Microorganisms

14 pages, 5075 KiB

Open AccessArticle

Exploring the Potential of Bacillus subtilis IS1 and B. amyloliquificiens IS6 to Manage Salinity Stress and Fusarium Wilt Disease in Tomato Plants by Induced Physiological Responses

by Waheed Akram, Shama Sharif, Areeba Rehman, Tehmina Anjum, Basharat Ali, Zill-e-Huma Aftab, Ayesha Shafqat, Laiba Afzal, Bareera Munir, Humaira Rizwana and Guihua Li

Microorganisms 2024, 12(10), 2092; https://doi.org/10.3390/microorganisms12102092 (registering DOI) - 19 Oct 2024

Abstract

The intensified concerns related to agrochemicals’ ecological and health risks have encouraged the exploration of microbial agents as eco-friendly alternatives. Some members of Bacillus spp. are potential plant-growth-promoting agents and benefit numerous crop plants globally. This study aimed to explore the beneficial effects [...] Read more.

The intensified concerns related to agrochemicals’ ecological and health risks have encouraged the exploration of microbial agents as eco-friendly alternatives. Some members of Bacillus spp. are potential plant-growth-promoting agents and benefit numerous crop plants globally. This study aimed to explore the beneficial effects of two Bacillus strains (B. subtilis strain IS1 and B. amyloliquificiens strain IS6) capable of alleviating the growth of tomato plants against salinity stress and Fusarium wilt disease. These strains were able to significantly promote the growth of tomato plants and biomass accumulation in pot trials in the absence of any stress. Under salinity stress conditions (150 mM NaCl), B. subtilis strain IS1 demonstrated superior performance and significantly increased shoot length (45.74%), root length (101.39%), fresh biomass (62.17%), and dry biomass (49.69%) contents compared to control plants. Similarly, B. subtilis strain IS1 (63.7%) and B. amyloliquificiens strain IS6 (32.1%) effectively suppressed Fusarium wilt disease and significantly increased plant growth indices compared to the pathogen control. Furthermore, these strains increased the production of chlorophyll, carotenoid, and total phenolic contents. They significantly affected the activities of enzymes involved in antioxidant machinery and the phenylpropanoid pathway. Hence, this study effectively demonstrates that these Bacillus strains can effectively alleviate the growth of tomato plants under multiple stress conditions and can be used to develop bio-based formulations for use in the fields. Full article

(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)

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14 pages, 590 KiB

Open AccessArticle

Parameter Estimation of Host Genomic and Gut Microbiota Contribution to Growth and Feed Efficiency Traits in Meat Rabbits

by Xinyang Tian, Junkun Zhou, Yinghe Qin, Kai Zhang, Wenqiang Sun, Song-Jia Lai, Xianbo Jia and Shi-Yi Chen

Microorganisms 2024, 12(10), 2091; https://doi.org/10.3390/microorganisms12102091 (registering DOI) - 19 Oct 2024

Abstract

Rabbits can efficiently utilize plant fibers that are indigestible to humans, and hence may contribute to the alleviation of feed–food competition. Therefore, it is economically and ecologically important to genetically improve the growth performance and feed efficiency of meat rabbits. In this study, [...] Read more.

Rabbits can efficiently utilize plant fibers that are indigestible to humans, and hence may contribute to the alleviation of feed–food competition. Therefore, it is economically and ecologically important to genetically improve the growth performance and feed efficiency of meat rabbits. In this study, we combined pedigree, genomic, and gut microbiota data to estimate genetic and microbial parameters for nine growth and feed efficiency traits of 739 New Zealand White rabbits, including body weight (BW) at 35 (BW35), 70 (BW70), and 84 (BW84) days of age, and average daily gain (ADG), feed conversion ratio (FCR), and residual feed intake (RFI) within two age intervals of 35–70 days (ADG70, FCR70, and RFI70) and 35–84 days (ADG84, FCR84, and RFI84). Based on single-step genomic best linear unbiased prediction, three BW traits and two ADG traits had the high estimates (±standard error, SE) of heritability, ranging from 0.44 ± 0.13 of BW35 to 0.66 ± 0.08 of BW70. Moderate heritabilities were observed for RFI70 (0.22 ± 0.07) and RFI84 (0.29 ± 0.07), whereas the estimates did not significantly deviate from zero for the two FCR traits. There was moderate positive genetic correlation (±SE) between BW70 and ADG70 (0.579 ± 0.086), but BW70 did not correlate with RFI70. Based on microbial best linear unbiased prediction, the estimates of microbiability did not significantly deviate from zero for any trait. Based on the combined use of genomic and gut microbiota data, the parameters obtained in this study could help us to implement efficient breeding schemes in meat rabbits. Full article

(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)

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10 pages, 248 KiB

Open AccessArticle

The Incidence and Characteristics of Oral Candidiasis in Patients Hospitalized for SARS-CoV-2 Infection During the Circulation of Alpha, Beta, and Delta Variants

by Elena Camelia Kouris, Sînziana Irina Mirea, Monica Luminița Luminos and Victor Daniel Miron

Microorganisms 2024, 12(10), 2090; https://doi.org/10.3390/microorganisms12102090 (registering DOI) - 18 Oct 2024

Viewed by 245

Abstract

Background: Oral candidiasis has been documented in patients with SARS-CoV-2 infection, with varying prevalence rates across geographic regions and patient demographics. This study aimed to ascertain the incidence, characteristics, and risk factors associated with the development of oral candidiasis in patients hospitalized for [...] Read more.

Background: Oral candidiasis has been documented in patients with SARS-CoV-2 infection, with varying prevalence rates across geographic regions and patient demographics. This study aimed to ascertain the incidence, characteristics, and risk factors associated with the development of oral candidiasis in patients hospitalized for SARS-CoV-2 infection in a tertiary infectious diseases hospital in Romania. Methods: A retrospective analysis was conducted on adult patients hospitalized between March 2020 and December 2022 with moderate or severe forms of SARS-CoV-2 infection, for whom a culture of lingual scrapings for Candida spp. was performed. Results: A total of 294 patients were deemed eligible for inclusion in the analysis, with an incidence rate of oral candidiasis of 17.0%. The incidence of oral candidiasis was 4.2 times higher in patients with severe forms of SARS-CoV-2 infection compared to those with moderate forms. Patients with a diagnosis of COVID-19 and oral candidiasis were more likely to receive antibiotics (98.0% vs. 86.1%, p = 0.017) and corticosteroids (100% vs. 83.6%, p = 0.003) than those without oral candidiasis. These findings were associated with a 19% higher relative risk of developing oral candidiasis for patients who received corticosteroid therapy compared to those who did not, and a 13% higher relative risk for those who were administered antibiotics compared to those who were not. The presence of respiratory insufficiency increased the odds of oral candidiasis association 4.7-fold (88.0% vs. 61.1%, p < 0.001). Conclusions: Although the data have been analyzed retrospectively, we have shown that individuals with severe forms of COVID-19 exhibited an elevated risk of developing oral candidiasis. The administration of antibiotics and corticosteroids was identified as a positive predictor for the development of oral candidiasis. The data presented here suggest that a key aspect of the therapeutic management of patients with SARS-CoV-2 infection should include the implementation of preventive measures to minimize the risk of secondary fungal infections. Full article

(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection—Third Edition)

13 pages, 3297 KiB

Open AccessArticle

Characterization and Antibacterial Activity of Silver Nanoparticles Synthesized from Oxya chinensis sinuosa (Grasshopper) Extract

by Se-Min Kim, Tai-Yong Kim, Yun-Sang Choi, Gyeongsik Ok and Min-Cheol Lim

Microorganisms 2024, 12(10), 2089; https://doi.org/10.3390/microorganisms12102089 - 18 Oct 2024

Viewed by 242

Abstract

In this study, silver nanoparticles (AgNPs) were synthesized using a green method from an extract of the edible insect Oxya chinensis sinuosa (O_extract). The formation of AgNPs (O_AgNPs) was confirmed via UV–vis spectroscopy, and their stability was assessed using Turbiscan analysis. The size [...] Read more.

