.65%, 12/103), Klebsiella ornithinolytica (8.74%, 9/103), Serratia fonticola (7.77%, 8/103) and Enterobacter cloacae (6.80%, 7/103) were identified. Among the isolated strains, 39.81% (41/103) were biofilm-forming, while 5.83% (6/103) were ESBL-producing. Isolates were most resistant to erythromycin, cefixime, ceftriaxone and ampicillin (≥90%) followed by ciprofloxacin, gentamycin, doxycycline and levofloxacin (≥50%), and least resistant to imipenem (27.18%). In regard to virulence genes, Sfa was the most detected (28.15%), followed by IronB (22.23%), iucD (21.36%), Cnf (15.53%), PapG (9.71%), FocG (8.74%), Sat (6.79%), FyuA (5.82%) and Hyl (2.91%). These data may help improve the diagnosis of uropathogenic strains of Enterobacteriaceae, but also in designing effective strategies and measures for the prevention and management of severe, recurrent, or complicated urinary tract infections in Benin. Full article

(This article belongs to the Special Issue Virulence Factors and Antibiotic Resistance of Enterobacterales 2.0)

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14 pages, 1039 KiB

Open AccessArticle

Human Papillomavirus in Non-Small Cell Lung Carcinoma: Assessing Virus Presence in Tumor and Normal Tissues and Its Clinical Relevance

by Matvey M. Tsyganov, Marina K. Ibragimova, Evgeniy O. Rodionov, Olga V. Cheremisina, Sergei V. Miller, Sergei A. Tuzikov and Nikolai V. Litvyakov

Microorganisms 2023, 11(1), 212; https://doi.org/10.3390/microorganisms11010212 - 14 Jan 2023

Cited by 3 | Viewed by 1950

Abstract

The significance of the role of human papillomavirus (HPV) in the development of lung cancer remains an open question. The data from the literature do not provide conclusive evidence of HPV being involved in the pathogenesis of lung cancer. The aim of this [...] Read more.

The significance of the role of human papillomavirus (HPV) in the development of lung cancer remains an open question. The data from the literature do not provide conclusive evidence of HPV being involved in the pathogenesis of lung cancer. The aim of this work was to detect the presence of HPV infections with a high carcinogenic risk in patients with non-small cell lung cancer (NSCLC). Materials and methods: the study involved 274 patients with stage IIA–IIIB non-small cell lung cancer. We analyzed normal and tumor tissues as well as blood from each patient. DNA was extracted from patients’ specimens, and HPV detection and genotyping was carried out using commercially available kits by PCR. Results: HPV was detected in 12.7% of the patients (35/274 of all cases). We detected nine different types of human papillomavirus in the patients, namely, types 16, 18, 31, 35, 45, 51, 52, 56, and 59. The HPV-positive samples had a clinically insignificant viral load and were predominantly integrated. The relationship between the presence of HPV and its virological parameters and the clinical and pathological parameters of the patients was established. A metastatic-free survival analysis showed that all patients with HPV in the tumor tissue had a higher 5-year survival rate (94%) compared with the HPV-negative patients (78%). The result was not statistically significant (p = 0.08). Conclusions: data showing a 12.7% human papillomavirus representation among patients with non-small cell lung cancer were obtained. The presence/absence of a viral component in patients with lung cancer was a clinically significant parameter. HPV types 16, 18, and 56, which are the most oncogenic, were most often detected. Full article

(This article belongs to the Special Issue Oncogenic Role of Viruses and Bacteria)

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26 pages, 5673 KiB

Open AccessEditor’s ChoiceArticle

The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny

by Katharina Keiz, Sebastian Ulrich, Jasmin Wenderlein, Patrick Keferloher, Anna Wiesinger, Klaus Neuhaus, Ilias Lagkouvardos, Helmut Wedekind and Reinhard K. Straubinger

Microorganisms 2023, 11(1), 211; https://doi.org/10.3390/microorganisms11010211 - 14 Jan 2023

Cited by 3 | Viewed by 2470

Abstract

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge [...] Read more.

