Microorganisms

15 pages, 3345 KiB

Open AccessProject Report

Looking for Pathogens in Dust from North Africa Arriving in the French West Indies Using Metabarcoding and Cultivable Analysis

by Yann Reynaud, Andric Gelasse, Luc Multigner, Philippe Quénel, Antoine Talarmin and Stéphanie Guyomard-Rabenirina

Microorganisms 2024, 12(10), 2111; https://doi.org/10.3390/microorganisms12102111 - 21 Oct 2024

Viewed by 695

Abstract

Periodically, the French West Indies receive dust originating from North Africa (NA). Microorganisms associated with desert dust can be transported over long distances through the atmosphere and could represent a means for the remote colonization of new habitats by putatively pathogenic microorganisms. The [...] Read more.

Periodically, the French West Indies receive dust originating from North Africa (NA). Microorganisms associated with desert dust can be transported over long distances through the atmosphere and could represent a means for the remote colonization of new habitats by putatively pathogenic microorganisms. The aim of this study was to determine the diversity and frequency of microbial agents (bacteria, eukaryotes) in NA dusts and the potential threat toward human and/or animal health by comparing microbial air composition during dust events and in control samples. In 2017 and 2018, 16 samples were collected during seven NA dust episodes and there were 9 controls. The microbial composition of the samples was characterized using a cultivable approach and by metabarcoding analyses (16S and 18S). A greater bacterial load and greater diversity were observed during the dust events, and some genera were significantly associated with the events. Some, such as Geodermatophilus, can be considered signature species of NA dust. No pathogenic species were found with the cultivable approach, whereas the metabarcoding analyses highlighted the presence of several potentially pathogenic species or known human pathogens such as Naegleria fowleri. Full article

(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)

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9 pages, 575 KiB

Open AccessArticle

A New Real-Time PCR Test (Flora Select™) and Nugent Score for the Diagnosis of Bacterial Vaginosis During Pregnancy

by Hideto Yamada, Shigeki Shimada, Hajime Ota, Yuta Kobayashi, Yoshiyuki Fukushi, Shinichiro Wada and Soromon Kataoka

Microorganisms 2024, 12(10), 2110; https://doi.org/10.3390/microorganisms12102110 - 21 Oct 2024

Viewed by 634

Abstract

This prospective cohort study aimed to evaluate the performance of Flora select™ (FS), a newly developed real-time PCR test, for the assessment of the vaginal microbiome during early pregnancy. Five hundred and fifty-six pregnant women underwent examinations of FS, Nugent score—a Gram-staining scoring [...] Read more.

This prospective cohort study aimed to evaluate the performance of Flora select™ (FS), a newly developed real-time PCR test, for the assessment of the vaginal microbiome during early pregnancy. Five hundred and fifty-six pregnant women underwent examinations of FS, Nugent score—a Gram-staining scoring system for the diagnosis of bacterial vaginosis (BV)—and conventional bacterial culture between 8 weeks and 12 gestational weeks. Nugent scores of 0–3, 4–6, and ≥7 were found in 469 (84.2%), 41 (7.4%), and 47 (8.5%) of the women, respectively. Relative dominance rates of Lactobacillus species of high (≥80% medium (50%≤, <80%), and low (0.1≤, <50%), and no detection (<0.1%) were 63.0%, 8.8%, 17.1%, and 11.2%, respectively. Gardnerella, Prevotella, Atopobium, Streptococcus, Ureaplasma, and Mycoplasma species were detected in 23.9%, 17.6%, 17.1%, 7.0%, 23.0%, and 4.9% of the women, respectively. Gardnerella species were detected in all women with Nugent scores ≥7 and Ureaplasma were detected in 40.4% of them. BV-associated bacterial species were also detected in 70.7% of women with Nugent scores of 4–6. Gardnerella, Prevotella, Atopobium, Streptococcus, Ureaplasma, and Mycoplasma species were highly prevalent in women with Nugent scores ≥4 or Lactobacillus species <50%. FS detected Gardnerella, Prevotella, and Atopobium species more effectively than conventional bacterial culture. FS could determine relative dominance rates of Lactobacillus species in the vaginal microbiome, and simultaneously detect four kinds of BV-associated bacteria, Ureaplasma and Mycoplasma species. Therefore, FS may be clinically useful for the screening of the vaginal microbiome during pregnancy to prevent preterm birth and for the assessment of the vaginal microbiome after BV treatments. Full article