In this study, silver nanoparticles (AgNPs) were synthesized using a green method from an extract of the edible insect Oxya chinensis sinuosa (O_extract). The formation of AgNPs (O_AgNPs) was confirmed via UV–vis spectroscopy, and their stability was assessed using Turbiscan analysis. The size and morphology of the synthesized particles were characterized using transmission electron microscopy and field-emission scanning electron microscopy. Dynamic light scattering and zeta potential analyses further confirmed the size distribution and dispersion stability of the particles. The average particle size was 111.8 ± 1.5 nm, indicating relatively high stability. The synthesized O_AgNPs were further characterized using X-ray photoelectron spectroscopy (XPS), high-resolution X-ray diffraction (HR-XRD), and Fourier transform infrared (FTIR) spectroscopy. XPS analysis confirmed the chemical composition of the O_AgNP surface, whereas HR-XRD confirmed its crystallinity. FTIR analysis suggested that the O_extract plays a crucial role in the synthesis process. The antibacterial activity of the O_AgNPs was demonstrated using a disk diffusion assay, which revealed effective activity against common foodborne pathogens, including Salmonella Typhimurium, Escherichia coli, Staphylococcus aureus, and Bacillus cereus. O_AgNPs exhibited clear antibacterial activity, with inhibition zones of 15.08 ± 0.45 mm for S. Typhimurium, 15.03 ± 0.15 mm for E. coli, 15.24 ± 0.66 mm for S. aureus, and 13.30 ± 0.16 mm for B. cereus. These findings suggest that the O_AgNPs synthesized from the O_extract have potential for use as antibacterial agents against foodborne bacteria. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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16 pages, 3289 KiB

Open AccessArticle

The Impact of Winter Cover Crops on Soil Nematode Communities and Food Web Stability in Corn and Soybean Cultivation

by Jerry Akanwari, Md Rashedul Islam and Tahera Sultana

Microorganisms 2024, 12(10), 2088; https://doi.org/10.3390/microorganisms12102088 - 18 Oct 2024

Viewed by 179

Abstract

There is increasing adoption of winter cover crops (WCCs) in corn and soybean production in Canada, primarily to reduce erosion and increase soil organic matter content. WCCs have the potential to influence nematode communities by increasing free-living nematodes and decreasing plant-parasitic nematodes or [...] Read more.

There is increasing adoption of winter cover crops (WCCs) in corn and soybean production in Canada, primarily to reduce erosion and increase soil organic matter content. WCCs have the potential to influence nematode communities by increasing free-living nematodes and decreasing plant-parasitic nematodes or vice versa. However, the mechanism by which WCCs change nematode community assemblages still remains a key question in soil food web ecology. We tested the hypothesis that the long-term use of rye (Secale cereale), barley (Hordeum vulgare) and oat (Avena sativa) as monocultures or mixtures promotes nematode communities and improves overall soil health conditions compared to winter fallow. The results from this study revealed that the use of WCCs generally promoted a higher abundance and diversity of nematode communities, whereas plant parasitic nematodes were the most abundant in winter fallow. Moreover, the mixtures of WCCs had more similar nematode communities compared to rye alone and winter fallow. The structure and enrichment indices were higher with WCCs, indicating higher nutrient cycling and soil suppressiveness, which are signs of healthy soil conditions. Furthermore, WCCs significantly reduced the populations of root lesion nematode Pratylenchus, although their numbers recovered and increased during the main crop stages. Additionally, mixtures of WCCs promoted the highest abundance of the stunt nematode Tylenchorhynchus, whereas winter fallow had a higher abundance of the spiral nematode Helicotylenchus during the fallow period and the main crop stages. The results show that the long-term use of cover crops can have a positive impact on nematode communities and the soil food web, but these changes depend on the type of WCCs and how they are used. Full article

(This article belongs to the Topic Evaluating the Functional Value of Agroecosystems under Different Management Scenarios)

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13 pages, 2282 KiB

Open AccessReview

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii—A Blueprint for Nitrogen-Fixing Plants?

by Sayre Barron, Florence Mus and John W. Peters

Microorganisms 2024, 12(10), 2087; https://doi.org/10.3390/microorganisms12102087 - 18 Oct 2024

Viewed by 192

Abstract

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen [...] Read more.

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants. Full article

(This article belongs to the Special Issue Nitrogen-Fixing Microorganisms)

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15 pages, 4532 KiB

Open AccessArticle

Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis

by Linqi Wang, Qinyu Wang and Yan Zhou

Microorganisms 2024, 12(10), 2086; https://doi.org/10.3390/microorganisms12102086 - 18 Oct 2024

Viewed by 219

Abstract

Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, [...] Read more.

Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, genetic evidence supporting this mechanism remains insufficient. In this study, we identified over 55,000 oral translocation genes (OTGs) associated with colorectal cancer (CRC) and inflammatory bowel disease (IBD). These genes are primarily involved in signal transduction and cell wall biosynthesis and show consistency in their functions between IBD and CRC. Furthermore, we found that Leclercia adecarboxylata, a newly discovered opportunistic pathogen, has a significantly high abundance in the gut microbiota of colorectal cancer patients. OTGs of this pathogen were enriched in 15 metabolic pathways, including those associated with amino acid and cofactor metabolism. These findings, for the first time, provide evidence at the genetic level of the transfer of oral pathogens to the intestine and offer new insights into the understanding of the roles of oral pathogens in the development of gastrointestinal cancers. Full article

(This article belongs to the Special Issue Understanding of the Microbiome at the Genome Level)

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6 pages, 182 KiB

Open AccessBrief Report

Clinical and Drug Resistance Characteristics of Providencia Infections

by Meenal Malviya, Pramodini Kale-Pradhan, Meredith Coyle, Christopher Giuliano and Leonard B. Johnson

Microorganisms 2024, 12(10), 2085; https://doi.org/10.3390/microorganisms12102085 - 18 Oct 2024

Viewed by 222

Abstract

Background: Providencia is a G ram-negative bacillus that most frequently colonizes the urinary tract and is often resistant to many antimicrobials. This study aimed to evaluate the resistance patterns of Providencia spp. and clinical outcomes due to the paucity of data. Methods: [...] Read more.

Background: Providencia is a G ram-negative bacillus that most frequently colonizes the urinary tract and is often resistant to many antimicrobials. This study aimed to evaluate the resistance patterns of Providencia spp. and clinical outcomes due to the paucity of data. Methods: A multi-center, descriptive, retrospective chart review of adult patients with Providencia spp. infections was conducted from 1 January 2020 to 31 May 2022. The primary outcome was to describe the drug resistance patterns of Providencia spp. isolates. This study’s secondary outcome was to evaluate the clinical outcomes of patients with Providencia spp. infections. Results: Of the 312 patients screened, 244 were excluded primarily for polymicrobial infections. The mean age was 70 years, and 39 (56.5%) were males. Of the 68 included cases, 46 (67.6%) were P. stuartii, 20 (29.4%) were P. rettgeri, and 2 (2.9%) were P. alcalifaciens. The most common infections were bacteremia 38 (55.8%), followed by 27 (39.7%) urinary tract infections and 3 (4.4%) wound infections. In this study, 45 patients (65.2%) had urinary catheters. The primary antibiotics used for treatment consisted of ceftriaxone (25 (36.2%)), cefepime (20 (29%)), and meropenem (10 (14.5%)). Only 5 of 68 (7.2%) cases were multidrug- resistant and required meropenem. In total, 19 patients (27.1%) died during their admission, but none were related to Providencia infections. A total of 10 of the 68 patients (14.5%) were readmitted within 30 days for reasons unrelated to the progression or recurrence of Providencia infections. Conclusions:Providencia bacteremia is predominantly seen in elderly patients. Third- generation cephalosporins remain an appropriate choice of antibiotics for Providencia spp. Providencia stuartii was the only species with multidrug resistance. Full article

(This article belongs to the Special Issue Clinical Microbial Infection and Antimicrobial Resistance)

16 pages, 337 KiB

Open AccessReview

Overview of Antimicrobial Resistant ESKAPEE Pathogens in Food Sources and Their Implications from a One Health Perspective

by Naomi Oyenuga, José Francisco Cobo-Díaz, Avelino Alvarez-Ordóñez and Elena-Alexandra Alexa

Microorganisms 2024, 12(10), 2084; https://doi.org/10.3390/microorganisms12102084 - 18 Oct 2024

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Abstract

Antimicrobial resistance is an increasing societal burden worldwide, with ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species and Escherichia coli) pathogens overwhelming the healthcare sectors and more recently becoming predominantly a [...] Read more.