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended. Full article

(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)

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18 pages, 4115 KiB

Open AccessArticle

Duration of Immunity Induced after Vaccination of Cattle with a Live Attenuated or Inactivated Lumpy Skin Disease Virus Vaccine

by Andy Haegeman, Ilse De Leeuw, Laurent Mostin, Willem Van Campe, Wannes Philips, Mehdi Elharrak, Nick De Regge and Kris De Clercq

Microorganisms 2023, 11(1), 210; https://doi.org/10.3390/microorganisms11010210 - 13 Jan 2023

Cited by 6 | Viewed by 8200

Abstract

Vaccines have proven themselves as an efficient way to control and eradicate lumpy skin disease (LSD). In addition to the safety and efficacy aspects, it is important to know the duration for which the vaccines confer protective immunity, as this impacts the design [...] Read more.

Vaccines have proven themselves as an efficient way to control and eradicate lumpy skin disease (LSD). In addition to the safety and efficacy aspects, it is important to know the duration for which the vaccines confer protective immunity, as this impacts the design of an efficient control and eradication program. We evaluated the duration of immunity induced by a live attenuated vaccine (LSDV LAV) and an inactivated vaccine (LSDV Inac), both based on LSDV. Cattle were vaccinated and challenged after 6, 12 and 18 months for LSDV LAV or after 6 and 12 months for the LSDV Inac. The LSDV LAV elicited a strong immune response and protection for up to 18 months, as no clinical signs or viremia could be observed after a viral LSDV challenge in any of the vaccinated animals. A good immune response and protection were similarly seen for the LSDV Inac after 6 months. However, two animals developed clinical signs and viremia when challenged after 12 months. In conclusion, our data support the annual booster vaccination when using the live attenuated vaccine, as recommended by the manufacturer, which could potentially even be prolonged. In contrast, a bi-annual vaccination seems necessary when using the inactivated vaccine. Full article

(This article belongs to the Special Issue Control of Viral Infections: Pathogenesis, Immunity, Vaccines and Antivirals)

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14 pages, 4691 KiB

Open AccessArticle

A Search for Tick-Associated, Bronnoya-like Virus Spillover into Sheep

by Bianca Elena Bratuleanu, Cristian Raileanu, Delphine Chrétien, Pablo Guardado-Calvo, Thomas Bigot, Gheorghe Savuta, Sarah Temmam and Marc Eloit

Microorganisms 2023, 11(1), 209; https://doi.org/10.3390/microorganisms11010209 - 13 Jan 2023

Cited by 2 | Viewed by 2286

Abstract

Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the order Bunyavirales were discovered in numerous tick species. In this study, we used metatranscriptomics to detect the virome, including novel viruses, associated [...] Read more.

Tick-borne diseases are responsible for many vector-borne diseases within Europe. Recently, novel viruses belonging to a new viral family of the order Bunyavirales were discovered in numerous tick species. In this study, we used metatranscriptomics to detect the virome, including novel viruses, associated with Ixodes ricinus collected from Romania and France. A bunyavirus-like virus related to the Bronnoya virus was identified for the first time in these regions. It presents a high level of amino-acid conservation with Bronnoya-related viruses identified in I. ricinus ticks from Norway and Croatia and with the Ixodes scapularis bunyavirus isolated from a tick cell line in Japan in 2014. Phylogenetic analyses revealed that the Bronnoya viruses’ sub-clade is distinct from several Bunyavirales families, suggesting that it could constitute a novel family within the order. To determine if Bronnoya viruses could constitute novel tick-borne arboviruses, a Luciferase immunoprecipitation assay for detecting antibodies in the viral glycoprotein of the Romanian Bronnoya virus was used to screen sera from small ruminants exposed to tick bites. No positive serum was detected, suggesting that this virus is probably not able to infect small ruminants. This study represents the first serological investigation of mammalian infections with a Bronnoya-like virus and an initial step in the identification of potential new emergences of tick-borne arboviruses. Full article

