Microorganisms

15 pages, 11618 KiB

Open AccessArticle

Oral Administration of Lactobacillus sakei CVL-001 Improves Recovery from Dextran Sulfate Sodium-Induced Colitis in Mice by Microbiota Modulation

by Dong-Yeon Kim, Tae-Sung Lee, Do-Hyeon Jung, Eun-Jung Song, Ah-Ra Jang, Ji-Yeon Park, Jae-Hun Ahn, In-Su Seo, Seung-Ju Song, Yeong-Jun Kim, Yun-Ji Lee, Yeon-Ji Lee and Jong-Hwan Park

Microorganisms 2023, 11(5), 1359; https://doi.org/10.3390/microorganisms11051359 - 22 May 2023

Cited by 6 | Viewed by 2550

Abstract

Inflammatory bowel disease (IBD) is an intestinal chronic inflammatory disease, and its incidence is steadily increasing. IBD is closely related to the intestinal microbiota, and probiotics are known to be a potential therapeutic agent for IBD. In our study, we evaluated the protective [...] Read more.

Inflammatory bowel disease (IBD) is an intestinal chronic inflammatory disease, and its incidence is steadily increasing. IBD is closely related to the intestinal microbiota, and probiotics are known to be a potential therapeutic agent for IBD. In our study, we evaluated the protective effect of Lactobacillus sakei CVL-001, isolated from Baechu kimchi, on dextran sulfated sodium (DSS)-induced colitis in mice. The oral administration of L. sakei CVL-001 according to the experimental schedule alleviated weight loss and disease activity in the mice with colitis. Furthermore, the length and histopathology of the colon improved. The expression of tumor necrosis factor (TNF)-α and interleukin (IL)-1β genes decreased in the colons of mice that were administered L. sakei CVL-001, whereas that of IL-10 increased. The expressions of genes coding for E-cadherin, claudin3, occludin, and mucin were also restored. In co-housed conditions, L. sakei CVL-001 administration did not improve disease activity, colon length, and histopathology. Microbiota analysis revealed that L. sakei CVL-001 administration increased the abundance of microbiota and altered Firmicutes/Bacteroidetes ratio, and decreased Proteobacteria. In conclusion, L. sakei CVL-001 administration protects mice from DSS-induced colitis by regulating immune response and intestinal integrity via gut microbiota modulation. Full article

(This article belongs to the Special Issue Probiotic and Postbiotic Properties of Lactobacillus)

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10 pages, 723 KiB

Open AccessArticle

Clinical, Laboratory, and Radiographic Features Can Help Predict Mycoplasma pneumoniae Lower Respiratory Tract Infection in Children

by Jasna Rodman Berlot, Špela Dolenc, Uroš Krivec and Darja Keše

Microorganisms 2023, 11(5), 1358; https://doi.org/10.3390/microorganisms11051358 - 22 May 2023

Cited by 1 | Viewed by 1742

Abstract

Mycoplasma pneumoniae (Mp) is a common cause of lower respiratory tract infection (LRTI) in children that is difficult to distinguish from LRTI of other etiologies. We aimed to determine if a combination of clinical, laboratory, and chest radiographic features can help identify patients [...] Read more.

Mycoplasma pneumoniae (Mp) is a common cause of lower respiratory tract infection (LRTI) in children that is difficult to distinguish from LRTI of other etiologies. We aimed to determine if a combination of clinical, laboratory, and chest radiographic features can help identify patients at higher risk of Mp LRTI. We reviewed medical charts of children referred to our tertiary hospital with suspected acute mycoplasmal LRTI. Pharyngeal swabs obtained from patients were tested by Mp PCR. We compared epidemiological and clinical data of children with positive and negative Mp PCR results. In addition, a multivariable logistic regression analysis was performed to predict Mp LRTI based on the patient’s age, duration of symptoms, presence of extrapulmonary manifestations, laboratory findings, and chest radiographic findings. We included 65 children with Mp PCR-negative and 49 with Mp PCR-positive LRTI and no viral co-detection. Children with Mp LRTI were older (median age 5.8 vs. 2.2 years, p < 0.001), had a longer duration of symptoms on referral (median 7 vs. 4 days, p < 0.001), and lower median WBC (9.9 vs. 12.7 × 10⁹/L, p < 0.001). On chest radiograph, unilateral infiltrates were more frequently observed in the Mp PCR-positive group (57.5% vs. 24.1%, p = 0.001). Age, duration of symptoms, and chest radiographic findings had the highest predictive value for Mp LRTI in a multivariable logistic regression model. Our analysis suggests that a combination of clinical, laboratory, and chest radiographic features can be used to assess the likelihood of Mp LRTI and assist in decision-making for which children need further tests or macrolide antibiotic treatment. Full article

(This article belongs to the Special Issue Mycoplasma Pathogenicity, Persistence and Virulence)

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14 pages, 1943 KiB

Open AccessArticle

Chitinolytic Enzymes of the Hyperparasite Fungus Aphanocladium album: Genome-Wide Survey and Characterization of A Selected Enzyme

by Claudia Leoni, Caterina Manzari, Matteo Chiara, Pasqua Veronico, Giovanni Luigi Bruno, Graziano Pesole, Luigi R. Ceci and Mariateresa Volpicella

Microorganisms 2023, 11(5), 1357; https://doi.org/10.3390/microorganisms11051357 - 22 May 2023

Viewed by 1821

Abstract

The filamentous fungus Aphanocladium album is known as a hyperparasite of plant pathogenic fungi; hence, it has been studied as a possible agent for plant protection. Chitinases secreted by A. album have proven to be essential for its fungicidal activity. However, no complete [...] Read more.

The filamentous fungus Aphanocladium album is known as a hyperparasite of plant pathogenic fungi; hence, it has been studied as a possible agent for plant protection. Chitinases secreted by A. album have proven to be essential for its fungicidal activity. However, no complete analysis of the A. album chitinase assortment has been carried out, nor have any of its chitinases been characterized yet. In this study, we report the first draft assembly of the genome sequence of A. album (strain MX-95). The in silico functional annotation of the genome allowed the identification of 46 genes encoding chitinolytic enzymes of the GH18 (26 genes), GH20 (8 genes), GH75 (8 genes), and GH3 (4 genes) families. The encoded proteins were investigated by comparative and phylogenetic analysis, allowing clustering in different subgroups. A. album chitinases were also characterized according to the presence of different functional protein domains (carbohydrate-binding modules and catalytic domains) providing the first complete description of the chitinase repertoire of A. album. A single chitinase gene was then selected for complete functional characterization. The encoded protein was expressed in the yeast Pichia pastoris, and its activity was assayed under different conditions of temperature and pH and with different substrates. It was found that the enzyme acts mainly as a chitobiosidase, with higher activity in the 37–50 °C range. Full article

(This article belongs to the Section Plant Microbe Interactions)

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29 pages, 7655 KiB

Open AccessArticle

The Effects of Different Feeding Regimes on Body Composition, Gut Microbial Population, and Susceptibility to Pathogenic Infection in Largemouth Bass

by Yao Zheng, Haojun Zhu, Quanjie Li and Gangchun Xu

Microorganisms 2023, 11(5), 1356; https://doi.org/10.3390/microorganisms11051356 - 22 May 2023

Cited by 3 | Viewed by 1740

Abstract

This study investigated the effects of dietary commercial feed (n = 50,025 in triplicate, named group PF for soil dike pond, sampling n = 7; n = 15,000 in triplicate, WF for water tank, n = 8), iced fish (n = [...] Read more.