(This article belongs to the Special Issue Detection of Pathogenic Microorganism)

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14 pages, 3655 KiB

Open AccessArticle

The Consumption of Lacticaseibacillus rhamnosus HDB1258 Changes Human Gut Microbiota and Induces Immune Enhancement Through NK Cell Activation

by Jin-Joo Lee, Kyung-Min Kim, Hyeon-Jeong Kim, Johann Sohn, Ji-Won Song, Hye-Yeon Koo and Seunghun Lee

Microorganisms 2024, 12(10), 2109; https://doi.org/10.3390/microorganisms12102109 - 21 Oct 2024

Viewed by 733

Abstract

The gut microbiota can play an important role in enhancing the host’s complex immune system. In this regard, many studies indicate that probiotics consumption has a beneficial impact on alterations in the composition of the gut microbiota. Our previous study demonstrated that the [...] Read more.

The gut microbiota can play an important role in enhancing the host’s complex immune system. In this regard, many studies indicate that probiotics consumption has a beneficial impact on alterations in the composition of the gut microbiota. Our previous study demonstrated that the oral administration of Lacticaseibacillus rhamnosus HDB1258 (HDB1258) enhances immune cell activity and alters the composition of gut microbiota in C57BL/6 mice, thereby showing its potential as a novel immunostimulatory ingredient. Therefore, this clinical trial assessed the effects of HDB1258 on human natural killer (NK) cell activity and changes in gut microbiota. It also investigated the correlation between gut microbiota and NK cell activity following HDB1258 supplementation. Participants (n = 71) were randomized into placebo and HDB1258 groups, and NK cell activity and gut microbiota were investigated at baseline (week 0) and endline (week 8). The present study showed that HDB1258 significantly increased NK cell activity and resulted in positive regulatory effects on the gut microbial balance in subjects compared to the placebo group. HDB1258 affected the gut microbial balance by inducing the growth of beneficial bacteria such as Lactococcus and Sutterella. Especially, the changes in Escherichia–Shigella composition were negatively correlated with the changes in NK cell activity after HDB1258 consumption. There was also a positive correlation between the NK cell activity in the HDB1258 group and the composition of Prevotella 9 and Adlercreutzia. These findings suggest that HDB1258 may improve the host’s intestinal environment by regulating gut bacteria related to immune response and promote NK cell activation. This study was registered at clinical research information service (CRIS: KCT0008204). Full article

(This article belongs to the Special Issue Probiotics, Prebiotics, and Gut Microbes)

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8 pages, 840 KiB

Open AccessCase Report

Baggio–Yoshinari Syndrome: A Report of Five Cases

by Virginia Lucia Nazario Bonoldi, Natalino Hajime Yoshinari, Giusto Trevisan and Serena Bonin

Microorganisms 2024, 12(10), 2108; https://doi.org/10.3390/microorganisms12102108 - 21 Oct 2024

Viewed by 446

Abstract

Compared to classic Lyme disease (LD), Baggio–Yoshinari syndrome (BYS) has the following distinctive characteristics: it is transmitted in the Amazon area and Northeast, Central-West, Southeast, and South regions of Brazil by hard ticks, notably Amblyomma cajannense or Rhipicefalus sp. The absence of Ixodes [...] Read more.

Compared to classic Lyme disease (LD), Baggio–Yoshinari syndrome (BYS) has the following distinctive characteristics: it is transmitted in the Amazon area and Northeast, Central-West, Southeast, and South regions of Brazil by hard ticks, notably Amblyomma cajannense or Rhipicefalus sp. The absence of Ixodes sp. ticks in areas at risk of BYS in Brazil is probably the main reason for the disease’s differences from LD in the United States, Europe, and Asia. Biodiversity and climate probably favor the formation of atypical pleomorphic Borrelias, which have not yet been cultivated or isolated. Clinically, the first manifestation of BYS is the erythema migrans as in the classic forms of Lyme disease, but BYS is distinguished from LD by its prolonged clinical evolution, with a high frequency of relapses and the appearance of autoimmune manifestations. Prevalent symptoms are headache and erythema nodosum. Five clinical cases of BYS in patients who contracted the disease in the Brazilian Amazon rainforest are described here. This syndrome should be considered among differential diagnoses in patients bitten by ticks in Brazil who present with erythema migrans and/or headache. It is important to pursue an early diagnosis because symptoms respond well to antibiotics in the early stages; if treatment is started late, a chronic course with articular and neurological sequelae can be detected. Full article