(This article belongs to the Special Issue Advanced Research on Ticks and Tick-Borne Diseases)

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18 pages, 3496 KiB

Open AccessArticle

Response of Intestinal Microbiota of Tiger Puffer (Takifugu rubripes) to the Fish Oil Finishing Strategy

by Yaoyao Kong, Zhangbin Liao, Xiuhua Ma, Mengqing Liang, Houguo Xu, Kangsen Mai and Yanjiao Zhang

Microorganisms 2023, 11(1), 208; https://doi.org/10.3390/microorganisms11010208 - 13 Jan 2023

Cited by 4 | Viewed by 2596

Abstract

The fish oil finishing (FOF) strategy, that is, re-feeding fish with fish oil (FO)-based diet after a certain period of feeding with alternative lipid source-based diets. On tiger puffer, the present study investigated the response of intestinal microbiota to FOF. Fish were fed [...] Read more.

The fish oil finishing (FOF) strategy, that is, re-feeding fish with fish oil (FO)-based diet after a certain period of feeding with alternative lipid source-based diets. On tiger puffer, the present study investigated the response of intestinal microbiota to FOF. Fish were fed four diets based on FO, soybean oil, palm oil and beef tallow as lipid sources, respectively, firstly for 50 days (growing-out period), and then fed the FO-based diet for 30 more days (FOF period). The results showed that dietary terrestrially sourced oils impaired the intestinal function in the growing-out period. However, the activities of amylase, trypsin and anti-oxidative enzymes (SOD, CAT, T-AOC), as well as gene expression of inflammatory cytokines (IL-1β, TNF-α, TGF-β) and tight junction protein (Claudin4, Claudin7, Claudin18, JAM, ZO-1) in the intestine were significantly recovered by FOF. The 16S rDNA sequencing analysis showed that FOF improved the similarity of bacterial community among the groups. The MetaStat analysis confirmed that FOF regulated the abundance of butyric acid-producing bacteria (Lachnospiraceae, Eubacterium, Butyricicoccus, Clostridium and Roseburia) and bacteria related to digestion and absorption (Sphingomonas, Romboutsia and Brevibacillus). In conclusion, FOF can recover the intestine function. The intestinal microbiota probably participated in and played a key role in the recovery process. Full article

(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals)

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20 pages, 6529 KiB

Open AccessArticle

Genome Characterization of Bacteriophage KPP-1, a Novel Member in the Subfamily Vequintavirinae, and Use of Its Endolysin for the Lysis of Multidrug-Resistant Klebsiella variicola In Vitro

by Amal Senevirathne, Jehee Lee, Mahanama De Zoysa and Chamilani Nikapitiya

Microorganisms 2023, 11(1), 207; https://doi.org/10.3390/microorganisms11010207 - 13 Jan 2023

Cited by 3 | Viewed by 3240

Abstract

Multidrug-resistant members of the Klebsiella pneumoniae complex have become a threat to human lives and animals, including aquatic animals, owing to the limited choice of antimicrobial treatments. Bacteriophages are effective natural tools available to fight against multidrug-resistant bacteria. The bacteriophage KPP-1 was found [...] Read more.

Multidrug-resistant members of the Klebsiella pneumoniae complex have become a threat to human lives and animals, including aquatic animals, owing to the limited choice of antimicrobial treatments. Bacteriophages are effective natural tools available to fight against multidrug-resistant bacteria. The bacteriophage KPP-1 was found to be strictly lytic against K. variicola, a multidrug-resistant isolate, producing clear plaques. The genome sequence analysis of KPP-1 revealed that it comprised 143,369 base pairs with 47% overall GC content. A total of 272 genes (forward 161, complementary 111) encode for 17 tRNAs and 255 open reading frames (ORFs). Among them, 32 ORFs could be functionally annotated using the National Center for Biotechnology Information (NCBI) Protein Basic Local Alignment Search Tool (BLASTp) algorithm while 223 were found to code for hypothetical proteins. Comparative genomic analysis revealed that the closest neighbor of KPP-1 can be found in the genus Mydovirus of the subfamily Vequintavirinae. KPP-1 not only markedly suppressed the growth of the host but also worked synergistically with ampicillin. Useful genes for pathogen control such as endolysin (locus tag: KPP_11591) were found to have activity against multidrug-resistant isolate of K. variicola. Further studies are necessary to develop a strategy to control the emerging pathogen K. variicola using bacteriophages such as KPP-1. Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