This study investigated the effects of dietary commercial feed (n = 50,025 in triplicate, named group PF for soil dike pond, sampling n = 7; n = 15,000 in triplicate, WF for water tank, n = 8), iced fish (n = 50,025 in triplicate, PI, n = 7), and a combination of both (n = 50,025 in triplicate, PFI, n = 8) on different metabolic parameters of the largemouth bass, Micropterus salmoides (0.67 ± 0.09 g, culture period from June 2017 to July 2018). Throughout the experimental period, different areas of water (including input water of the front, middle of the pond, and from the drain off at the back) and their mixed samples were simultaneously analyzed to find the source of the main infectious bacteria. Various feeding strategies may differentially affect body composition and shape the gut microbiota, but the mode of action has not been determined. Results showed that no significant differences were found in the growth performance except for the product yield using a different culture mode (PFI vs. WF). For muscle composition, the higher ∑SFA, ∑MUFA, ∑n-6PUFA, and 18:3n-3/18:2n-6 levels were detected in largemouth bass fed with iced fish, while enrichment in ∑n-3PUFA and ∑HUFA was detected in largemouth bass fed with commercial feed. For the gut microbiota, Fusobacteria, Proteobacteria, and Firmicutes were the most dominant phyla among all the gut samples. The abundance of Firmicutes and Tenericutes significantly decreased and later increased with iced fish feeding. The relative abundance of species from the Clostridia, Mollicutes, Mycoplasmatales, and families (Clostridiaceae and Mycoplasmataceae) significantly increased in the feed plus iced fish (PFI) group relative to that in the iced fish (PI) group. Pathways of carbohydrate metabolism and the digestive system were enriched in the commercial feed group, whereas infectious bacterial disease resistance-related pathways were enriched in the iced fish group, corresponding to the higher rate of death, fatty liver disease, and frequency and duration of cyanobacteria outbreaks. Feeding with iced fish resulted in more activities in the digestive system and energy metabolism, more efficient fatty acid metabolism, had higher ∑MUFA, and simultaneously had the potential for protection against infectious bacteria from the environment through a change in intestinal microbiota in the pond of largemouth bass culturing. Finally, the difference in feed related to the digestive system may contribute to the significant microbiota branch in the fish gut, and the input and outflow of water affects the intestinal flora in the surrounding water and in the gut, which in turn affects growth and disease resistance. Full article

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

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14 pages, 4192 KiB

Open AccessArticle

Tryptophanase Expressed by Salmonella Halts Breast Cancer Cell Growth In Vitro and Inhibits Production of Immunosuppressive Kynurenine

by Eljoie Anice Cada Hababag, Allea Cauilan, David Quintero and David Bermudes

Microorganisms 2023, 11(5), 1355; https://doi.org/10.3390/microorganisms11051355 - 22 May 2023

Cited by 1 | Viewed by 2453

Abstract

Tryptophan is an essential amino acid required for tumor cell growth and is also the precursor to kynurenine, an immunosuppressive molecule that plays a role in limiting anticancer immunity. Tryptophanase (TNase) is an enzyme expressed by different bacterial species that converts tryptophan into [...] Read more.

Tryptophan is an essential amino acid required for tumor cell growth and is also the precursor to kynurenine, an immunosuppressive molecule that plays a role in limiting anticancer immunity. Tryptophanase (TNase) is an enzyme expressed by different bacterial species that converts tryptophan into indole, pyruvate and ammonia, but is absent in the Salmonella strain VNP20009 that has been used as a therapeutic delivery vector. We cloned the Escherichia coli TNase operon tnaCAB into the VNP20009 (VNP20009-tnaCAB), and were able to detect linear production of indole over time, using Kovács reagent. In order to conduct further experiments using the whole bacteria, we added the antibiotic gentamicin to stop bacterial replication. Using a fixed number of bacteria, we found that there was no significant effect of gentamicin on stationary phase VNP20009-tnaCAB upon their ability to convert tryptophan to indole over time. We developed a procedure to extract indole from media while retaining tryptophan, and were able to measure tryptophan spectrophotometrically after exposure to gentamicin-inactivated whole bacterial cells. Using the tryptophan concentration equivalent to that present in DMEM cell culture media, a fixed number of bacteria were able to deplete 93.9% of the tryptophan in the culture media in 4 h. In VNP20009-tnaCAB depleted tissue culture media, MDA-MB-468 triple negative breast cancer cells were unable to divide, while those treated with media exposed only to VNP20009 continued cell division. Re-addition of tryptophan to conditioned culture media restored tumor cell growth. Treatment of tumor cells with molar equivalents of the TNase products indole, pyruvate and ammonia only caused a slight increase in tumor cell growth. Using an ELISA assay, we confirmed that TNase depletion of tryptophan also limits the production of immunosuppressive kynurenine in IFNγ-stimulated MDA-MB-468 cancer cells. Our results demonstrate that Salmonella VNP20009 expressing TNase has improved potential to stop tumor cell growth and reverse immunosuppression. Full article

(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)

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26 pages, 8581 KiB

Open AccessArticle

Synergistic Immunostimulatory Activities of Probiotic Strains, Leuconostoc lactis and Weissella cibaria, and the Prebiotic Oligosaccharides They Produce

by Seoyoung Jeong, Ayeon Kwon, Huijin Jeong and Young-Seo Park

Microorganisms 2023, 11(5), 1354; https://doi.org/10.3390/microorganisms11051354 - 22 May 2023

Cited by 1 | Viewed by 1870

Abstract

Synbiotics contain health-beneficial bacteria, i.e., probiotics and prebiotics selectively utilized by the probiotics. Herein, three probiotic strains, Leuconostoc lactis CCK940, L. lactis SBC001, and Weissella cibaria YRK005, and the oligosaccharides produced by these strains (CCK, SBC, and YRK, respectively) were used to prepare [...] Read more.

Synbiotics contain health-beneficial bacteria, i.e., probiotics and prebiotics selectively utilized by the probiotics. Herein, three probiotic strains, Leuconostoc lactis CCK940, L. lactis SBC001, and Weissella cibaria YRK005, and the oligosaccharides produced by these strains (CCK, SBC, and YRK, respectively) were used to prepare nine synbiotic combinations. Macrophages (RAW 264.7) were treated with these synbiotic combinations and the corresponding lactic acid bacteria and oligosaccharides alone to evaluate the treatments’ immunostimulatory activities. The level of nitric oxide (NO) production was significantly higher in the macrophages treated with the synbiotics than in those treated with the corresponding probiotic strains and the oligosaccharide alone. The immunostimulatory activities of the synbiotics increased regardless of the probiotic strain and the type of oligosaccharide used. The expressions of tissue necrosis factor-α, interleukin-1β, cyclooxygenase-2, inducible NO synthase genes, and extracellular-signal-regulated and c-Jun N-terminal kinases were significantly higher in the macrophages treated with the three synbiotics than in those treated with the corresponding strains or with the oligosaccharides alone. These results indicate that the synergistic immunostimulatory activities of probiotics and the prebiotics they produced in the studied synbiotic preparations resulted from the activation of the mitogen-activated protein-kinase-signaling pathway. This study suggests the combined use of these probiotics and prebiotics in the development of synbiotic preparations as health supplements. Full article

(This article belongs to the Special Issue Dialogue of Probiotics with the Host 2.0)

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10 pages, 787 KiB

Open AccessArticle

Antibiotics Resistance and Adhesive Properties of Clinical Staphylococcus aureus Isolated from Wound Infections

by Khulood Fahad Alabbosh, Tarek Zmantar, Abdulrahman S. Bazaid, Mejdi Snoussi and Emira Noumi

Microorganisms 2023, 11(5), 1353; https://doi.org/10.3390/microorganisms11051353 - 22 May 2023

Cited by 2 | Viewed by 1704

Abstract

Staphylococcus aureus (S. aureus) is a ubiquitous pathogen responsible for several severe infections. This study aimed to investigate the adhesive properties and antibiotic resistance among clinical S. aureus isolated from Hail Hospital Province, Kingdom of Saudi Arabia (KSA), using molecular approaches. [...] Read more.