(This article belongs to the Section Medical Microbiology)

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18 pages, 3215 KiB

Open AccessArticle

Inoculation with Azospirillum brasilense as a Strategy to Reduce Nitrogen Fertilization in Cultivating Purple Maize (Zea mays L.) in the Inter-Andean Valleys of Peru

by Tatiana Condori, Susan Alarcón, Lucero Huasasquiche, Cayo García-Blásquez, César Padilla-Castro, José Velásquez and Richard Solórzano

Microorganisms 2024, 12(10), 2107; https://doi.org/10.3390/microorganisms12102107 - 21 Oct 2024

Viewed by 534

Abstract

Purple maize has gained global significance due to its numerous nutraceutical benefits. However, sustaining its production typically requires high doses of nitrogen fertilizers, which, when applied in excess, can contaminate vital resources such as soil and water. Inoculation with nitrogen-fixing microorganisms, such as [...] Read more.

Purple maize has gained global significance due to its numerous nutraceutical benefits. However, sustaining its production typically requires high doses of nitrogen fertilizers, which, when applied in excess, can contaminate vital resources such as soil and water. Inoculation with nitrogen-fixing microorganisms, such as those from the Azospirillum genus, has emerged as an alternative to partially or fully replace nitrogen fertilizers. This study aimed to evaluate the inoculation effect with A. brasilense and varying nitrogen fertilization levels on the yield and quality of purple maize. The experiment was carried out using a randomized complete block design (RCBD) with a 2 × 5 factorial arrangement and five replications. Treatments comprised two inoculation levels (control without inoculation and inoculation with A. brasilense) under five nitrogen doses (0, 30, 60, 90, and 120 kg∙ha⁻¹, applied as urea). Inoculation with A. brasilense resulted in a 10.5% increase in plant height, a 16.7% increase in root length, a 21.3% increase in aboveground fresh biomass, a 30.1% increase in root fresh biomass, and a 27.7% increase in leaf nitrogen concentration compared to the non-inoculated control. Regarding yield, the inoculated plants surpassed the control in both purple maize yield (kg∙ha⁻¹) and cob weight by 21.8% and 11.6%, respectively. Across all fertilization levels and parameters assessed, the inoculated treatments outperformed the control. Furthermore, for parameters, namely plant height, leaf nitrogen content, and cob dimensions (length, diameter, and weight), the A. brasilense inoculation treatment with 90 kg N∙ha⁻¹ was statistically equivalent or superior to the non-inoculated control with 120 kg N∙ha⁻¹. These results indicate that inoculation with A. brasilense positively impacted purple maize at all nitrogen levels tested and improved nitrogen use efficiency, enabling a reduction of 30 kg N∙ha⁻¹ without compromising performance in key parameters. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)

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16 pages, 2484 KiB

Open AccessArticle

Coinfection of Toxoplasma gondii and Other Microorganisms: A Systematic Review and Meta-Analysis

by María de la Luz Galván-Ramírez, Eber Eduardo Soto-Hernández and Rocío Bojórquez-Pérez

Microorganisms 2024, 12(10), 2106; https://doi.org/10.3390/microorganisms12102106 - 21 Oct 2024

Viewed by 826

Abstract

Toxoplasmosis is a disease caused by the intracellular protozoan Toxoplasma gondii, which has infected a third of the global population. Immunocompromised individuals and children with congenital disorders are most likely to be impacted by toxoplasmosis, and accurate diagnosis is essential. Toxoplasmosis is [...] Read more.