Antimicrobial resistance is an increasing societal burden worldwide, with ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species and Escherichia coli) pathogens overwhelming the healthcare sectors and more recently becoming predominantly a concern for their persistence in food and food industries, including agricultural settings and animal husbandry environments. The aim of this review is to explore the mechanisms by which the ESKAPEE group gained its multidrug resistance profiles, to analyse their occurrence in different foods and other related reservoirs, including water, and to address the current challenges due to their spread within the food production chain. Moreover, the repertoire of surveillance programmes available focused on monitoring their occurrence, common reservoirs and the spread of antimicrobial resistance are described in this review paper. Evidence from the literature suggests that restricting our scope in relation to multidrug resistance in ESKAPEE pathogens to healthcare and healthcare-associated facilities might actually impede unveiling the actual issues these pathogens can exhibit, for example, in food and food-related reservoirs. Furthermore, this review addresses the need for increasing public campaigns aimed at addressing this challenge, which must be considered in our fight against antimicrobial resistance shown by the ESKAPEE group in food and food-related sectors. Full article

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

20 pages, 5447 KiB

Open AccessArticle

Plastic Polymers and Antibiotic Resistance in an Antarctic Environment (Ross Sea): Are We Revealing the Tip of an Iceberg?

by Gabriella Caruso, Maurizio Azzaro, Ombretta Dell’Acqua, Maria Papale, Angelina Lo Giudice and Pasqualina Laganà

Microorganisms 2024, 12(10), 2083; https://doi.org/10.3390/microorganisms12102083 - 17 Oct 2024

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Abstract

Microbial colonization of plastic polymers in Antarctic environments is an under-investigated issue. While several studies are documenting the spread of plastic pollution in the Ross Sea, whether the formation of a plastisphere (namely the complex microbial assemblage colonizing plastics) may favor the spread [...] Read more.

Microbial colonization of plastic polymers in Antarctic environments is an under-investigated issue. While several studies are documenting the spread of plastic pollution in the Ross Sea, whether the formation of a plastisphere (namely the complex microbial assemblage colonizing plastics) may favor the spread of antibiotic-resistant bacteria (ARB) in this marine environment is unknown yet. A colonization experiment was performed in this ecosystem, aiming at exploring the potential role of plastic polymers as a reservoir of antibiotic resistance. To this end, the biofilm-producing activity and the antibiotic susceptibility profiles of bacterial strains isolated from biofilms colonizing submerged polyvinylchloride and polyethylene panels were screened. The colonization experiment was carried out at two different sites of the Ross Sea, namely Road Bay and Tethys Bay. Most of bacterial isolates were able to produce biofilm; several multidrug resistances were detected in the bacterial members of biofilms associated to PVC and PE (also named as the plastisphere), as well as in the bacterial strains isolated from the surrounding water. The lowest percentage of ARB was found in the PE-associated plastisphere from the not-impacted (control) Punta Stocchino station, whereas the highest one was detected in the PVC-associated plastisphere from the Tethys Bay station. However, no selective enrichment of ARB in relation to the study sites or to either type of plastic material was observed, suggesting that resistance to antibiotics was a generalized widespread phenomenon. Resistance against to all the three classes of antibiotics assayed in this study (i.e., cell wall antibiotics, nucleic acids, and protein synthesis inhibitors) was observed. The high percentage of bacterial isolates showing resistance in remote environments like Antarctic ones, suffering increasing anthropic pressure, points out an emerging threat with a potential pathogenic risk that needs further deepening studies. Full article

(This article belongs to the Special Issue Microbial Colonization in Marine Environments)

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14 pages, 968 KiB

Open AccessArticle

Impact of Forage Sources on Ruminal Bacteriome and Carcass Traits in Hanwoo Steers During the Late Fattening Stages

by Ryukseok Kang, Jaeyong Song, Joong Kook Park, Sukjun Yun, Jeong Heon Lee, Jun Sang Ahn, Chaemin Yu, Geonwoo Kim, Jongsik Jeong, Myeong-Gwan Oh, Wanho Jo, Woohyung Lee, Mekonnen Tilahun and Tansol Park

Microorganisms 2024, 12(10), 2082; https://doi.org/10.3390/microorganisms12102082 - 17 Oct 2024

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Abstract

This study examined the effects of different forage sources on the ruminal bacteriome, growth performance, and carcass characteristics of Hanwoo steers during the fattening stage. In Korea, where high-concentrate feeding is common, selecting suitable forage is crucial for sustainable beef production. Fifteen 23-month-old [...] Read more.

This study examined the effects of different forage sources on the ruminal bacteriome, growth performance, and carcass characteristics of Hanwoo steers during the fattening stage. In Korea, where high-concentrate feeding is common, selecting suitable forage is crucial for sustainable beef production. Fifteen 23-month-old Hanwoo steers, weighing an average of 679.27 ± 43.60 kg, were fed the following five different forage sources: oat hay (OAT), rye silage (RYE), Italian ryegrass (IRS), barley forage (BAR), and rice straw silage (RSS), alongside 1.5 kg of dry matter concentrate daily for five months. Carcass traits were evaluated post-slaughter, and rumen fluid samples were analyzed using full-length 16S rRNA gene sequencing to determine the bacteriome composition. The forage source significantly affected the alpha-diversity indices and bacteriome biomarkers linked to the feed efficiency and ruminal fermentation. Differences in the backfat thickness and meat yield index were noted, with alpha-diversity indices correlating with carcass traits. The phylum Planctomycetota, especially the family Thermoguttaceae, was linked to nitrogen fixation in high-protein diets like IRS, while the genus Limimorpha emerged as a biomarker for the meat yield. These findings highlight the importance of forage selection during late fattening to optimize beef production, considering diet and bacteriome shifts. Full article

(This article belongs to the Section Virology)

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17 pages, 5594 KiB

Open AccessArticle

The Effects of swnH1 Gene Function of Endophytic Fungus Alternaria oxytropis OW 7.8 on Its Swainsonine Biosynthesis

by Dan Li, Xinlei Zhao, Ping Lu and Yu Min

Microorganisms 2024, 12(10), 2081; https://doi.org/10.3390/microorganisms12102081 - 17 Oct 2024

Viewed by 282

Abstract

The swnH1 gene in the endophytic fungus Alternaria oxytropis OW 7.8 isolated from Oxytropis glabra was identified, and the gene knockout mutant ΔswnH1 was first constructed in this study. Compared with A. oxytropis OW 7.8, the ΔswnH1 mutant exhibited altered colony [...] Read more.