Staphylococcus aureus (S. aureus) is a ubiquitous pathogen responsible for several severe infections. This study aimed to investigate the adhesive properties and antibiotic resistance among clinical S. aureus isolated from Hail Hospital Province, Kingdom of Saudi Arabia (KSA), using molecular approaches. This study was conducted according to the ethical committee at Hail’s guidelines on twenty-four S. aureus isolates. A polymerase chain reaction (PCR) was performed to identify genes encoding the β-lactamase resistance (blaZ), methicillin resistance (mecA), fluoroquinolone resistance (norA), nitric oxide reductase (norB), fibronectin (fnbA and fnbB), clumping factor (clfA) and intracellular adhesion factors (icaA and icaD). This qualitative study tested adhesion based on exopolysaccharide production on Congo red agar (CRA) medium and biofilm formation on polystyrene by S. aureus strains. Among 24 isolates, the cna and blaz were the most prevalent (70.8%), followed by norB (54.1%), clfA (50.0%), norA (41.6%), mecA and fnbB (37.5%) and fnbA (33.3%). The presence of icaA/icaD genes was demonstrated in almost all tested strains in comparison to the reference strain, S. aureus ATCC 43300. The phenotypic study of adhesion showed that all tested strains had moderate biofilm-forming capacity on polystyrene and represented different morphotypes on a CRA medium. Five strains among the twenty-four harbored the four genes of resistance to antibiotics (mecA, norA, norB and blaz). Considering the genes of adhesion (cna, clfA, fnbA and fnbB), these genes were present in 25% of the tested isolates. Regarding the adhesive properties, the clinical isolates of S. aureus formed biofilm on polystyrene, and only one strain (S17) produced exopolysaccharides on Congo red agar. All these results contribute to an understanding that the pathogenesis of clinical S. aureus isolates is due to their antibiotic resistance and adhesion to medical material. Full article

(This article belongs to the Special Issue Biology and Pathogenesis of Staphylococcus Infection (2nd Edition))

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17 pages, 1527 KiB

Open AccessArticle

Structure of Microbial Communities and Biological Activity in Tundra Soils of the Euro-Arctic Region (Rybachy Peninsula, Russia)

by Maria V. Korneykova, Vladimir A. Myazin, Nadezhda V. Fokina, Alexandra A. Chaporgina, Dmitry A. Nikitin and Andrey V. Dolgikh

Microorganisms 2023, 11(5), 1352; https://doi.org/10.3390/microorganisms11051352 - 22 May 2023

Cited by 4 | Viewed by 1974

Abstract

The relevance of the Arctic regions’ study is rapidly increasing due to the sensitive response of fragile ecosystems to climate change and anthropogenic pressure. The microbiome is an important component that determines the soils’ functioning and an indicator of changes occurring in ecosystems. [...] Read more.

The relevance of the Arctic regions’ study is rapidly increasing due to the sensitive response of fragile ecosystems to climate change and anthropogenic pressure. The microbiome is an important component that determines the soils’ functioning and an indicator of changes occurring in ecosystems. Rybachy Peninsula is the northernmost part of the continental European Russia and is almost completely surrounded by Barents Sea water. For the first time, the microbial communities of the Entic Podzol, Albic Podzol, Rheic Histosol and Folic Histosol as well as anthropogenically disturbed soils (chemical pollution and human impact, growing crops) on the Rybachy Peninsula were characterized using plating and fluorescence microscopy methods, in parallel with the enzymatic activity of soils. The amount and structure of soil microbial biomass, such as the total biomass of fungi and prokaryote, the length and diameter of fungal and actinomycete mycelium, the proportion of spores and mycelium in the fungal biomass, the number of spores and prokaryotic cells, the proportion of small and large fungal spores and their morphology were determined. In the soils of the peninsula, the fungal biomass varied from 0.121 to 0.669 mg/g soil. The biomass of prokaryotes in soils ranged from 9.22 to 55.45 μg/g of soil. Fungi predominated, the proportion of which in the total microbial biomass varied from 78.5 to 97.7%. The number of culturable microfungi ranged from 0.53 to 13.93 × 10³ CFU/g in the topsoil horizons, with a maximum in Entic Podzol and Albic Podzol soils and a minimum in anthropogenically disturbed soil. The number of culturable copiotrophic bacteria varied from 41.8 × 10³ cells/g in a cryogenic spot to 5551.3 × 10³ cells /g in anthropogenically disturbed soils. The number of culturable oligotrophic bacteria ranged from 77.9 to 12,059.6 × 10³ cells/g. Changes in natural soils because of anthropogenic impact and a change in vegetation types have led to a change in the structure of the community of soil microorganisms. Investigated tundra soils had high enzymatic activity in native and anthropogenic conditions. The β-glucosidase and urease activity were comparable or even higher than in the soils of more southern natural zone, and the activity of dehydrogenase was 2–5 times lower. Thus, despite the subarctic climatic conditions, local soils have a significant biological activity upon which the productivity of ecosystems largely depends. The soils of the Rybachy Peninsula have a powerful enzyme pool due to the high adaptive potential of soil microorganisms to the extreme conditions of the Arctic, which allows them to perform their functions even under conditions of anthropogenic interference. Full article

(This article belongs to the Special Issue Soil Microbial Diversity and Its Ecological Functions)

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20 pages, 2020 KiB

Open AccessArticle

Petroleum-Degrading Fungal Isolates for the Treatment of Soil Microcosms

by Dalel Daâssi and Fatimah Qabil Almaghrabi

Microorganisms 2023, 11(5), 1351; https://doi.org/10.3390/microorganisms11051351 - 22 May 2023

Cited by 4 | Viewed by 2846

Abstract

The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the same petroleum-polluted soil and ligninolytic fungal strains were screened and applied in the treatment of soil-contaminated microcosms [...] Read more.

The main purpose of this study was to degrade total petroleum hydrocarbons (TPHs) from contaminated soil in batch microcosm reactors. Native soil fungi isolated from the same petroleum-polluted soil and ligninolytic fungal strains were screened and applied in the treatment of soil-contaminated microcosms in aerobic conditions. The bioaugmentation processes were carried out using selected hydrocarbonoclastic fungal strains in mono or co-cultures. Results demonstrated the petroleum-degrading potential of six fungal isolates, namely KBR1 and KBR8 (indigenous) and KBR1-1, KB4, KB2 and LB3 (exogenous). Based on the molecular and phylogenetic analysis, KBR1 and KB8 were identified as Aspergillus niger [MW699896] and tubingensis [MW699895], while KBR1-1, KB4, KB2 and LB3 were affiliated with the genera Syncephalastrum sp. [MZ817958], Paecilomyces formosus [MW699897], Fusarium chlamydosporum [MZ817957] and Coniochaeta sp. [MW699893], respectively. The highest rate of TPH degradation was recorded in soil microcosm treatments (SMT) after 60 days by inoculation with Paecilomyces formosus 97 ± 2.54%, followed by bioaugmentation with the native strain Aspergillus niger (92 ± 1.83%) and then by the fungal consortium (84 ± 2.21%). The statistical analysis of the results showed significant differences. Full article

(This article belongs to the Special Issue Microbial Communities in Waste Treatment)

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5 pages, 200 KiB

Open AccessEditorial

Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants

by Sunghyun Yoon, Sandeep Kondakala, Minjae Kim, Steven L. Foley, Ohgew Kweon and Seongjae Kim

Microorganisms 2023, 11(5), 1350; https://doi.org/10.3390/microorganisms11051350 - 22 May 2023

Viewed by 1818

Abstract

Microbial contamination is the inadvertent presence of microbes or their byproducts in materials or environments [...] Full article

(This article belongs to the Special Issue Detection, Genophenotypic Characterization, and Antimicrobial Resistance of Microbial Contaminants)

11 pages, 962 KiB

Open AccessCommunication

Total Osteopontin and Its Isoform OPN4 Are Differently Expressed in Respiratory Samples during Influenza A(H1N1)pdm09 Infection and Progression

by Jéssica Santa Cruz de Carvalho Martins, Thiago das Chagas Sousa, Maria de Lourdes de Aguiar Oliveira, Etel Rodrigues Pereira Gimba, Marilda Mendonça Siqueira and Aline da Rocha Matos

Microorganisms 2023, 11(5), 1349; https://doi.org/10.3390/microorganisms11051349 - 20 May 2023

Viewed by 1545

Abstract

Influenza A virus (IAV) infection affects the human respiratory tract, causing an acute and highly contagious disease. Individuals with comorbidities and in the extremes of age are classified as risk groups for serious clinical outcomes. However, part of the severe infections and fatalities [...] Read more.