Toxoplasmosis is a disease caused by the intracellular protozoan Toxoplasma gondii, which has infected a third of the global population. Immunocompromised individuals and children with congenital disorders are most likely to be impacted by toxoplasmosis, and accurate diagnosis is essential. Toxoplasmosis is associated with HIV, schizophrenia, and diabetes. However, few studies have analyzed the association with other microorganisms. The purpose of this study was to determine the prevalence of coinfection of Toxoplasma gondii with other pathogens. From November 1997 to June 2024, PubMed, Science Direct, LAT index, Web of Science, Google Scholar, and Research Gate were searched. The keywords used were “Toxoplasma and microorganism coinfection”, “Toxoplasma coinfection and parasites”, “Toxoplasma coinfection and Protozoans or Bacteria or Helminths or Nematodes or Trematodes or Mycobacterium”, “Toxoplasma gondii in coinfection with virus”, and “Human Toxoplasmosis and coinfection”. Next, OpenMeta Analyst Software version 12.11 was used for meta-analysis, creating forest plots, and determining heterogeneity I². A total of 17,535 patients in 48 articles, of whom 5848 were seropositive to T. gondii, were included in this review. Population studies showed that the prevalence of virus infection was most frequent (32%), followed by parasites (18.4%), bacteria (29.7%), and fungi (5.8%). The pooled prevalence of coinfection was found to be 29.1%, with a lower bound of 0.232, an upper bound of 0.350, a standard error of 0.030, and p < 0.001. Heterogeneity (I²) was 99.12%, p < 0.001, with a global variance tau2 = 0.042. Toxoplasma gondii is an opportunist that mainly affects immunocompromised populations. The main coinfections were found to be viral infections, with HIV ranking first, followed by cytomegalovirus, hepatitis B and C, rubella, herpes simplex 1 and 2, SARS-CoV-2, and coxsackie virus. Full article

(This article belongs to the Section Public Health Microbiology)

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11 pages, 2173 KiB

Open AccessArticle

Learning from the rDNA Operon: A Reanalysis of the Acanthamoeba palestinensis Group

by Daniele Corsaro

Microorganisms 2024, 12(10), 2105; https://doi.org/10.3390/microorganisms12102105 - 21 Oct 2024

Viewed by 487

Abstract

The molecular classification of Acanthamoeba is currently based on the analysis of 18S rDNA sequences, delimiting around twenty genotypes (T1–T23). In some cases, however, the resolution of 18S is limited, and other genetic markers could be useful for unravelling poorly resolved lineages. In [...] Read more.

The molecular classification of Acanthamoeba is currently based on the analysis of 18S rDNA sequences, delimiting around twenty genotypes (T1–T23). In some cases, however, the resolution of 18S is limited, and other genetic markers could be useful for unravelling poorly resolved lineages. In this study, the partial large subunit (LSU) of rDNA and ITS were used to re-examine the Acanthamoeba palestinensis group (T2/T6 lineage), which consists of various poorly defined lineages, including the T2 and T6 genotypes. New sequences overlapping 18S, ITS, and LSU were recovered. The analysis placed previously identified partial ITS-LSU sequences as T2/T6 and further confirmed the separation of the OX1 lineage from T2. In addition, analysis of the second internal transcribed spacer (ITS-2) suggests that multiple species may be present within the T6 and OX1 lineages. The results obtained from the T2/T6 lineage analysis confirm the utility of partial LSU and ITS for the study of Acanthamoeba, suggesting their advantage for disentangling complex lineages. Full article

(This article belongs to the Special Issue Advances in Acanthamoeba, Second Edition)

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13 pages, 337 KiB

Open AccessArticle

Antibiotic Susceptibility-Guided Concomitant Therapy Regimen with Vonoprazan, High-Dose Amoxicillin, Clarithromycin, and Metronidazole for Helicobacter pylori Eradication as Fourth-Line Regimen: An Interventional Study

by Soichiro Sue, Takeshi Sato, Mao Matsubayashi, Hiroaki Kaneko, Kuniyasu Irie and Shin Maeda

Microorganisms 2024, 12(10), 2104; https://doi.org/10.3390/microorganisms12102104 - 21 Oct 2024

Viewed by 573

Abstract

This is the first registered intervention study for vonoprazan, high-dose amoxicillin, clarithromycin, and metronidazole 14-day concomitant therapy based on a susceptibility test of Helicobacter pylori. We conducted this study as a fourth-line rescue regimen in Japan. Methods: Twenty patients who underwent three [...] Read more.