The swnH1 gene in the endophytic fungus Alternaria oxytropis OW 7.8 isolated from Oxytropis glabra was identified, and the gene knockout mutant ΔswnH1 was first constructed in this study. Compared with A. oxytropis OW 7.8, the ΔswnH1 mutant exhibited altered colony and mycelium morphology, slower growth rate, and no swainsonine (SW) in mycelia, indicating that the function of the swnH1 gene promoted SW biosynthesis. Five differential expressed genes (DEGs) closely associated with SW synthesis were identified by transcriptomic analysis of A. oxytropis OW 7.8 and ΔswnH1, with sac, swnR, swnK, swnN, and swnH2 down-regulating. Six differential metabolites (DEMs) closely associated with SW synthesis were identified by metabolomic analysis, with P450, PKS-NRPS, saccharopine, lipopolysaccharide kinase, L-PA, α-aminoadipic, and L-stachydrine down-regulated, while L-proline was up-regulated. The SW biosynthetic pathways in A. oxytropis OW 7.8 were predicted and refined. The results lay the foundation for in-depth exploration of the molecular mechanisms and metabolic pathways of SW synthesis in fungi and provide reference for future control of SW in locoweeds, which would benefit the development of animal husbandry and the sustainable use of grassland ecosystems. Full article

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

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15 pages, 8383 KiB

Open AccessArticle

Continuous and Dynamic Circulation of West Nile Virus in Mosquito Populations in Bucharest Area, Romania, 2017–2023

by Sorin Dinu, Ioana Georgeta Stancu, Ani Ioana Cotar, Cornelia Svetlana Ceianu, Georgiana Victorița Pintilie, Ioannis Karpathakis, Elena Fălcuță, Ortansa Csutak and Florian Liviu Prioteasa

Microorganisms 2024, 12(10), 2080; https://doi.org/10.3390/microorganisms12102080 - 17 Oct 2024

Viewed by 368

Abstract

West Nile virus (WNV) is a mosquito-borne pathogen with a worldwide distribution. Climate change and human activities have driven the expansion of WNV into new territories in Europe during the last two decades. Romania is endemic for WNV circulation since at least 1996 [...] Read more.

West Nile virus (WNV) is a mosquito-borne pathogen with a worldwide distribution. Climate change and human activities have driven the expansion of WNV into new territories in Europe during the last two decades. Romania is endemic for WNV circulation since at least 1996 when the presence of lineage 1 was documented during an unprecedented outbreak. Lineage 2 was first identified in this country during a second significant human outbreak in 2010. Its continuous circulation is marked by clade replacement, and even co-circulation of different strains of the same clade was observed until 2016. The present study aims to fill the information gap regarding the WNV strains that were circulating in Romania between 2017 and 2023, providing chiefly viral sequences obtained from mosquito samples collected in the Bucharest metropolitan area, complemented by human and bird viral sequences. WNV was detected mainly in Culex pipiens mosquitoes, the vectors of this virus in the region, but also in the invasive Aedes albopictus mosquito species. Lineage 2 WNV was identified in mosquito samples collected between 2017 and 2023, as well as in human sera from patients in southern and central Romania during the outbreaks of 2017 and 2018. Both 2a and 2b sub-lineages were identified, with evidence of multiple clusters and sub-clusters within sub-lineage 2a, highlighting the complex and dynamic circulation of WNV in Romania, as a consequence of distinct introduction events from neighboring countries followed by in situ evolution. Full article

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

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16 pages, 5268 KiB

Open AccessArticle

Pathogenicity of Citrobacter freundii Causing Mass Mortalities of Macrobrachium rosenbergii and Its Induced Host Immune Response

by Anting Chen, Qieqi Qian, Xiaoyu Cai, Jia Yin, Yan Liu, Qi Dong, Xiaojian Gao, Qun Jiang and Xiaojun Zhang

Microorganisms 2024, 12(10), 2079; https://doi.org/10.3390/microorganisms12102079 - 17 Oct 2024

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Abstract

Citrobacter freundii is an opportunistic pathogen of freshwater aquatic animals, which severely restricts the sustainable development of the aquaculture industry. In this study, a dominant strain, named FSNM-1, was isolated from the hepatopancreas of diseased Macrobrachium rosenbergii. This strain was identified as [...] Read more.

Citrobacter freundii is an opportunistic pathogen of freshwater aquatic animals, which severely restricts the sustainable development of the aquaculture industry. In this study, a dominant strain, named FSNM-1, was isolated from the hepatopancreas of diseased Macrobrachium rosenbergii. This strain was identified as C. freundii based on a comprehensive analysis of its morphological, physiological, and biochemical features and molecular identification. Challenge experiments were conducted to assess the pathogenicity of C. freundii to M. rosenbergii. The results showed that the FSNM-1 strain had high virulence to M. rosenbergii with a median lethal dose (LD₅₀) of 1.1 × 10⁶ CFU/mL. Histopathological analysis revealed that C. freundii infection caused different degrees of inflammation in the hepatopancreas, gills, and intestines of M. rosenbergii. The detection of virulence-related genes revealed that the FSNM-1 strain carried colonization factor antigen (cfa1, cfa2), ureases (ureG, ureF, ureD, ureE), and outer membrane protein (ompX), and virulence factor detection showed that the FSNM-1 strain had lecithinase, amylase, lipase, gelatinase, and hemolysin activities but did not produce protease and DNase activities. To investigate the immune response of M. rosenbergii to C. freundii, the expression levels of ALF3, MyD88, SOD, proPO, TRAF6, and TNF immune-related genes were monitored at different points of time in the hepatopancreas, gills, intestines, and hemocytes of M. rosenbergii after infection. The results demonstrated a significant upregulation in the expression levels of the ALF3, MyD88, SOD, proPO, TRAF6, and TNF genes in M. rosenbergii at the early stage of C. freundii infection. This study highlights C. freundii as a major pathogen causing mass mortality in M. rosenbergii and provides valuable insights into its virulence mechanisms and the host’s immune response. Full article

(This article belongs to the Special Issue Pathogens and Aquaculture)

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15 pages, 3915 KiB

Open AccessArticle

The pH and Sucrose Influence Rhamnolipid Action Toward Planktonic and Biofilms of Listeria monocytogenes

by Tathiane Ferroni Passos and Marcia Nitschke

Microorganisms 2024, 12(10), 2078; https://doi.org/10.3390/microorganisms12102078 - 17 Oct 2024

Viewed by 346

Abstract

Bacterial resistance and persistence in food environments are major concerns for the industry, which constantly seeks new strategies to reduce microbial contamination. Rhamnolipids (RL) biosurfactants are considered sustainable and green alternatives to synthetics; furthermore, they have demonstrated potential for controlling various foodborne pathogens. [...] Read more.

Bacterial resistance and persistence in food environments are major concerns for the industry, which constantly seeks new strategies to reduce microbial contamination. Rhamnolipids (RL) biosurfactants are considered sustainable and green alternatives to synthetics; furthermore, they have demonstrated potential for controlling various foodborne pathogens. Food environments are typically exposed to diverse pH, solutes, temperatures, and water activity (a_w) levels that may favor the survival of pathogens. Therefore, it is crucial to consider these factors in evaluating the performance of novel antimicrobials. Our study examined the influence of pH and sucrose on the antimicrobial activity of RL against both planktonic and biofilm of Listeria monocytogenes. We found that the presence of sucrose can enhance the antimicrobial effectiveness of RL against both planktonic and sessile bacteria. The addition of sugar particularly improved RL action at pH 6 and 7. Moreover, we observed that the type and size of RL self-assembly structures depend on the pH and sucrose concentration. These findings suggest potential for developing RL-based innovative methods to control L. monocytogenes in sugar-rich or -low a_w foods and environments. Full article

(This article belongs to the Special Issue Advances in Microbial Surfactants: Production and Applications)

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10 pages, 2028 KiB

Open AccessReview

My Early Years of Yeast Mitochondrial Genetics

by Ian G. Macreadie

Microorganisms 2024, 12(10), 2077; https://doi.org/10.3390/microorganisms12102077 - 17 Oct 2024

Viewed by 259

Abstract

There have been massive technological advances in molecular biology and genetics over the past five decades. I have personally experienced these advances and here I reflect on those origins, from my perspective, studying yeast mitochondrial genetics leading up to deciphering the functions of [...] Read more.