Influenza A virus (IAV) infection affects the human respiratory tract, causing an acute and highly contagious disease. Individuals with comorbidities and in the extremes of age are classified as risk groups for serious clinical outcomes. However, part of the severe infections and fatalities are observed among young healthy individuals. Noteworthy, influenza infections lack specific prognostic biomarkers that would predict the disease severity. Osteopontin (OPN) has been proposed as a biomarker in a few human malignancies and its differential modulation has been observed during viral infections. However, OPN expression levels in the primary site of IAV infection have not been previously investigated. Therefore, we evaluated the transcriptional expression patterns of total OPN (tOPN) and its splicing isoforms (OPNa, OPNb, OPNc, OPN4, and OPN5) in 176 respiratory secretion samples collected from human influenza A(H1N1)pdm09 cases and a group of 65 IAV-negative controls. IAV samples were differentially classified according to their disease severity. tOPN was more frequently detected in IAV samples (34.1%) when compared with the negative controls (18.5%) (p < 0.05), as well as in fatal (59.1%) versus non-fatal IAV samples (30.5%) (p < 0.01). OPN4 splice variant transcript was more prevalent in IAV cases (78.4%) than in the negative controls (66.1%) (p = 0.05) and in severe cases (85.7%) in relation to the non-severe ones (69.2%) (p < 0.01). OPN4 detection was also associated with severity symptoms such as dyspnea (p < 0.05), respiratory failure (p < 0.05), and oxygen saturation < 95% (p < 0.05). In addition, the OPN4 expression level was increased in the fatal cases of respiratory samples. Our data indicated that tOPN and OPN4 had a more pronounced expression pattern in IAV respiratory samples, pointing to the potential use of these molecules as biomarkers to evaluate disease outcomes. Full article

(This article belongs to the Special Issue Recent Advances of Respiratory Infections)

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12 pages, 1764 KiB

Open AccessArticle

Investigating the Impacts of UVC Radiation on Natural and Cultured Biofilms: An assessment of Cell Viability

by Cierra R. Braga, Kailey N. Richard, Harrison Gardner, Geoffrey Swain and Kelli Z. Hunsucker

Microorganisms 2023, 11(5), 1348; https://doi.org/10.3390/microorganisms11051348 - 20 May 2023

Cited by 2 | Viewed by 1583

Abstract

Biofilms are conglomerates of cells, water, and extracellular polymeric substances which can lead to various functional and financial setbacks. As a result, there has been a drive towards more environmentally friendly antifouling methods, such as the use of ultraviolet C (UVC) radiation. When [...] Read more.

Biofilms are conglomerates of cells, water, and extracellular polymeric substances which can lead to various functional and financial setbacks. As a result, there has been a drive towards more environmentally friendly antifouling methods, such as the use of ultraviolet C (UVC) radiation. When applying UVC radiation, it is important to understand how frequency, and thus dose, can influence an established biofilm. This study compares the impacts of varying doses of UVC radiation on both a monocultured biofilm consisting of Navicula incerta and field-developed biofilms. Both biofilms were exposed to doses of UVC radiation ranging from 1626.2

mJ / {cm}^{2}

to 9757.2

mJ / {cm}^{2}

and then treated with a live/dead assay. When exposed to UVC radiation, the N. incerta biofilms demonstrated a significant reduction in cell viability compared to the non-exposed samples, but all doses had similar viability results. The field biofilms were highly diverse, containing not only benthic diatoms but also planktonic species which may have led to inconsistencies. Although they are different from each other, these results provide beneficial data. Cultured biofilms provide insight into how diatom cells react to varying doses of UVC radiation, whereas the real-world heterogeneity of field biofilms is useful for determining the dosage needed to effectively prevent a biofilm. Both concepts are important when developing UVC radiation management plans that target established biofilms. Full article

(This article belongs to the Section Biofilm)

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17 pages, 3235 KiB

Open AccessArticle

Evaluation of Rouxiella badensis Subsp Acadiensis (Canan SV-53) as a Potential Probiotic Bacterium

by Ivanna Novotny-Nuñez, Gabriela Perdigón, Chantal Matar, María José Martínez Monteros, Nour Yahfoufi, Silvia Inés Cazorla and Carolina Maldonado-Galdeano

Microorganisms 2023, 11(5), 1347; https://doi.org/10.3390/microorganisms11051347 - 20 May 2023

Cited by 3 | Viewed by 1651

Abstract

The advent of omic platforms revealed the significant benefits of probiotics in the prevention of many infectious diseases. This led to a growing interest in novel strains of probiotics endowed with health characteristics related to microbiome and immune modulation. Therefore, autochthonous bacteria in [...] Read more.

The advent of omic platforms revealed the significant benefits of probiotics in the prevention of many infectious diseases. This led to a growing interest in novel strains of probiotics endowed with health characteristics related to microbiome and immune modulation. Therefore, autochthonous bacteria in plant ecosystems might offer a good source for novel next-generation probiotics. The main objective of this study was to analyze the effect of Rouxiella badensis acadiensis Canan (R. acadiensis) a bacterium isolated from the blueberry biota, on the mammalian intestinal ecosystem and its potential as a probiotic microorganism. R. acadiensis, reinforced the intestinal epithelial barrier avoiding bacterial translocation from the gut to deep tissues, even after feeding BALB/c mice for a prolonged period of time. Moreover, diet supplementation with R. acadiensis led to increases in the number of Paneth cells, well as an increase in the antimicrobial peptide α defensin. The anti-bacterial effect of R. acadiensis against Staphylococcus aureus and Salmonella enterica serovar Typhimurium was also reported. Importantly, R. acadiensis-fed animals showed better survival in an in vivo Salmonella enterica serovar Typhimurium challenge compared with those that received a conventional diet. These results demonstrated that R. acadiensis possesses characteristics of a probiotic strain by contributing to the reinforcement and maintenance of intestinal homeostasis. Full article

(This article belongs to the Section Gut Microbiota)

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12 pages, 2397 KiB

Open AccessArticle

Antiherpetic Activity of Taurisolo^®, a Grape Pomace Polyphenolic Extract

by Carla Zannella, Annalisa Chianese, Giuseppe Annunziata, Annalisa Ambrosino, Anna De Filippis, Gian Carlo Tenore, Ettore Novellino, Mariano Stornaiuolo and Massimiliano Galdiero

Microorganisms 2023, 11(5), 1346; https://doi.org/10.3390/microorganisms11051346 - 20 May 2023

Cited by 4 | Viewed by 2042

Abstract

Herpes simplex virus (HSV) is widespread in the population, causing oral or genital ulcers and, rarely, severe complications such as encephalitis, keratitis, and neonatal herpes. Current available anti-HSV drugs are acyclovir and its derivatives, although long-term therapy with these agents can lead to [...] Read more.

Herpes simplex virus (HSV) is widespread in the population, causing oral or genital ulcers and, rarely, severe complications such as encephalitis, keratitis, and neonatal herpes. Current available anti-HSV drugs are acyclovir and its derivatives, although long-term therapy with these agents can lead to drug resistance. Thus, the discovery of novel antiherpetic compounds merits additional studies. In recent decades, much scientific effort has been invested in the discovery of new synthetic or natural compounds with promising antiviral properties. In our study, we tested the antiviral potential of a novel polyphenol-based nutraceutical formulation (named Taurisolo^®) consisting of a water polyphenol extract of grape pomace. The evaluation of the antiviral activity was carried out by using HSV-1 and HSV-2 in plaque assay experiments to understand the mechanism of action of the extract. Results were confirmed by real-time PCR, transmission electron microscope (TEM), and fluorescence microscope. Taurisolo^® was able to block the viral infection by acting on cells when added together with the virus and also when the virus was pretreated with the extract, demonstrating an inhibitory activity directed to the early phases of HSV-1 and HSV-2 infection. Altogether, these data evidence for the first time the potential use of Taurisolo^® as a topical formulation for both preventing and healing herpes lesions. Full article

(This article belongs to the Special Issue Antimicrobial Properties of Plants-Derived Natural Products)

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20 pages, 1782 KiB

Open AccessArticle

Study of Antimicrobial Resistance, Biofilm Formation, and Motility of Pseudomonas aeruginosa Derived from Urine Samples

by Telma de Sousa, Michel Hébraud, Olimpia Alves, Eliana Costa, Luís Maltez, José Eduardo Pereira, Ângela Martins, Gilberto Igrejas and Patricia Poeta

Microorganisms 2023, 11(5), 1345; https://doi.org/10.3390/microorganisms11051345 - 19 May 2023

Cited by 13 | Viewed by 3767

Abstract

Pseudomonas aeruginosa causes urinary tract infections associated with catheters by forming biofilms on the surface of indwelling catheters. Therefore, controlling the spread of the bacteria is crucial to preventing its transmission in hospitals and the environment. Thus, our objective was to determine the [...] Read more.