This is the first registered intervention study for vonoprazan, high-dose amoxicillin, clarithromycin, and metronidazole 14-day concomitant therapy based on a susceptibility test of Helicobacter pylori. We conducted this study as a fourth-line rescue regimen in Japan. Methods: Twenty patients who underwent three rounds of eradication therapies (first- or second-line 7-day triple therapy consisting of amoxicillin and clarithromycin, or metronidazole- and sitafloxacin-based third-line therapy) and had failed eradication based on a urea breath test or fecal antigen test were recruited. All patients underwent endoscopic examination and culture tests before starting eradication therapy. The intervention was concomitant therapy consisting of vonoprazan 20 mg bid, amoxicillin 500 mg qid, clarithromycin 400 mg bid, and metronidazole 250 mg bid for 14 days, which were modified based on the susceptibility test, and the resistant drugs were removed from the regimen. Patients with negative culture results were treated with quadruple therapy. The primary outcome was the eradication rate (UMIN000025765, jRCTs 031180208). Results: The eradication rate of susceptibility-testing-based fourth-line eradication therapy was 63.2% (95%CI: 38.4–83.7%) in intent-to-treat analysis and 70.6% (95%CI: 44.0–89.7%) in per-protocol analysis. Thirteen patients received quadruple therapy, with eradication rates of 61.5% and 75.0%, respectively. No serious adverse events were reported. Conclusions: This vonoprazan-based concomitant therapy modified by the susceptibility test is a potential option as fourth-line eradication after first-line clarithromycin-based 7-day triple, second-line metronidazole-based 7-day triple, and third-line sitafloxacin-based 7-day triple therapy failure. Full article

(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)

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13 pages, 1528 KiB

Open AccessArticle

Impact of Various Washing Protocols on the Mitigation of Escherichia coli Contamination in Raw Salad Vegetables

by Fahad M. Alreshoodi, Bassam Alsuliman, Norah M. Alotaibi, Afnan Althobaiti, Lenah E. Mukhtar, Sarah Alsaleh, Abdullah A. Alajlan, Saleh I. Alakeel, Fahad M. Alshabrmi, Tarique Sarwar and Sulaiman M. Alajel

Microorganisms 2024, 12(10), 2103; https://doi.org/10.3390/microorganisms12102103 - 21 Oct 2024

Viewed by 1136

Abstract

Vegetables are an essential component of a balanced diet. The consumption of ready-to-eat foods may lead to the risk of infections and illnesses due to microbial contamination. To mitigate the potential of microbial contamination risks, it is critical to promote safe handling practices [...] Read more.

Vegetables are an essential component of a balanced diet. The consumption of ready-to-eat foods may lead to the risk of infections and illnesses due to microbial contamination. To mitigate the potential of microbial contamination risks, it is critical to promote safe handling practices among consumers. In this study, our research evaluated the efficacy of different vegetable washing methods, specifically with lettuce, tomato, and cucumber, to establish optimal practices for reducing microbial contamination. This study consisted of two phases. Initially, a survey was distributed to 150 volunteers using snowball sampling to assess everyday vegetable handling and washing methods. The survey’s results identified four predominant methods: washing with a 5% vinegar solution for 3 min followed by tap water rinse (37.3% of participants), rinsing with tap water for 1 min (29.3%), washing with a 5% salt solution (vegetable soap) for 3 min followed by a tap water rinse (16.6%), and a 3 min tap water rinse (14%). A minor segment (3.33%) reported not washing their vegetables at all. The survey’s findings guided the second phase, which tested the aforementioned washing protocols’ effectiveness in reducing Escherichia coli (E. coli) levels on spiked contaminated salad vegetables. The tested vegetables were sterilized using UV light, inoculated with 0.5 McFarland E. coli, and then washed using the four identified methods. After that, E. coli enumeration after washing was performed using 3M™ Petrifilm and the comparison was analyzed via one-way ANOVA. During this study, it was revealed that the cucumbers had the highest E. coli contamination levels in comparison to the lettuce and tomato after washing. Interestingly, by comparing the three washing methods, it was found that washing the vegetables with vinegar proved to be the most effective solution for reducing microbial presence on both lettuce and cucumbers. Notably, the natural smoothness of tomato skin led to no significant differences in contamination levels across washing methods. In summary, vinegar washing effectively reduces microbial contamination from salad vegetables, highlighting the need for informed consumer practices to prevent foodborne outbreaks. This study emphasizes the importance of monitoring contamination sources and using safe washing techniques. Full article