There have been massive technological advances in molecular biology and genetics over the past five decades. I have personally experienced these advances and here I reflect on those origins, from my perspective, studying yeast mitochondrial genetics leading up to deciphering the functions of the mitochondrial genome. The yeast contributions commenced in the middle of the last century with pure genetics, correlating mutants with phenotypes, in order to discover genes, just like the early explorations to discover new lands. The quest was to explore the mitochondrial genome and find its genes and their products. It was most fortunate that DNA sequencing technologies became available in the late 1970s, and laboratories were restructured enormously to keep pace with the emerging technologies. There were considerable costs in equipping laboratories, purchasing ultracentrifuges and restriction endonucleases, and undertaking DNA sequencing; additionally, workers required special safety gear. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Microbial Molecular Genetics)

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16 pages, 1120 KiB

Open AccessReview

Parasites and Microbiota: Dual Interactions and Therapeutic Perspectives

by Hayat S. Al-Rashidi and Eman S. El-Wakil

Microorganisms 2024, 12(10), 2076; https://doi.org/10.3390/microorganisms12102076 - 16 Oct 2024

Viewed by 440

Abstract

The human gut hosts a diverse and active community of bacteria that symbiotically support the physiology, metabolism, and immunity of the intestinal lining. Nevertheless, a dynamic community of parasites (helminths and protozoa) may share a habitat with gut-dwelling microbiota. Both microbiota and parasites [...] Read more.

The human gut hosts a diverse and active community of bacteria that symbiotically support the physiology, metabolism, and immunity of the intestinal lining. Nevertheless, a dynamic community of parasites (helminths and protozoa) may share a habitat with gut-dwelling microbiota. Both microbiota and parasites can significantly change the physical and immunological environment of the gut, thus generating several mechanisms of interaction. Studying this field is crucial for understanding the pathogenesis of parasitic diseases. Additionally, intestinal microbiota and gut-dwelling parasites may interact with each other and with the host immunity to alleviate or exacerbate the disease. These interactions can alter the pathogenicity of both parasites and microbiota, thereby changing the infection outcomes and the overall disease profile. Parasites and microbiota interactions occur via several mechanisms, including physical alteration in both the gastrointestinal microenvironment and the adaptive and innate immune responses. By modulating the microbiota, treating parasitic infections and microbiota dysbiosis may be improved through knowing the mechanisms and consequences of the interactions between intestinal parasites and the microbiota. Thus, new biological tools of treatment including probiotics can be introduced, particularly with the emergence of drug resistance and adverse effects. Full article

(This article belongs to the Special Issue Microbiota: From the Environment to Humans, 2nd Edition)

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17 pages, 3882 KiB

Open AccessArticle

Structure and Function of Soil Bacterial Communities in the Different Wetland Types of the Liaohe Estuary Wetland

by Yunlong Zheng, Fangli Su, Haifu Li, Fei Song, Chao Wei and Panpan Cui

Microorganisms 2024, 12(10), 2075; https://doi.org/10.3390/microorganisms12102075 - 16 Oct 2024

Viewed by 422

Abstract

Soil bacterial communities play a crucial role in the functioning of estuarine wetlands. Investigating the structure and function of these communities across various wetland types, along with the key factors influencing them, is essential for understanding the relationship between bacteria and wetland ecosystems. [...] Read more.

Soil bacterial communities play a crucial role in the functioning of estuarine wetlands. Investigating the structure and function of these communities across various wetland types, along with the key factors influencing them, is essential for understanding the relationship between bacteria and wetland ecosystems. The Liaohe Estuary Wetland formed this study’s research area, and soil samples from four distinct wetland types were utilized: suaeda wetlands, reed wetlands, pond returning wetlands, and tidal flat wetlands. The structure and function of the soil bacterial communities were examined using Illumina MiSeq high-throughput sequencing technology in conjunction with the PICRUSt analysis method. The results indicate that different wetland types significantly affect the physical and chemical properties of soil, as well as the structure and function of bacterial communities. The abundance and diversity of soil bacterial communities were highest in the suaeda wetland and lowest in the tidal flat wetland. The dominant bacterial phyla identified were Proteobacteria and Bacteroidota. Furthermore, the dominant bacterial genera identified included RSA9, SZUA_442, and SP4260. The primary functional pathways associated with the bacterial communities involved the biosynthesis of valine, leucine, and isoleucine, as well as lipoic acid metabolism, which are crucial for the carbon and nitrogen cycles. This study enhances our understanding of the mutual feedback between river estuary wetland ecosystems and environmental changes, providing a theoretical foundation for the protection and management of wetlands. Full article

(This article belongs to the Section Environmental Microbiology)

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17 pages, 6889 KiB

Open AccessArticle

Legionella in Primary School Hot Water Systems from Two Municipalities in the Danish Capital Region

by Niss Skov Nielsen, Peter Fojan, Rasmus Lund Jensen, Haseebullah Wahedi and Alireza Afshari

Microorganisms 2024, 12(10), 2074; https://doi.org/10.3390/microorganisms12102074 - 16 Oct 2024

Viewed by 360

Abstract

Legionella contamination in public water systems poses significant health risks, particularly in schools where vulnerable populations, including children, regularly use these facilities. This study investigates the presence of Legionella in the hot water systems from 49 primary schools across two municipalities in the [...] Read more.

Legionella contamination in public water systems poses significant health risks, particularly in schools where vulnerable populations, including children, regularly use these facilities. This study investigates the presence of Legionella in the hot water systems from 49 primary schools across two municipalities in the Danish capital region. Water samples were collected from taps in each school, and both first-flush and stabile temperature samples were analysed for Legionella contents. The findings revealed that 97% of schools in Municipality 1 and 100% in Municipality 2 had Legionella in their hot water systems. The content of Legionella colonies was significantly higher in schools in Municipality 1, which was probably because of overall lower water temperatures. At stabile temperatures, 76% and 50% of the schools in the two municipalities exceeded the European Union’s recommended limit of 1000 CFU/L. Stabile peripheral water temperatures were achieved after 3 min. Tap water temperatures above 54 °C and central tank temperatures above 59 °C were associated with Legionella contents below 1000 CFU/L. This study highlights the need for more stringent Legionella control procedures in schools, including higher water temperatures and refining Legionella reducing interventions with the addition of regular flow and draining procedures. Full article

(This article belongs to the Special Issue Legionella pneumophila: A Microorganism with Thousand Faces, 2nd Edition)

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10 pages, 459 KiB

Open AccessArticle

Impact of PCV13 and PPSV23 Vaccination on Invasive Pneumococcal Disease in Adults with Treated Rheumatoid Arthritis: A Population-Based Study

by Carlos A. Alvarez, Ronald G. Hall 2nd, Suzy Lin, Aaron R. Perkins and Eric M. Mortensen

Microorganisms 2024, 12(10), 2073; https://doi.org/10.3390/microorganisms12102073 - 16 Oct 2024

Viewed by 316

Abstract

On-time receipt of pneumococcal vaccines is essential in patients with rheumatoid arthritis (RA) as immunosuppressive medications increase their risk of invasive pneumococcal disease (IPD). However, data regarding the impact of timely administration of these vaccines on the risk of developing IPD are lacking [...] Read more.

On-time receipt of pneumococcal vaccines is essential in patients with rheumatoid arthritis (RA) as immunosuppressive medications increase their risk of invasive pneumococcal disease (IPD). However, data regarding the impact of timely administration of these vaccines on the risk of developing IPD are lacking for RA patients. We conducted a retrospective cohort study to assess the impact of on-time vaccination for pneumococcal conjugate vaccine (PCV) 13 and pneumococcal polysaccharide vaccine (PPSV) 23 in patients treated for RA on the development of IPD using national Veterans Affairs data from 2010 to 2018. Patients > 18 years of age, diagnosed with RA, and newly initiated on RA treatment were included. Pneumococcal vaccine compliance was assessed by measuring on-time receipt of PCV13 and PPSV23 vaccinations. A total of 33,545 patients were included in the cohort. Non-compliance with PCV recommendations was associated with an increased risk of IPD in a multivariable logistic regression model. This finding was consistent whether IPD status was ascertained by International Classification of Diseases coding (OR 2.42, 95%CI 2.14–2.73) or microbiologic data (OR 1.64, 95%CI 1.26–2.14). Providers should actively seek opportunities to provide pneumococcal vaccinations to patients with RA, as their on-time administration is associated with a decreased risk of IPD. Full article

(This article belongs to the Section Medical Microbiology)

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10 pages, 798 KiB

Open AccessArticle

The Determination of the Rapid and Effective Activity of an Air Sanitizer against Aerosolized Bacteria Using a Room-Sized Aerobiology Chamber

by Bahram Zargar, M. Khalid Ijaz, Anthony Kevek, Mark Miller, Julie McKinney and Syed A. Sattar

Microorganisms 2024, 12(10), 2072; https://doi.org/10.3390/microorganisms12102072 - 16 Oct 2024

Viewed by 324

Abstract

Air sanitization is an important non-pharmaceutical intervention for mitigating the risk of indoor pathogen spreading. A dipropylene glycol-containing air sanitizer was tested against aerosolized Staphylococcus aureus and Klebsiella pneumoniae. The bacteria, suspended in a soil load, were aerosolized using a six-jet Collison [...] Read more.