Pseudomonas aeruginosa causes urinary tract infections associated with catheters by forming biofilms on the surface of indwelling catheters. Therefore, controlling the spread of the bacteria is crucial to preventing its transmission in hospitals and the environment. Thus, our objective was to determine the antibiotic susceptibility profiles of twenty-five P. aeruginosa isolates from UTIs at the Medical Center of Trás-os-Montes and Alto Douro (CHTMAD). Biofilm formation and motility are also virulence factors studied in this work. Out of the twenty-five P. aeruginosa isolates, 16% exhibited multidrug resistance, being resistant to at least three classes of antibiotics. However, the isolates showed a high prevalence of susceptibility to amikacin and tobramycin. Resistance to carbapenem antibiotics, essential for treating infections when other antibiotics fail, was low in this study, Notably, 92% of the isolates demonstrated intermediate sensitivity to ciprofloxacin, raising concerns about its efficacy in controlling the disease. Genotypic analysis revealed the presence of various β-lactamase genes, with class B metallo-β-lactamases (MBLs) being the most common. The bla_NDM, bla_S_PM, and bla_VIM-VIM2 genes were detected in 16%, 60%, and 12% of the strains, respectively. The presence of these genes highlights the emerging threat of MBL-mediated resistance. Additionally, virulence gene analysis showed varying prevalence rates among the strains. The exoU gene, associated with cytotoxicity, was found in only one isolate, while other genes such as exoS, exoA, exoY, and exoT had a high prevalence. The toxA and lasB genes were present in all isolates, whereas the lasA gene was absent. The presence of various virulence genes suggests the potential of these strains to cause severe infections. This pathogen demonstrated proficiency in producing biofilms, as 92% of the isolates were found to be capable of doing so. Currently, antibiotic resistance is one of the most serious public health problems, as options become inadequate with the continued emergence and spread of multidrug-resistant strains, combined with the high rate of biofilm production and the ease of dissemination. In conclusion, this study provides insights into the antibiotic resistance and virulence profiles of P. aeruginosa strains isolated from human urine infections, highlighting the need for continued surveillance and appropriate therapeutic approaches. Full article

(This article belongs to the Special Issue Molecular Epidemiology of Antimicrobial Resistance, 2nd Edition)

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34 pages, 1433 KiB

Open AccessReview

Fermented Beverage Benefits: A Comprehensive Review and Comparison of Kombucha and Kefir Microbiome

by Ann Qi Chong, Siew Wen Lau, Nyuk Ling Chin, Rosnita A. Talib and Roseliza Kadir Basha

Microorganisms 2023, 11(5), 1344; https://doi.org/10.3390/microorganisms11051344 - 19 May 2023

Cited by 20 | Viewed by 9217

Abstract

Beverage fermentation is an ancient ritual that has been practised for millennia. It was slowly disappearing from households and communities due to the advancement of manufacturing technology and the marketing of soft drinks until the recent revival of the beverage fermentation culture due [...] Read more.

Beverage fermentation is an ancient ritual that has been practised for millennia. It was slowly disappearing from households and communities due to the advancement of manufacturing technology and the marketing of soft drinks until the recent revival of the beverage fermentation culture due to an increase in the demand for health drinks amid the COVID-19 pandemic. Kombucha and kefir are two well-known fermented beverages that are renowned for their myriad of health benefits. The starter materials for making these beverages contain micro-organisms that act like microscopic factories producing beneficial nutrients that have antimicrobial and anticancer effects. The materials modulate the gut microbiota and promote positive effects on the gastrointestinal tract. Due to wide variations in the substrates and types of micro-organisms involved in the production of both kombucha and kefir, this paper compiles a compendium of the micro-organisms present and highlights their nutritional roles. Full article

(This article belongs to the Special Issue Latest Review Papers in Food Microbiology 2023)

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11 pages, 1521 KiB

Open AccessArticle

Localization of C Cycle Enzymes in Arable and Forest Phaeozems within Levels of Soil Microstructure

by Anna Yudina, Olga Ovchinnikova, Vladimir Cheptsov and Dmitry Fomin

Microorganisms 2023, 11(5), 1343; https://doi.org/10.3390/microorganisms11051343 - 19 May 2023

Cited by 2 | Viewed by 1538

Abstract

Soil microbial and enzyme activities are closely related to the spatial variability of soil environmental conditions at the microscale (μm-mm). The origin and localization of the enzymes are somewhat neglected when the measured activity is used to evaluate specific soil functions. The activity [...] Read more.

Soil microbial and enzyme activities are closely related to the spatial variability of soil environmental conditions at the microscale (μm-mm). The origin and localization of the enzymes are somewhat neglected when the measured activity is used to evaluate specific soil functions. The activity of four hydrolytic enzymes (β-glucosidase, Cellobiohydrolase, Chitinase, Xylanase) and microbial diversity based on community-level physiological profiling were determined in samples of arable and native Phaeozems with increasing physical impact to soil solids. The level of impact on the soil solids had a significant effect on enzyme activity and depended on both the enzyme type and soil land use. The highest proportion of the activity of Xylanase and Cellobiohydrolase of arable Phaeozem was determined at the dispersion energy in the range of 450–650 J·mL⁻¹ and was associated with the primary soil particles’ hierarchy level. The highest proportions of β-glucosidase and Chitinase activities were determined for forest Phaeozem after applying energies lower than 150 J·mL⁻¹ and characterizing the level of soil microaggregates. The increased activity of Xylanase and Cellobiohydrolase in primary soil particles of arable soil compared to those in forest soil might be a reflection of the substrates being unavailable to decomposition, leading to enzyme accumulation on the solid surface. For the Phaeozems, the lower the level of soil microstructure organization, the greater the differences observed between soils of different land use type, i.e., microbial communities, associated with lower microstructure levels, were more specific to land use type. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 812 KiB

Open AccessArticle

Favipiravir Suppresses Zika Virus (ZIKV) through Activity as a Mutagen

by Evelyn J. Franco, Eleonora Cella, Xun Tao, Kaley C. Hanrahan, Taj Azarian and Ashley N. Brown

Microorganisms 2023, 11(5), 1342; https://doi.org/10.3390/microorganisms11051342 - 19 May 2023

Cited by 4 | Viewed by 1534

Abstract

In a companion paper, we demonstrated that the nucleoside analogue favipiravir (FAV) suppressed Zika virus (ZIKV) replication in three human-derived cell lines—HeLa, SK-N-MC, and HUH-7. Our results revealed that FAV’s effect was most pronounced in HeLa cells. In this work, we aimed to [...] Read more.

In a companion paper, we demonstrated that the nucleoside analogue favipiravir (FAV) suppressed Zika virus (ZIKV) replication in three human-derived cell lines—HeLa, SK-N-MC, and HUH-7. Our results revealed that FAV’s effect was most pronounced in HeLa cells. In this work, we aimed to explain variation in FAV activity, investigating its mechanism of action and characterizing host cell factors relevant to tissue-specific differences in drug effect. Using viral genome sequencing, we show that FAV therapy was associated with an increase in the number of mutations and promoted the production of defective viral particles in all three cell lines. Our findings demonstrate that defective viral particles made up a larger portion of the viral population released from HeLa cells both at increasing FAV concentrations and at increasing exposure times. Taken together, our companion papers show that FAV acts via lethal mutagenesis against ZIKV and highlight the host cell’s influence on the activation and antiviral activity of nucleoside analogues. Furthermore, the information gleaned from these companion papers can be applied to gain a more comprehensive understanding of the activity of nucleoside analogues and the impact of host cell factors against other viral infections for which we currently have no approved antiviral therapies. Full article

(This article belongs to the Special Issue Recent Advances in Antivirals for Emerging Viruses 2.0)

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26 pages, 8016 KiB

Open AccessArticle

Identification of Fungicide Combinations Targeting Plasmopara viticola and Botrytis cinerea Fungicide Resistance Using Machine Learning

by Junrui Zhang and Sandun D. Fernando

Microorganisms 2023, 11(5), 1341; https://doi.org/10.3390/microorganisms11051341 - 19 May 2023

Cited by 7 | Viewed by 2027

Abstract

Downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea) are fungal diseases that significantly impact grape production globally. Cytochrome b plays a significant role in the mitochondrial respiratory chain of the two fungi that cause these diseases [...] Read more.

Downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea) are fungal diseases that significantly impact grape production globally. Cytochrome b plays a significant role in the mitochondrial respiratory chain of the two fungi that cause these diseases and is a key target for quinone outside inhibitor (QoI)-based fungicide development. Since the mode of action (MOA) of QoI fungicides is restricted to a single active site, the risk of developing resistance to these fungicides is deemed high. Consequently, using a combination of fungicides is considered an effective way to reduce the development of QoI resistance. Currently, there is little information available to help in the selection of appropriate fungicides. This study used a combination of in silico simulations and quantitative structure–activity relationship (QSAR) machine learning algorithms to screen the most potent QoI-based fungicide combinations for wild-type (WT) and the G143A mutation of fungal cytochrome b. Based on in silico studies, mandestrobin emerged as the top binder for both WT Plasmopara viticola and WT Botrytis cinerea cytochrome b. Famoxadone appeared to be a versatile binder for G143A-mutated cytochrome b of both Plasmopara viticola and Botrytis cinerea. Thiram emerged as a reasonable, low-risk non-QoI fungicide that works on WT and G143A-mutated versions of both fungi. QSAR analysis revealed fenpropidin, fenoxanil, and ethaboxam non-QoIs to have a high affinity for G143A-mutated cytochrome b of Plasmopara viticola and Botrytis cinerea. Above-QoI and non-QoI fungicides can be considered for field studies in a fungicide management program against Plasmopara viticola- and Botrytis cinerea-based fungal infections. Full article

(This article belongs to the Special Issue Advances in Antibiotic and Drug-Resistance Mechanisms)

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11 pages, 916 KiB

Open AccessReview

Mutualistic Relationships between Microorganisms and Eusocial Wasps (Hymenoptera, Vespidae)

by Stefano Turillazzi, Niccolò Meriggi and Duccio Cavalieri

Microorganisms 2023, 11(5), 1340; https://doi.org/10.3390/microorganisms11051340 - 19 May 2023

Cited by 3 | Viewed by 1909

Abstract

Eusocial wasps are represented in the Vespidae by the subfamilies Stenogastrinae, Vespinae and Polistinae. These wasps present colonies that are sometimes composed of thousands of individuals which live in nests built with paper materials. The high density of the adult and larval population, [...] Read more.

Eusocial wasps are represented in the Vespidae by the subfamilies Stenogastrinae, Vespinae and Polistinae. These wasps present colonies that are sometimes composed of thousands of individuals which live in nests built with paper materials. The high density of the adult and larval population, as well as the stable micro environment of the nests, make very favourable conditions for the flourishing of various types of microorganisms. These microorganisms, which may be pathogens, are beneficial and certainly contribute to model the sociality of these insects. The mutualistic relationships that we observe in some species, especially in Actinomycete bacteria and yeasts, could have important fallouts for the development of new medicines and for the use of these insects in agricultural environments. Full article

(This article belongs to the Special Issue Macro and Microorganism Interactions 2.0)

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27 pages, 1234 KiB

Open AccessReview

Epizootic Hemorrhagic Disease Virus: Current Knowledge and Emerging Perspectives

by Luis Jiménez-Cabello, Sergio Utrilla-Trigo, Gema Lorenzo, Javier Ortego and Eva Calvo-Pinilla

Microorganisms 2023, 11(5), 1339; https://doi.org/10.3390/microorganisms11051339 - 19 May 2023

Cited by 18 | Viewed by 7261

Abstract

Epizootic Hemorrhagic Disease (EHD) of ruminants is a viral pathology that has significant welfare, social, and economic implications. The causative agent, epizootic hemorrhagic disease virus (EHDV), belongs to the Orbivirus genus and leads to significant regional disease outbreaks among livestock and wildlife in [...] Read more.

Epizootic Hemorrhagic Disease (EHD) of ruminants is a viral pathology that has significant welfare, social, and economic implications. The causative agent, epizootic hemorrhagic disease virus (EHDV), belongs to the Orbivirus genus and leads to significant regional disease outbreaks among livestock and wildlife in North America, Asia, Africa, and Oceania, causing significant morbidity and mortality. During the past decade, this viral disease has become a real threat for countries of the Mediterranean basin, with the recent occurrence of several important outbreaks in livestock. Moreover, the European Union registered the first cases of EHDV ever detected within its territory. Competent vectors involved in viral transmission, Culicoides midges, are expanding its distribution, conceivably due to global climate change. Therefore, livestock and wild ruminants around the globe are at risk for this serious disease. This review provides an overview of current knowledge about EHDV, including changes of distribution and virulence, an examination of different animal models of disease, and a discussion about potential treatments to control the disease. Full article

(This article belongs to the Special Issue Climate Change and Emerging Arboviruses)

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26 pages, 2392 KiB

Open AccessReview

Inside Current Winemaking Challenges: Exploiting the Potential of Conventional and Unconventional Yeasts

by Nunzio A. Fazio, Nunziatina Russo, Paola Foti, Alessandra Pino, Cinzia Caggia and Cinzia L. Randazzo

Microorganisms 2023, 11(5), 1338; https://doi.org/10.3390/microorganisms11051338 - 19 May 2023

Cited by 12 | Viewed by 3463

Abstract

Wine represents a complex matrix in which microbial interactions can strongly impact the quality of the final product. Numerous studies have focused on optimizing microbial approaches for addressing new challenges to enhance quality, typicity, and food safety. However, few studies have investigated yeasts [...] Read more.

Wine represents a complex matrix in which microbial interactions can strongly impact the quality of the final product. Numerous studies have focused on optimizing microbial approaches for addressing new challenges to enhance quality, typicity, and food safety. However, few studies have investigated yeasts of different genera as resources for obtaining wines with new, specific traits. Currently, based on the continuous changes in consumer demand, yeast selection within conventional Saccharomyces cerevisiae and unconventional non-Saccharomyces yeasts represents a suitable opportunity. Wine fermentation driven by indigenous yeasts, in the various stages, has achieved promising results in producing wines with desired characteristics, such as a reduced content of ethanol, SO₂, and toxins, as well as an increased aromatic complexity. Therefore, the increasing interest in organic, biodynamic, natural, or clean wine represents a new challenge for the wine sector. This review aims at exploring the main features of different oenological yeasts to obtain wines reflecting the needs of current consumers in a sustainability context, providing an overview, and pointing out the role of microorganisms as valuable sources and biological approaches to explore potential and future research opportunities. Full article

(This article belongs to the Special Issue Latest Review Papers in Food Microbiology 2023)

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15 pages, 1895 KiB

Open AccessArticle

Importance of Pre-Milking Udder Hygiene to Reduce Transfer of Clostridial Spores from Teat Skin to Raw Milk

by Johanna Burtscher, Tamara Rudavsky, Ulrike Zitz, Viktoria Neubauer and Konrad J. Domig

Microorganisms 2023, 11(5), 1337; https://doi.org/10.3390/microorganisms11051337 - 19 May 2023

Cited by 5 | Viewed by 2299

Abstract

Butyric acid producing clostridia (BAPC) cause the so-called late-blowing defect, a serious quality problem in semi-hard and hard cheeses. Late-blown cheeses are characterized by undesired slits and cracks, irregular eyes, and off-flavors due to excessive amounts of gas and organic acids produced by [...] Read more.