(This article belongs to the Special Issue Overview of Foodborne Pathogens and Antimicrobial Resistance)

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14 pages, 2126 KiB

Open AccessReview

Listeria in Pregnancy—The Forgotten Culprit

by Vladimír Kraus, Jr., Beáta Čižmárová and Anna Birková

Microorganisms 2024, 12(10), 2102; https://doi.org/10.3390/microorganisms12102102 - 21 Oct 2024

Viewed by 645

Abstract

Listeria monocytogenes is a Gram-positive bacterium that causes listeriosis, a severe foodborne illness that is particularly dangerous during pregnancy. It thrives in diverse environments, including refrigerated conditions and food production facilities, due to its adaptability to varying temperatures, pH levels, and salt concentrations. [...] Read more.

Listeria monocytogenes is a Gram-positive bacterium that causes listeriosis, a severe foodborne illness that is particularly dangerous during pregnancy. It thrives in diverse environments, including refrigerated conditions and food production facilities, due to its adaptability to varying temperatures, pH levels, and salt concentrations. Its virulence stems from the ability to invade host cells, particularly macrophages and epithelial cells, and avoid, or at least postpone, immune detection by utilizing virulence factors such as internalins, listeriolysin O, and actin assembly-inducing protein. This intracellular motility and biofilm formation make LM a persistent pathogen in food safety and public health. Pregnant women are at a much higher risk of listeriosis, which can result in serious fetal complications such as miscarriage, stillbirth, and preterm labor due to LM’s affinity for placental tissues. The vertical transmission of LM from mother to fetus can lead to neonatal listeriosis, which can result in sepsis and meningitis, with high mortality rates if not promptly treated. Early diagnosis and treatment with antibiotics, such as ampicillin or gentamicin, are crucial for maternal and neonatal outcomes. Full article

(This article belongs to the Special Issue Microbial Infections during Pregnancy: Second Edition)

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17 pages, 5038 KiB

Open AccessArticle

Potentially Pathogenic Vibrio spp. in Algal Wrack Accumulations on Baltic Sea Sandy Beaches

by Marija Kataržytė, Greta Gyraitė, Greta Kalvaitienė, Diana Vaičiūtė, Otilija Budrytė and Martynas Bučas

Microorganisms 2024, 12(10), 2101; https://doi.org/10.3390/microorganisms12102101 - 21 Oct 2024

Viewed by 605

Abstract

The Vibrio bacteria known to cause infections to humans and wildlife have been largely overlooked in coastal environments affected by beach wrack accumulations from seaweed or seagrasses. This study presents findings on the presence and distribution of potentially pathogenic Vibrio species on coastal [...] Read more.

The Vibrio bacteria known to cause infections to humans and wildlife have been largely overlooked in coastal environments affected by beach wrack accumulations from seaweed or seagrasses. This study presents findings on the presence and distribution of potentially pathogenic Vibrio species on coastal beaches that are used for recreation and are affected by red-algae-dominated wrack. Using species-specific primers and 16S rRNA gene amplicon sequencing, we identified V. vulnificus, V. cholerae (non-toxigenic), and V. alginolyticus, along with 14 operational taxonomic units (OTUs) belonging to the Vibrio genus in such an environment. V. vulnificus and V. cholerae were most frequently found in water at wrack accumulation sites and within the wrack itself compared to sites without wrack. Several OTUs were exclusive to wrack accumulation sites. For the abundance and presence of V. vulnificus and the presence of V. cholerae, the most important factors in the water were the proportion of V. fucoides in the wrack, chl-a, and CDOM. Specific Vibrio OTUs correlated with salinity, water temperature, cryptophyte, and blue-green algae concentrations. To better understand the role of wrack accumulations in Vibrio abundance and community composition, future research should include different degradation stages of wrack, evaluate the link with nutrient release, and investigate microbial food-web interactions within such ecosystems, focusing on potentially pathogenic Vibrio species that could be harmful both for humans and wildlife. Full article