Air sanitization is an important non-pharmaceutical intervention for mitigating the risk of indoor pathogen spreading. A dipropylene glycol-containing air sanitizer was tested against aerosolized Staphylococcus aureus and Klebsiella pneumoniae. The bacteria, suspended in a soil load, were aerosolized using a six-jet Collison nebulizer with pressurized air. The 25-m³ (~900 ft³) aerobiology chamber was maintained at 22 ± 2 °C and 50 ± 5% relative humidity per the U.S. Environmental Protection Agency’s 2012 Guidelines on air sanitizers. An initial 2-min air sample was collected from the chamber using a slit-to-agar sampler containing 150-mm Petri plates, with Trypticase soy agar (TSA) containing neutralizers to quench the microbicidal activity of the air sanitizer, to determine the initial bacterial challenge in the air. The air sanitizer was sprayed into the chamber from pressurized cans. Additional air samples were collected from the chamber over 10 min to detect surviving bacteria. The TSA plates were then incubated aerobically at 36 ± 1 °C for 90 ± 4 h and scored for bacterial colony-forming units. A 30-s spray of the air sanitizer reduced infectious S. aureus and K. pneumoniae titers by 3.0 log₁₀ (99.9%) in 3.2 ± 0.3 min and 1.2 ± 0.0 min, respectively. Based on these findings, the EPA granted registration of the air sanitizer as the first product of its kind for indoor air sanitization. Full article

(This article belongs to the Special Issue Disinfection and Sterilization of Microorganisms (2nd Edition))

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14 pages, 2516 KiB

Open AccessArticle

Comparative Analysis of Fecal Microbiota Between Adolescents with Early-Onset Psychosis and Adults with Schizophrenia

by Lucero Nuncio-Mora, Humberto Nicolini, Nuria Lanzagorta, Cynthia García-Jaimes, Fernanda Sosa-Hernández, Vanessa González-Covarrubias, Héctor Cabello-Rangel, Emmanuel Sarmiento, David C. Glahn and Alma Genis-Mendoza

Microorganisms 2024, 12(10), 2071; https://doi.org/10.3390/microorganisms12102071 - 16 Oct 2024

Viewed by 514

Abstract

Studies of the composition of the gut microbiome have consistently shown that psychiatric disorders such as schizophrenia are associated with gut dysbiosis. However, research focusing on adolescents with early-onset psychosis remains limited. This study aimed to characterize the microbial communities and their potential [...] Read more.

Studies of the composition of the gut microbiome have consistently shown that psychiatric disorders such as schizophrenia are associated with gut dysbiosis. However, research focusing on adolescents with early-onset psychosis remains limited. This study aimed to characterize the microbial communities and their potential metabolic functions in these populations. We identified that genera Desulfovibrionaceae_Incertae_Sedis, Paraprevotella, and several genera from the Oscillospiraceae family were significantly more abundant in patients with schizophrenia compared to non-psychotic individuals, while Dorea showed decreased levels in schizophrenia patients. Furthermore, patients with early-onset psychosis demonstrated a significant reduction in Staphylococcus abundance. Additionally, we observed an increase in Prevotellaceae Leyella and Prevotellaceae Incertae Sedis in patients receiving atypical antipsychotic treatment, along with a rise in the genus Weissella among those treated with sertraline. Conversely, patients on valproate treatment exhibited decreased levels of Desulfovibrionaceae Incertae Sedis, while showing increased levels of Kandleria and Howardella. Functional prediction analysis using PICRUSt2 revealed significant differences in the expression of key enzymes associated with fatty acid metabolism. Gene orthology analysis identified 10 differentially expressed genes in the early-onset psychosis and schizophrenia groups. Our findings underscore the importance of considering dietary factors, pharmacological treatments, and microbial composition in understanding the gut–brain axis in psychiatric disorders. Full article

(This article belongs to the Section Gut Microbiota)

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11 pages, 1243 KiB

Open AccessReview

The Effect of Aloe vera on Skin and Its Commensals: Contribution of Acemannan in Curing Acne Caused by Propionibacterium acnes

by Suraj Pal, Mayank Raj, Medha Singh, Kumar Saurav, Chetan Paliwal, Subhasish Saha, Anil Kumar Sharma and Manoj Singh

Microorganisms 2024, 12(10), 2070; https://doi.org/10.3390/microorganisms12102070 (registering DOI) - 16 Oct 2024

Viewed by 296

Abstract

Aloe vera is one of the most significant therapeutical plant species that belongs to the family Liliaceae. Aloe vera is composed of a high amount of water, with the remainder being dry matter. The dry matter contains a lot of bioactive compounds like [...] Read more.

Aloe vera is one of the most significant therapeutical plant species that belongs to the family Liliaceae. Aloe vera is composed of a high amount of water, with the remainder being dry matter. The dry matter contains a lot of bioactive compounds like carbohydrates, fats, and enzymes, with various therapeutic and antimicrobial properties. It can enhance the proliferation of cells and prevent cell damage by anti-oxidative properties (stimulating the secretion of superoxide dismutase and peroxidase). Human skin is colonized by microbes like fungi (Candida albicans), bacteria (Propionibacterium acnes, Staphylococcus aureus), and mites. These commensals are responsible for skin characteristics such as acidic pH, the pungent smell of sweat, etc. Human fetuses lack skin microbiota, and their skin is colonized after birth. Commensals present on the skin have a crucial role in training the human immune system against other pathogenic microbes. Propionibacterium acnes act as an opportunistic pathogen when the balance between the commensals is disturbed. We also emphasize the recent progress in identifying the aloe metabolite biosynthesis pathways and the associated enzyme machinery. The hyperproliferation of Propionibacterium acnes causes acne, and acemannan plays a significant role in its cure. Hence, we need to consider a new treatment approach based on the root cause of this dysbiosis. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions)

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18 pages, 5966 KiB

Open AccessArticle

Co-Regulation Mechanism of Host p53 and Fos in Transcriptional Activation of ILTV Immediate-Early Gene ICP4

by Zheyi Liu, Xuefeng Li, Lu Cui, Shufeng Feng, Zongxi Han, Yu Zhang, Shengwang Liu and Hai Li

Microorganisms 2024, 12(10), 2069; https://doi.org/10.3390/microorganisms12102069 (registering DOI) - 16 Oct 2024

Viewed by 269

Abstract

Infectious laryngotracheitis virus (ILTV) exhibits a cascade expression pattern of encoded genes, and ICP4 is the only immediate-early gene of ILTV, which plays a crucial role in initiating the subsequent viral genes. Therefore, studying the transcriptional regulation mechanism of ICP4 holds promise for [...] Read more.