Butyric acid producing clostridia (BAPC) cause the so-called late-blowing defect, a serious quality problem in semi-hard and hard cheeses. Late-blown cheeses are characterized by undesired slits and cracks, irregular eyes, and off-flavors due to excessive amounts of gas and organic acids produced by clostridia. Clostridial transfer to raw milk can occur during milking through dirty teats. Therefore, teat cleaning before milking is a key factor in preventing clostridial contamination of the milk. However, different cleaning methods are used, and little information is available on the efficacy of routine teat cleaning in reducing clostridial endospores. The main objectives of this study were to assess the extent of udder contamination with BAPC spores and to investigate the efficacy of routine teat cleaning on BAPC spore counts in milk. In a longitudinal study, eight dairy farms were visited during five sampling events. Clostridial spore counts were quantified from teat skin before and after routine teat cleaning, in pooled quarter milk samples from individual cows, and in bulk tank milk samples using a most probable number method. In addition, farm management data were collected periodically through a survey, and average cow cleanliness was assessed by a veterinarian. On average, teat cleaning resulted in a 0.6 log unit reduction in BAPC spores on teat skin, and a strong positive correlation was found between BAPC spore concentrations on teat skin after cleaning and in pooled quarter milk samples. Seasonal variations and the potential influence of differences in farm management were also noted. Interestingly, average cow cleanliness correlated strongly with BAPC spore levels in milk, suggesting the potential for a quick and rough estimation method of clostridial contamination that could be implemented by farmers. Full article

(This article belongs to the Section Food Microbiology)

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12 pages, 4516 KiB

Open AccessArticle

Ectothiorhodospira lacustris sp. nov., a New Purple Sulfur Bacterium from Low-Mineralized Soda Lakes That Contains a Unique Pathway for Nitric Oxide Reduction

by Irina A. Bryantseva, John A. Kyndt, Vladimir M. Gorlenko and Johannes F. Imhoff

Microorganisms 2023, 11(5), 1336; https://doi.org/10.3390/microorganisms11051336 - 19 May 2023

Cited by 2 | Viewed by 2160

Abstract

Several strains of a Gram-negative, anaerobic photoautotrophic, motile, rod-shaped bacterium, designated as B14B, A-7R, and A-7Y were isolated from biofilms of low-mineralized soda lakes in central Mongolia and Russia (southeast Siberia). They had lamellar stacks as photosynthetic structures and bacteriochlorophyll a as the [...] Read more.

Several strains of a Gram-negative, anaerobic photoautotrophic, motile, rod-shaped bacterium, designated as B14B, A-7R, and A-7Y were isolated from biofilms of low-mineralized soda lakes in central Mongolia and Russia (southeast Siberia). They had lamellar stacks as photosynthetic structures and bacteriochlorophyll a as the major photosynthetic pigment. The strains were found to grow at 25–35 °C, pH 7.5–10.2 (optimum, pH 9.0), and with 0–8% (w/v) NaCl (optimum, 0%). In the presence of sulfide and bicarbonate, acetate, butyrate, yeast extract, lactate, malate, pyruvate, succinate, and fumarate promoted growth. The DNA G + C content was 62.9–63.0 mol%. While the 16S rRNA gene sequences confirmed that the new strains belonged to the genus Ectothiorhodospira of the Ectothiorhodospiraceae, comparison of the genome nucleotide sequences of strains B14B, A-7R, and A-7Y revealed that the new isolates were remote from all described Ectothiorhodospira species both in dDDH (19.7–38.8%) and in ANI (75.0–89.4%). The new strains are also genetically differentiated by the presence of a nitric oxide reduction pathway that is lacking from all other Ectiothiorhodospiraceae. We propose to assign the isolates to the new species, Ectothiorhodospira lacustris sp. nov., with the type strain B14B^T (=DSM 116064^T = KCTC 25542^T = UQM 41491^T). Full article

(This article belongs to the Special Issue Phototrophic Bacteria 2.0)

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34 pages, 1097 KiB

Open AccessReview

Viability of Probiotic Microorganisms and the Effect of Their Addition to Fruit and Vegetable Juices

by Maria Spinasse Maia, Manueli Monciozo Domingos and Jackline Freitas Brilhante de São José

Microorganisms 2023, 11(5), 1335; https://doi.org/10.3390/microorganisms11051335 - 19 May 2023

Cited by 11 | Viewed by 5070

Abstract

Consumers’ recent interest in healthier diets has increased the demand for food products with functional properties, such as probiotics. However, most probiotic food types available on the market are of dairy origin, which limits their consumption by individuals with food intolerances and by [...] Read more.

Consumers’ recent interest in healthier diets has increased the demand for food products with functional properties, such as probiotics. However, most probiotic food types available on the market are of dairy origin, which limits their consumption by individuals with food intolerances and by those who adhere to strict vegan and vegetarian diets. The aim of the current review is to assess both the limitations and impacts of the addition of probiotic microorganisms to fruit, vegetable, and/or mixed juices. Thus, an integrative literature review was herein carried out. A bibliographic survey was carried out in the following databases: Lilacs, Medline, Web of Science, Scopus, and Scielo. In addition, searches for studies published in English from 2010 to 2021 were carried out, based on the following meshes: “fruit”, ‘‘vegetable”, ‘‘juice”, and “probiotics”, which were used both in combination with each other and with Boolean operators such as “AND” and “OR”. Although 254 articles were initially found in the literature search, only 21 of them were selected to compose the final sample. The included studies mainly addressed microorganism viability and physicochemical analyses. Overall, fruit and/or vegetable juices can be suitable matrices used to help the development of probiotic food types. However, the microorganisms added to these products must be capable of adapting to and surviving in them to enable a product’s success. Therefore, factors such as pH, fiber content, amino acids, and phenolic compounds play an essential role in the survival of probiotic microorganisms. Given the wide variety of analyses, a comparison between parameters was the major limitation of the present study. Future studies should focus on filling the gaps persisting in the development of probiotic fruit and/or vegetable juices as well as mixed juices. Full article

(This article belongs to the Special Issue New Perspectives on the Action of Probiotics against Food Contaminants)

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19 pages, 1453 KiB

Open AccessReview

Probiotics and Commensal Bacteria Metabolites Trigger Epigenetic Changes in the Gut and Influence Beneficial Mood Dispositions

by Luis Vitetta, Matthew Bambling and Esben Strodl

Microorganisms 2023, 11(5), 1334; https://doi.org/10.3390/microorganisms11051334 - 18 May 2023

Cited by 6 | Viewed by 3639

Abstract

The effect of the intestinal microbiome on the gut–brain axis has received considerable attention, strengthening the evidence that intestinal bacteria influence emotions and behavior. The colonic microbiome is important to health and the pattern of composition and concentration varies extensively in complexity from [...] Read more.

The effect of the intestinal microbiome on the gut–brain axis has received considerable attention, strengthening the evidence that intestinal bacteria influence emotions and behavior. The colonic microbiome is important to health and the pattern of composition and concentration varies extensively in complexity from birth to adulthood. That is, host genetics and environmental factors are complicit in shaping the development of the intestinal microbiome to achieve immunological tolerance and metabolic homeostasis from birth. Given that the intestinal microbiome perseveres to maintain gut homeostasis throughout the life cycle, epigenetic actions may determine the effect on the gut–brain axis and the beneficial outcomes on mood. Probiotics are postulated to exhibit a range of positive health benefits including immunomodulating capabilities. Lactobacillus and Bifidobacterium are genera of bacteria found in the intestines and so far, the benefits afforded by ingesting bacteria such as these as probiotics to people with mood disorders have varied in efficacy. Most likely, the efficacy of probiotic bacteria at improving mood has a multifactorial dependency, relying namely on several factors that include the agents used, the dose, the pattern of dosing, the pharmacotherapy used, the characteristics of the host and the underlying luminal microbial environment (e.g., gut dysbiosis). Clarifying the pathways linking probiotics with improvements in mood may help identify the factors that efficacy is dependent upon. Adjunctive therapies with probiotics for mood disorders could, through DNA methylation molecular mechanisms, augment the intestinal microbial active cohort and endow its mammalian host with important and critical co-evolutionary redox signaling metabolic interactions, that are embedded in bacterial genomes, and that in turn can enhance beneficial mood dispositions. Full article

(This article belongs to the Special Issue Functional Foods, Prebiotics and Probiotics Strengthening Intestinal Microbiome Health)

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12 pages, 701 KiB

Open AccessArticle

Changes in the Incidence of Invasive Pneumococcal Disease in Calgary, Canada, during the SARS-CoV-2 Pandemic 2020–2022

by Leah J. Ricketson and James D. Kellner

Microorganisms 2023, 11(5), 1333; https://doi.org/10.3390/microorganisms11051333 - 18 May 2023

Cited by 7 | Viewed by 2272

Abstract

We describe the impact of non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic on invasive pneumococcal disease (IPD) in Calgary. IPD declined significantly worldwide during 2020 and 2021. This may be due to the reduced transmission of and decrease in circulating viruses that often [...] Read more.