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23 pages, 7930 KiB

Open AccessArticle

Calendula officinalis—A Great Source of Plant Growth Promoting Endophytic Bacteria (PGPEB) and Biological Control Agents (BCA)

by Polina C. Tsalgatidou, Eirini-Evangelia Thomloudi, Kallimachos Nifakos, Costas Delis, Anastasia Venieraki and Panagiotis Katinakis

Microorganisms 2023, 11(1), 206; https://doi.org/10.3390/microorganisms11010206 - 13 Jan 2023

Cited by 8 | Viewed by 4324

Abstract

The application of beneficial bacteria may present an alternative approach to chemical plant protection and fertilization products as they enhance growth and resistance to biotic and abiotic stresses. Plant growth-promoting bacteria are found in the rhizosphere, epiphytically or endophytically (Plant Growth Promoting Endophytic [...] Read more.

The application of beneficial bacteria may present an alternative approach to chemical plant protection and fertilization products as they enhance growth and resistance to biotic and abiotic stresses. Plant growth-promoting bacteria are found in the rhizosphere, epiphytically or endophytically (Plant Growth Promoting Endophytic Bacteria, PGPEB). In the present study, 36 out of 119 isolated endophytic bacterial strains from roots, leaves and flowers of the pharmaceutical plant Calendula officinalis were further identified and classified into Bacillus, Pseudomonas, Pantoea, Stenotrophomonas and Rhizobium genera. Selected endophytes were evaluated depending on positive reaction to different plant growth promoting (PGP) traits, motility, survival rate and inhibition of phytopathogenic fungi in vitro and ex vivo (tomato fruit). Bacteria were further assessed for their plant growth effect on Arabidopsis thaliana seedlings and on seed bio-primed tomato plantlets, in vitro. Our results indicated that many bacterial endophytes increased seed germination, promoted plant growth and changed root structure by increasing lateral root density and length and root hair formation. The most promising antagonistic PGPEB strains (Cal.r.29, Cal.l.30, Cal.f.4, Cal.l.11, Cal.f.2.1, Cal.r.19 and Cal.r.11) are indicated as effective biological control agents (BCA) against Botrytis cinerea on detached tomato fruits. Results underlie the utility of beneficial endophytic bacteria for sustainable and efficient crop production and disease control. Full article

(This article belongs to the Special Issue Plant Growth-Promoting Bacteria and Plant-Soil Interactions in Harsh Environments)

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9 pages, 671 KiB

Open AccessArticle

The Association between Mycoplasma pneumoniae Genotype and Cutaneous Disease

by Jasna Rodman Berlot, Tatjana Mrvič, Mitja Košnik and Darja Keše

Microorganisms 2023, 11(1), 205; https://doi.org/10.3390/microorganisms11010205 - 13 Jan 2023

Cited by 4 | Viewed by 2043

Abstract

Mycoplasma pneumoniae (Mp) can cause several extrapulmonary manifestations, most frequently dermatological ones. It is largely unknown whether Mp genotype determines Mp-induced cutaneous disease. The aim of our study was to assess the association between Mp genotype and this clinical outcome. [...] Read more.