Infectious laryngotracheitis virus (ILTV) exhibits a cascade expression pattern of encoded genes, and ICP4 is the only immediate-early gene of ILTV, which plays a crucial role in initiating the subsequent viral genes. Therefore, studying the transcriptional regulation mechanism of ICP4 holds promise for effectively blocking ILTV infection and spread. Host transcriptional factors p53 and Fos are proven to regulate a variety of viral infections, and our previous studies have demonstrated their synergistic effects in regulating ILTV infection. In this study, we constructed eukaryotic expression vectors for p53 and Fos as well as their specific siRNAs and transfected them into a chicken hepatoma cell line. The results showed that knocking down p53 or Fos significantly inhibited ICP4 transcription, while overexpressing p53 or Fos had an opposite effect. A further CoIP and ChIP-qPCR assay suggested p53 and Fos physically interacted with each other, and jointly bound to the upstream transcriptional regulatory region of ICP4. To elucidate the specific mechanisms of p53 and Fos in regulating ICP4 transcription, we designed p53 and Fos protein mutants by mutating their DNA binding domains, which significantly reduced their binding ability to DNA without affecting their interaction. The results showed that Fos directly bound to the promoter region of ICP4 as a binding target of p53, and the p53–Fos protein complex acted as a transcriptional co-regulator of ICP4. Studying the transcriptional process and regulatory pattern of ICP4 is of great significance for understanding the molecular mechanism of ILTV infection, and thus for finding effective methods to control and prevent it. Full article

(This article belongs to the Special Issue State-of-the-Art Veterinary Microbiology in China (2023, 2024))

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17 pages, 2557 KiB

Open AccessArticle

Three-Year Monitoring of Microorganisms’ Composition and Concentration in Atmospheric Aerosols of Novosibirsk City and Suburbs

by Irina Andreeva, Aleksandr Safatov, Olga Totmenina, Sergei Olkin, Maxim Rebus, Galina Buryak, Tatiana Alikina, Olga Baturina and Marsel Kabilov

Microorganisms 2024, 12(10), 2068; https://doi.org/10.3390/microorganisms12102068 (registering DOI) - 15 Oct 2024

Viewed by 343

Abstract

The atmospheric environment is formed under the influence of local and distant sources as a result of horizontal and vertical transport. In the present work, microbiological analysis of 604 samples of atmospheric aerosol collected in the period from September 2020 to September 2023 [...] Read more.

The atmospheric environment is formed under the influence of local and distant sources as a result of horizontal and vertical transport. In the present work, microbiological analysis of 604 samples of atmospheric aerosol collected in the period from September 2020 to September 2023 at four sites differing in anthropogenic load, located in Novosibirsk and the region, was carried out. Day and night aerosol samples were collected during 12 h every two weeks by filtration using Sartorius reinforced Teflon membranes, then sown on a set of nutrient media. The taxonomic affiliation of the isolated microbial isolates was determined based on phenotypic characteristics and analysis of 16S rRNA gene nucleotide sequences. Changes in the composition and concentration of culturable microorganisms depending on the season, time of day, and site of aerosol sampling were observed. In winter, lower fungi and bacteria of the genera Bacillus, Staphylococcus, Micrococcus dominated with an average concentration from zero to 12.5 CFU/m³ of aerosol. In the warm period, the concentration and diversity of cocci, spore-forming and non-spore-forming bacteria, actinomycetes, and fungi (up to 1970 CFU/m³), among which pathogenic microorganisms were found, increased sharply in aerosols. The use of 16S metabarcoding techniques has greatly expanded the range of aerosols’ microbial diversity detectable. Full article

(This article belongs to the Section Environmental Microbiology)

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24 pages, 2369 KiB

Open AccessArticle

Diversity and Functional Roles of Root-Associated Endophytic Fungi in Two Dominant Pioneer Trees Reclaimed from a Metal Mine Slag Heap in Southwest China

by Bo Bi, Yuqing Xiao, Xiaonan Xu, Qianqian Chen, Haiyan Li, Zhiwei Zhao and Tao Li

Microorganisms 2024, 12(10), 2067; https://doi.org/10.3390/microorganisms12102067 (registering DOI) - 15 Oct 2024

Viewed by 343

Abstract

The utilization of fast-growing, economically valuable woody plants with strong stress resistance, such as poplar and willow, to revegetate severely metal-contaminated mine tailings not only offers a productive and profitable use of abandoned polluted soil resources but also facilitates the phytoremediation of these [...] Read more.

The utilization of fast-growing, economically valuable woody plants with strong stress resistance, such as poplar and willow, to revegetate severely metal-contaminated mine tailings not only offers a productive and profitable use of abandoned polluted soil resources but also facilitates the phytoremediation of these polluted soils. This study examines the diversity and functional roles of endophytic fungi naturally colonizing the roots of an artificially established Populus yunnanensis forest and the naturally reclaimed pioneer species Coriaria sinica on an abandoned tailing dam in southwest China. Culture-independent analyses revealed that the root systems of both plant species were abundantly colonized by arbuscular mycorrhizal fungi and endophytic fungi, forming rich and diverse endophytic fungal communities predominantly represented by the genera Ilyonectria, Tetracladium, Auricularia, and unclassified members of Helotiales. However, the composition of root endophytic fungal communities differed significantly between the two plant species. Using a culture-dependent approach, a total of 192 culturable endophytic fungal strains were isolated from the roots. The dominant genera included Cadophora, Cladosporium, Cyphellophora, and Paraphoma, most of which were previously identified as dark septate endophytes (DSE). Six representative DSE strains were selected for further study, and significant cadmium tolerance and various plant growth-promoting traits were observed, including the solubilization of insoluble inorganic and organic phosphorus, indole-3-acetic acid (IAA) production, and siderophore synthesis. In greenhouse experiments, inoculating two DSE strains mitigated the inhibitory effects of metal-polluted tailing soil on the growth of P. yunnanensis. This was achieved by reducing heavy metal uptake in roots and limiting metal translocation to the above-ground tissues, thereby promoting plant growth and adaptability. Our findings suggest that as plants reclaim metal-polluted tailings, root-associated endophytic fungal communities also undergo natural succession, playing a critical role in enhancing the host plant’s tolerance to stress. Therefore, these restored root-associated fungi, particularly DSE, are essential functional components of the root systems in plants used for tailing reclamation. Full article

(This article belongs to the Special Issue Biotechnology for Environmental Remediation)

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21 pages, 1995 KiB

Open AccessArticle

Alginate–Bentonite Encapsulation of Extremophillic Bacterial Consortia Enhances Chenopodium quinoa Tolerance to Metal Stress

by Cesar Arriagada-Escamilla, Roxana Alvarado, Javier Ortiz, Reinaldo Campos-Vargas and Pablo Cornejo

Microorganisms 2024, 12(10), 2066; https://doi.org/10.3390/microorganisms12102066 (registering DOI) - 15 Oct 2024

Viewed by 515

Abstract

This study explores the encapsulation in alginate/bentonite beads of two metal(loid)-resistant bacterial consortia (consortium A: Pseudomonas sp. and Bacillus sp.; consortium B: Pseudomonas sp. and Bacillus sp.) from the Atacama Desert (northern Chile) and Antarctica, and their influence on physiological traits of Chenopodium [...] Read more.

This study explores the encapsulation in alginate/bentonite beads of two metal(loid)-resistant bacterial consortia (consortium A: Pseudomonas sp. and Bacillus sp.; consortium B: Pseudomonas sp. and Bacillus sp.) from the Atacama Desert (northern Chile) and Antarctica, and their influence on physiological traits of Chenopodium quinoa growing in metal(loid)-contaminated soils. The metal(loid) sorption capacity of the consortia was determined. Bacteria were encapsulated using ionic gelation and were inoculated in soil of C. quinoa. The morphological variables, photosynthetic pigments, and lipid peroxidation in plants were evaluated. Consortium A showed a significantly higher biosorption capacity than consortium B, especially for As and Cu. The highest viability of consortia was achieved with matrices A1 (3% alginate and 2% bentonite) and A3 (3% alginate, 2% bentonite and 2.5% LB medium) at a drying temperature of 25 °C and storage at 4 °C. After 12 months, the highest viability was detected using matrix A1 with a concentration of 10⁶ CFU g⁻¹. Further, a greenhouse experiment using these consortia in C. quinoa plants showed that, 90 days after inoculation, the morphological traits of both consortia improved. Chemical analysis of metal(loid) contents in the leaves indicated that consortium B reduced the absorption of Cu to 32.1 mg kg⁻¹ and that of Mn to 171.9 mg kg⁻¹. Encapsulation resulted in a significant increase in bacterial survival. This highlights the benefits of using encapsulated microbial consortia from extreme environments, stimulating the growth of C. quinoa, especially in soils with metal(loid) levels that can be a serious constraint for plant growth. Full article

(This article belongs to the Special Issue Rhizosphere Bacteria and Fungi that Promote Plant Growth)

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5 pages, 8713 KiB

Open AccessCase Report

Acute Retinal Necrosis Associated with Epstein–Barr Virus Successfully Treated with Antiviral Treatment: A Case Report

by Heejeong You and Joonhyung Kim

Microorganisms 2024, 12(10), 2065; https://doi.org/10.3390/microorganisms12102065 (registering DOI) - 15 Oct 2024

Viewed by 364

Abstract

Epstein–Barr virus (EBV) is a rare cause of acute retinal necrosis (ARN) and is known for its poor prognosis and limited response to conventional antiviral treatment. Herein, we report a case of EBV ARN successfully treated with conventional systemic acyclovir and intravitreal ganciclovir [...] Read more.