We describe the impact of non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic on invasive pneumococcal disease (IPD) in Calgary. IPD declined significantly worldwide during 2020 and 2021. This may be due to the reduced transmission of and decrease in circulating viruses that often co-infect with the opportunistic pneumococcus. Pneumococcus has not been shown to frequently co-infect or cause secondary infection with SARS-CoV-2. We examined and compared incidence rates in Calgary per quarter in the pre-vaccine, post-vaccine, 2020 and 2021 (pandemic) and 2022 (late pandemic) eras. We also conducted a time series analysis from 2000–2022 allowing for change in trend at introduction of vaccines and for initiation of NPIs during the COVID-19 pandemic. Incidence declined in 2020/2021 but by the end of 2022 had begun to rapidly recover to near pre-vaccine rates. This recovery may be related to the high rates of viral activity in the winter of 2022 along with childhood vaccines being delayed during the pandemic. However, a large proportion of the IPD caused in the last quarter of 2022 was serotype 4, which has caused outbreaks in the homeless population of Calgary in the past. Further surveillance will be important to understand IPD incidence trends in the post-pandemic landscape. Full article

(This article belongs to the Special Issue Infectious Disease Epidemiology and Modelling)

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12 pages, 683 KiB

Open AccessArticle

Phenotypic Variation in Clinical S. aureus Isolates Did Not Affect Disinfection Efficacy Using Short-Term UV-C Radiation

by Birte Knobling, Gefion Franke, Laura Carlsen, Cristina Belmar Campos, Henning Büttner, Eva M. Klupp, Philipp Maximilian Maurer and Johannes K. Knobloch

Microorganisms 2023, 11(5), 1332; https://doi.org/10.3390/microorganisms11051332 - 18 May 2023

Cited by 1 | Viewed by 1709

Abstract

Pigmentation, catalase activity and biofilm formation are virulence factors that cause resistance of Staphylococcus aureus to environmental stress factors including disinfectants. In recent years, automatic UV-C room disinfection gained greater importance in enhanced disinfection procedures to improve disinfection success in hospitals. In this [...] Read more.

Pigmentation, catalase activity and biofilm formation are virulence factors that cause resistance of Staphylococcus aureus to environmental stress factors including disinfectants. In recent years, automatic UV-C room disinfection gained greater importance in enhanced disinfection procedures to improve disinfection success in hospitals. In this study, we evaluated the effect of naturally occurring variations in the expression of virulence factors in clinical S. aureus isolates on tolerance against UV-C radiation. Quantification of staphyloxanthin expression, catalase activity and biofilm formation for nine genetically different clinical S. aureus isolates as well as reference strain S. aureus ATCC 6538 were performed using methanol extraction, a visual approach assay and a biofilm assay, respectively. Log₁₀ reduction values (LRV) were determined after irradiation of artificially contaminated ceramic tiles with 50 and 22 mJ/cm² UV-C using a commercial UV-C disinfection robot. A wide variety of virulence factor expression was observed, indicating differential regulation of global regulatory networks. However, no direct correlation with the strength of expression with UV-C tolerance was observed for either staphyloxanthin expression, catalase activity or biofilm formation. All isolates were effectively reduced with LRVs of 4.75 to 5.94. UV-C disinfection seems therefore effective against a wide spectrum of S. aureus strains independent of occurring variations in the expression of the investigated virulence factors. Due to only minor differences, the results of frequently used reference strains seem to be representative also for clinical isolates in S. aureus. Full article

(This article belongs to the Special Issue Research in Hospital Infection Control 2.0)

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17 pages, 4523 KiB

Open AccessEditor’s ChoiceArticle

Klebsiella aerogenes Adhesion Behaviour during Biofilm Formation on Monazite

by Arya Van Alin, Melissa K. Corbett, Homayoun Fathollahzadeh, M. Christian Tjiam, Andrew Putnis, Jacques Eksteen, Anna H. Kaksonen and Elizabeth Watkin

Microorganisms 2023, 11(5), 1331; https://doi.org/10.3390/microorganisms11051331 - 18 May 2023

Cited by 2 | Viewed by 1658

Abstract

The adsorption behaviour of micro-organisms during the initial attachment stage of biofilm formation affects subsequent stages. The available area for attachment and the chemophysical properties of a surface affect microbial attachment performance. This study focused on the initial attachment behaviour of Klebsiella aerogenes [...] Read more.

The adsorption behaviour of micro-organisms during the initial attachment stage of biofilm formation affects subsequent stages. The available area for attachment and the chemophysical properties of a surface affect microbial attachment performance. This study focused on the initial attachment behaviour of Klebsiella aerogenes on monazite by measuring the ratio of planktonic against sessile subpopulations (P:S ratio), and the potential role of extracellular DNA (eDNA). eDNA production, effects of physicochemical properties of the surface, particle size, total available area for attachment, and the initial inoculation size on the attachment behaviour were tested. K. aerogenes attached to monazite immediately after exposure to the ore; however, the P:S ratio significantly (p = 0.05) changed in response to the particle size, available area, and inoculation size. Attachment occurred preferentially on larger-sized (~50 µm) particles, and either decreasing the inoculation size or increasing the available area further promoted attachment. Nevertheless, a portion of the inoculated cells always remained in a planktonic state. K. aerogenes produced lower eDNA in response to the changed surface chemical properties when monazite was replaced by xenotime. Using pure eDNA to cover the monazite surface significantly (p ≤ 0.05) hindered bacterial attachment due to the repulsive interaction between the eDNA layer and bacteria. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Biofilms)

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Open AccessArticle

Gausemycin A-Resistant Staphylococcus aureus Demonstrates Affected Cell Membrane and Cell Wall Homeostasis

by Darya V. Poshvina, Diana S. Dilbaryan and Alexey S. Vasilchenko

Microorganisms 2023, 11(5), 1330; https://doi.org/10.3390/microorganisms11051330 - 18 May 2023

Cited by 1 | Viewed by 1749

Abstract

Antibiotic resistance is a significant and pressing issue in the medical field, as numerous strains of infectious bacteria have become resistant to commonly prescribed antibiotics. Staphylococcus aureus is a bacterium that poses a grave threat, as it is responsible for a large number [...] Read more.

Antibiotic resistance is a significant and pressing issue in the medical field, as numerous strains of infectious bacteria have become resistant to commonly prescribed antibiotics. Staphylococcus aureus is a bacterium that poses a grave threat, as it is responsible for a large number of nosocomial infections and has high mortality rates worldwide. Gausemycin A is a new lipoglycopeptide antibiotic that has considerable efficacy against multidrug-resistant S. aureus strains. Although the cellular targets of gausemycin A have been previously identified, detailing the molecular processes of action is still needed. We performed gene expression analysis to identify molecular mechanisms that may be involved in bacterial resistance to gausemycin A. In the present study, we observed that gausemycin A-resistant S. aureus in the late-exponential phase showed an increased expression of genes involved in cell wall turnover (sceD), membrane charge (dltA), phospholipid metabolism (pgsA), the two-component stress-response system (vraS), and the Clp proteolytic system (clpX). The increased expression of these genes implies that changes in the cell wall and cell membrane are essential for the bacterial resistance to gausemycin A. In the stationary phase, we observed a decrease in the expression of genes involved in the phospholipid metabolism (mprF) and Clp proteolytic system (clpX). Full article

(This article belongs to the Special Issue Research on Antimicrobial Activity of Natural Products)

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