Mycoplasma pneumoniae (Mp) can cause several extrapulmonary manifestations, most frequently dermatological ones. It is largely unknown whether Mp genotype determines Mp-induced cutaneous disease. The aim of our study was to assess the association between Mp genotype and this clinical outcome. We performed a retrospective study of children referred with signs of acute Mp infection from 1 January 2014 to 31 December 2014. We compared the characteristics of children presenting as cutaneous disease, upper (URTI) and lower respiratory tract infection (LRTI). In addition, we separately analyzed the data of patients presenting with Mp-induced cutaneous disease. We evaluated data from 435 patients (mean age 7.3 years, SD 3.4 years; 52.0% boys) who had Mp PCR-positive pharyngeal swab, P1 genotype and/or multilocus variable-number tandem-repeat analysis (MLVA) genotype defined and no viral co-detection, presenting as cutaneous disease (38/435), URTI (46/435) or LRTI (351/435). The majority of patients had urticarial (55%, 21/38) or maculopapular eruptions (37%, 14/38). We found no association between Mp genotype and clinical outcome of cutaneous disease, nor any specific dermatological presentation. In the group with cutaneous disease, 18% (7/38) required hospital admission because of rash. We found that infection with MLVA-3,6,6,2 strains was more common in admitted patients than in outpatients (40% vs. 4%, p = 0.017) and significantly affected the likelihood of hospital admission in a logistic regression model. The results of our cohort study suggest that Mp genotype does not determine Mp-induced cutaneous disease or a specific dermatological presentation. Nevertheless, infections with certain MLVA strains could induce more severe cutaneous disease requiring hospitalization. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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12 pages, 2619 KiB

Open AccessArticle

Legionnaires’ Disease in China Caused by Legionella pneumophila Corby

by Pei-Xing Xu, Hong-Yu Ren, Ran Li, Xiao-Jing Jin, Zhan-Cheng Gao and Tian Qin

Microorganisms 2023, 11(1), 204; https://doi.org/10.3390/microorganisms11010204 - 13 Jan 2023

Viewed by 2975

Abstract

Legionella pneumophila is an intracellular pathogen causing pneumonia in humans. In February 2022, Legionnaires’ disease caused by L. pneumophila strain Corby in a patient with lung adenocarcinoma was identified for the first time in China. This paper includes the case report and phenotypic [...] Read more.

Legionella pneumophila is an intracellular pathogen causing pneumonia in humans. In February 2022, Legionnaires’ disease caused by L. pneumophila strain Corby in a patient with lung adenocarcinoma was identified for the first time in China. This paper includes the case report and phenotypic and genomic analysis of the Corby (ICDC) strain. Its biological characteristics were evaluated by antibiotic sensitivity testing and cytology experiments, and genomic analysis was performed to understand its genetic evolution. The patient’s clinical manifestations included cough, fever, pulmonary infiltration, and significantly decreased activity endurance. After empirical antimicrobial therapy, infection indicators decreased. The Corby (ICDC) strain was susceptible to nine antibiotics and exhibited strong intracellular proliferation ability. A phylogenetic tree showed that the Corby (ICDC) strain was closely related to the Corby strain, but under the pressure of a complex environment, its genome had undergone more rearrangement and inversion. The type IF CRISPR-Cas system was identified in its genome, and spacer analysis indicated that it had been invaded by several foreign plasmids, bacteria, and viruses during evolution. Legionnaires’ disease caused by L. pneumophila strain Corby may be ignored in China, and it is urgent to improve long-term monitoring and investigation of aquatic environments and patients with respiratory infections to prevent a large-scale outbreak of Legionnaires’ disease. Full article

(This article belongs to the Special Issue Clinical and Environmental Surveillance for the Prevention of Legionellosis)

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15 pages, 2962 KiB

Open AccessArticle

Metabolic Engineering of Escherichia coli for High-Level Production of (R)-Acetoin from Low-Cost Raw Materials

by Mengxue Diao, Xianrui Chen, Jing Li, Ya’nan Shi, Bo Yu, Zhilin Ma, Jianxiu Li and Nengzhong Xie

Microorganisms 2023, 11(1), 203; https://doi.org/10.3390/microorganisms11010203 - 13 Jan 2023

Cited by 1 | Viewed by 3333

Abstract

Acetoin is an important four-carbon platform chemical with versatile applications. Optically pure (R)-acetoin is more valuable than the racemate as it can be applied in the asymmetric synthesis of optically active α-hydroxy ketone derivatives, pharmaceuticals, and liquid crystal composites. As a [...] Read more.