Epstein–Barr virus (EBV) is a rare cause of acute retinal necrosis (ARN) and is known for its poor prognosis and limited response to conventional antiviral treatment. Herein, we report a case of EBV ARN successfully treated with conventional systemic acyclovir and intravitreal ganciclovir injection. An 85-year-old man presented with visual disturbance of the right eye from 10 days prior. His visual acuity was 20/200 in the right eye and slit lamp examination showed keratic precipitates, 4+ anterior chamber cells, and 1+ anterior vitreous cells. Fundus examination revealed multiple retinal hemorrhages and yellow-whitish necrotic lesion. The patient was clinically diagnosed with ARN. A few days later, EBV DNA was identified in the aqueous humor and in the serum PCR assay. The patient received 350 mg of intravenous acyclovir three times a day with oral prednisolone, and an intravitreal ganciclovir injection (2 mg per dose) was given five times. Over the course of seven weeks, systemic acyclovir was switched to 1g of per-oral valaciclovir three times a day, and oral steroids were successfully tapered. His visual acuity improved to 20/100, and the previous necrotic lesion was markedly decreased in size. Intravenous acyclovir combined with intravitreal ganciclovir may yield successful treatment outcomes in acute retinal necrosis caused by EBV. Full article

(This article belongs to the Special Issue Ocular Microorganisms)

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8 pages, 933 KiB

Open AccessArticle

Effects of Inosine-5′-monophosphate Dehydrogenase (IMPDH/GuaB) Inhibitors on Borrelia burgdorferi Growth in Standard and Modified Culture Conditions

by Eric L. Siegel, Connor Rich, Sanchana Saravanan, Patrick Pearson, Guang Xu and Stephen M. Rich

Microorganisms 2024, 12(10), 2064; https://doi.org/10.3390/microorganisms12102064 (registering DOI) - 15 Oct 2024

Viewed by 378

Abstract

Borrelia burgdorferi’s inosine-5′-monophosphate dehydrogenase (IMPDH, GuaB encoded by the guaB gene) is a potential therapeutic target. GuaB is necessary for B. burgdorferi replication in mammalian hosts but not in standard laboratory culture conditions. Therefore, we cannot test novel GuaB inhibitors against B. [...] Read more.

Borrelia burgdorferi’s inosine-5′-monophosphate dehydrogenase (IMPDH, GuaB encoded by the guaB gene) is a potential therapeutic target. GuaB is necessary for B. burgdorferi replication in mammalian hosts but not in standard laboratory culture conditions. Therefore, we cannot test novel GuaB inhibitors against B. burgdorferi without utilizing mammalian infection models. This study aimed to evaluate modifications to a standard growth medium that may mimic mammalian conditions and induce the requirement of GuaB usage for replication. The effects of two GuaB inhibitors (mycophenolic acid, 6-chloropurine riboside at 125 μM and 250 μM) were assessed against B. burgdorferi (guaB+) grown in standard Barbour–Stoenner–Kelly-II (BSK-II) medium (6% rabbit serum) and BSK-II modified to 60% concentration rabbit serum (BSK-II/60% serum). BSK-II directly supplemented with adenine, hypoxanthine, and nicotinamide (75 μM each, BSK-II/AHN) was also considered as a comparison group. In standard BSK-II, neither mycophenolic acid nor 6-chloropurine riboside affected B. burgdorferi growth. Based on an ANOVA, a dose-dependent increase in drug effects was observed in the modified growth conditions (F = 4.471, p = 0.001). Considering higher drug concentrations at exponential growth, mycophenolic acid at 250 μM reduced spirochete replication by 48% in BSK-II/60% serum and by 50% in BSK-II/AHN (p < 0.001 each). 6-chloropurine riboside was more effective in both mediums than mycophenolic acid, reducing replication by 64% in BSK-II/60% serum and 65% in BSK-II/AHN (p < 0.001 each). These results demonstrate that modifying BSK-II medium with physiologically relevant levels of mammalian serum supports replication and induces the effects of GuaB inhibitors. This represents the first use of GuaB inhibitors against Borrelia burgdorferi, building on tests against purified B. burgdorferi GuaB. The strong effects of 6-chloropurine riboside indicate that B. burgdorferi can salvage and phosphorylate these purine derivative analogs. Therefore, this type of molecule may be considered for future drug development. Optimization of this culture system will allow for better assessment of novel Borrelia-specific GuaB inhibitor molecules for Lyme disease interventions. The use of GuaB inhibitors as broadcast sprays or feed baits should also be evaluated to reduce spirochete load in competent reservoir hosts. Full article

(This article belongs to the Special Issue Borreliosis and Other Tick-Borne Diseases in the Northern and Southern Hemispheres)

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11 pages, 952 KiB

Open AccessArticle

Safety Assessment and Evaluation of Probiotic Potential of Lactobacillus bulgaricus IDCC 3601 for Human Use

by Minjee Lee, Won-Yeong Bang, Han-Bin Lee, Soo-Yeon Yang, Kyu-Shik Lee, Hae-Ji Kang, Sun-Mee Hong and Jungwoo Yang

Microorganisms 2024, 12(10), 2063; https://doi.org/10.3390/microorganisms12102063 (registering DOI) - 15 Oct 2024

Viewed by 482

Abstract

Lactic acid bacteria (LAB) are probiotic microorganisms widely used for their health benefits in the food industry. However, recent concerns regarding their safety have highlighted the need for comprehensive safety assessments. In this study, we aimed to evaluate the safety of L. bulgaricus [...] Read more.

Lactic acid bacteria (LAB) are probiotic microorganisms widely used for their health benefits in the food industry. However, recent concerns regarding their safety have highlighted the need for comprehensive safety assessments. In this study, we aimed to evaluate the safety of L. bulgaricus IDCC 3601, isolated from homemade plain yogurt, via genomic, phenotypic, and toxicity-based analyses. L. bulgaricus IDCC 3601 possessed a single circular chromosome of 1,865,001 bp, with a GC content of 49.72%, and 1910 predicted coding sequences. No virulence or antibiotic resistance genes were detected. Although L. bulgaricus IDCC 3601 exhibited antibiotic resistance to gentamicin and kanamycin, this resistance is an intrinsic feature of this species. L. bulgaricus IDCC 3601 did not produce biogenic amines and did not exhibit hemolytic activity. Phenotypic analysis of enzyme activity and carbohydrate fermentation profiles revealed the metabolic features of L. bulgaricus IDCC 3601. Moreover, no deaths or abnormalities were observed in single-dose oral toxicity tests, suggesting that L. bulgaricus IDCC 3601 has no adverse effect on human health. Finally, L. bulgaricus IDCC 3601 inhibited the growth of potential carbapenem-resistant Enterobacteriaceae. Therefore, our results suggest that L. bulgaricus IDCC 3601 is a safe probiotic strain for human consumption. Full article

(This article belongs to the Special Issue Microbial Safety and Biotechnology in Food Production and Processing)

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Microorganisms, Volume 12, Issue 10 (October 2024) – 162 articles

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