Acetoin is an important four-carbon platform chemical with versatile applications. Optically pure (R)-acetoin is more valuable than the racemate as it can be applied in the asymmetric synthesis of optically active α-hydroxy ketone derivatives, pharmaceuticals, and liquid crystal composites. As a cytotoxic solvent, acetoin at high concentrations severely limits culture performance and impedes the acetoin yield of cell factories. In this study, putative genes that may improve the resistance to acetoin for Escherichia coli were screened. To obtain a high-producing strain, the identified acetoin-resistance gene was overexpressed, and the synthetic pathway of (R)-acetoin was strengthened by optimizing the copy number of the key genes. The engineered E. coli strain GXASR-49RSF produced 81.62 g/L (R)-acetoin with an enantiomeric purity of 96.5% in the fed-batch fermentation using non-food raw materials in a 3-L fermenter. Combining the systematic approach developed in this study with the use of low-cost feedstock showed great potential for (R)-acetoin production via this cost-effective biotechnological process. Full article

(This article belongs to the Special Issue Systems Metabolic Engineering of Industrial Microorganisms)

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11 pages, 1190 KiB

Open AccessArticle

Proteotyping of Campylobacter jejuni by MALDI-TOF MS and Strain Solution Version 2 Software

by Teruyo Ojima-Kato, Satomi Nagai, Akane Fujita, Junko Sakata and Hiroto Tamura

Microorganisms 2023, 11(1), 202; https://doi.org/10.3390/microorganisms11010202 - 12 Jan 2023

Viewed by 2533

Abstract

Identification of microorganisms by MALDI-TOF MS has become a popular method in the past 20 years. Strain Solution ver. 2 software appended with MALDI-TOF MS enables accurate discrimination of serotypes and strains beyond the genus and species level by creating a theoretical mass-based [...] Read more.

Identification of microorganisms by MALDI-TOF MS has become a popular method in the past 20 years. Strain Solution ver. 2 software appended with MALDI-TOF MS enables accurate discrimination of serotypes and strains beyond the genus and species level by creating a theoretical mass-based database. In this study, we constructed a theoretical mass database with the validated biomarkers to proteotype Campylobacter jejuni. Using 10 strains belonging to Campylobacter spp. available from culture collections and 41 Campylobacter jejuni strains isolated from humans and foods, the ribosomal protein subunits L36, L32, S14, L24, L23, L7/L12, and S11 could be selected as the effective biomarkers for the proteotyping of C. jejuni at MALDI-TOF MS. An accurate database of their theoretical mass-based values was constructed by matching these gene DNA sequences and the observed mass peaks. We attempted to automatically classify 41 strains isolated from nature using this database and Strain Solution ver. 2 software, and 38 strains (93%) were correctly classified into the intended group based on the theoretical mass-based values. Thus, the seven biomarkers found in this study and Strain Solution ver. 2 are promising for the proteotyping of C. jejuni by MALDI-TOF MS. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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14 pages, 1330 KiB

Open AccessArticle

Indigenous Yeasts from Rose Oil Distillation Wastewater and Their Capacity for Biotransformation of Phenolics

by Mila Rusanova, Krasimir Rusanov, Veronika Butterweck and Ivan Atanassov

Microorganisms 2023, 11(1), 201; https://doi.org/10.3390/microorganisms11010201 - 12 Jan 2023

Cited by 1 | Viewed by 2514

Abstract

The indigenous yeasts associated with the spontaneous fermentation of phenolic-rich rose oil distillation wastewater (RODW) generated after the industrial distillation of rose oil were studied. The ITS-rDNA sequence analysis of the samples collected from RODW fermented at semi-sterile conditions, a waste deposition lagoon [...] Read more.

The indigenous yeasts associated with the spontaneous fermentation of phenolic-rich rose oil distillation wastewater (RODW) generated after the industrial distillation of rose oil were studied. The ITS-rDNA sequence analysis of the samples collected from RODW fermented at semi-sterile conditions, a waste deposition lagoon and endophytic yeasts isolated from industrially cultivated Rosa damascena suggests that the spontaneous RODW fermentation is caused by yeasts from the genus Cyberlindnera found also as endophytes in the rose flowers. Phylogenetic analysis based on the nucleotide sequences of the translation elongation factor (TEF1α) and 18S- and 26S- rRNA genes further confirmed the taxonomic affiliation of the RODW yeast isolates with the genus Cyberlindnera. The RODW fermentation capacity of a selected set of indigenous yeast isolates was studied and compared with those of common yeast strains. The indigenous yeast isolates demonstrated a superior growth rate, resulting in a nearly double reduction in the phenolic content in the fermented RODW. The indigenous yeasts’ fermentation changed the RODW phenolics’ composition. The levels of some particular phenolic glycosides decreased through the depletion and fermentation of their sugar moiety. Hence, the relative abundance of the corresponding aglycons and other phenolic compounds increased. The capacity for the biotransformation of RODW phenolics by indigenous yeasts is discussed. Full article

(This article belongs to the Special Issue Microbial Biodegradation and Biotransformation 2.0)

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12 pages, 2495 KiB

Open AccessArticle

Detection of Old and New World Relapsing Fever Borreliae in Ornithodoros Ticks Collected from Warthog Burrows in Zambia

by Yongjin Qiu, Herman M. Chambaro, Kozue Sato, David Squarre, Edgar Simulundu, Masahiro Kajihara, Katendi Changula, Manyando Simbotwe, Hayato Harima, Joseph Ndebe, Ladslav Moonga, Ryo Nakao, Ayato Takada, Bernard Mudenda Hang’ombe, Hirofumi Sawa and Hiroki Kawabata

Microorganisms 2023, 11(1), 200; https://doi.org/10.3390/microorganisms11010200 - 12 Jan 2023

Viewed by 2556

Abstract

Relapsing fever (RF) is an arthropod-borne disease caused by Borrelia spirochete, which is one of the major public health concerns in endemic regions including Africa. However, information on Borrelia spirochetes is limited in Zambia. Here, we investigate the Borrelia spirochetes harbored by Ornithodoros ticks in [...] Read more.

Relapsing fever (RF) is an arthropod-borne disease caused by Borrelia spirochete, which is one of the major public health concerns in endemic regions including Africa. However, information on Borrelia spirochetes is limited in Zambia. Here, we investigate the Borrelia spirochetes harbored by Ornithodoros ticks in Zambian National Parks. We analyzed 182 DNA samples pooled from 886 Ornithodoros ticks. Of these, 43 tested positive, and their sequence revealed that the ticks harbored both Old and New World RF borreliae. This research presents the first evidence of Old-World RF borreliae in Zambia. The New World RF borreliae detected herein differed from the Candidatus Borrelia fainii previously reported in Zambia and were closely related to the pathogenic Borrelia sp. VS4 identified in Tanzania. Additionally, Borrelia theileri was recently reported in Zambia. Hence, at least four different Borrelia species occur in Zambia, and the organisms causing relapsing fever there might be more complex than previously thought. We empirically confirmed that real-time PCR with TaqMan minor groove binder probes accurately and simultaneously detected both Old and New World RF. In this manner, they could facilitate quantitative analyses of both types of RF borreliae. Subsequent investigations should endeavor to isolate the aforementioned Borrelia spp. and perform serosurveys on patients with RF. Full article

(This article belongs to the Special Issue Research on Ticks and Tick-Borne Pathogens)

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Microorganisms, Volume 11, Issue 1 (January 2023) – 229 articles

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