(This article belongs to the Special Issue Research on Diseases of Aquatic Organisms)

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15 pages, 7839 KiB

Open AccessArticle

A Novel Cold-Adapted Nitronate Monooxygenase from Psychrobacter sp. ANT206: Identification, Characterization and Degradation of 2-Nitropropane at Low Temperature

by Yatong Wang, Shumiao Hou, Qi Zhang, Yanhua Hou and Quanfu Wang

Microorganisms 2024, 12(10), 2100; https://doi.org/10.3390/microorganisms12102100 - 21 Oct 2024

Viewed by 589

Abstract

Aliphatic nitro compounds cause environmental pollution by being discharged into water with industrial waste. Biodegradation needs to be further explored as a green and pollution-free method of environmental remediation. In this study, we successfully cloned a novel nitronate monooxygenase gene (psnmo) [...] Read more.

Aliphatic nitro compounds cause environmental pollution by being discharged into water with industrial waste. Biodegradation needs to be further explored as a green and pollution-free method of environmental remediation. In this study, we successfully cloned a novel nitronate monooxygenase gene (psnmo) from the genomic DNA library of Psychrobacter sp. ANT206 and investigated its ability to degrade 2-nitropropane (2-NP). Homology modeling demonstrated that PsNMO had a typical I nitronate monooxygenase catalytic site and cold-adapted structural features, such as few hydrogen bonds. The specific activity of purified recombinant PsNMO (rPsNMO) was 97.34 U/mg, rPsNMO exhibited thermal instability and reached maximum catalytic activity at 30 °C. Moreover, rPsNMO was most active in 1.5 M NaCl and remained at 104% of its full activity in 4.0 M NaCl, demonstrating its significant salt tolerance. Based on this finding, a novel bacterial cold-adapted enzyme was obtained in this work. Furthermore, rPsNMO protected E. coli BL21 (DE3)/pET28a(+) from the toxic effects of 2-NP at 30 °C because the 2-NP degradation rate reached 96.1% at 3 h and the final product was acetone. These results provide a reliable theoretical basis for the low-temperature degradation of 2-NP by NMO. Full article

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

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12 pages, 2212 KiB

Open AccessArticle

Decontamination of Fused-Silica Surfaces by UVC Irradiation as Potential Application on Touchscreens

by Ben Sicks, Oksana Gurow, Florian Sommerfeld and Martin Hessling

Microorganisms 2024, 12(10), 2099; https://doi.org/10.3390/microorganisms12102099 - 21 Oct 2024

Viewed by 580

Abstract

The contamination of surfaces by antibiotic-resistant pathogens presents an escalating challenge, especially on touchscreens in public settings such as hospitals, airports, and means of transport. Traditional chemical cleaning agents are often ineffective and leave behind harmful residues. Thus, the application of optical radiation [...] Read more.

The contamination of surfaces by antibiotic-resistant pathogens presents an escalating challenge, especially on touchscreens in public settings such as hospitals, airports, and means of transport. Traditional chemical cleaning agents are often ineffective and leave behind harmful residues. Thus, the application of optical radiation is gaining relevance as a rapid, effective, and environmentally friendly disinfection method. This study examines the contamination of publicly accessible touchscreens and the efficacy of an irradiation approach for the radiation disinfection of microorganisms on quartz surfaces with UVC LEDs. In this setup, the LED radiation is laterally coupled into a quartz plate that serves as cover glass of a simplified touchscreen model. The process allows for the irradiation of microorganisms on the surface, without the user being exposed to hazardous radiation. To assess the efficacy of the disinfection process, a range of bacteria, mostly ESKAPE surrogates, such as Staphylococcus carnosus, Acinetobacter kookii, Escherichia coli, Enterococcus mundtii, and additionally Micrococcus luteus, were spread over a quartz plate with a homebuilt nebulization system. After operating the side-mounted LEDs for 30 s, a reduction in all bacteria except M. luteus by more than three orders of magnitude was observed. In the case of M. luteus, a significant reduction was achieved after 60 s (p < 0.05). This result demonstrates the potential of side-mounted UVC LEDs for rapid disinfection of touchscreens between two users and thus for reducing the spread of pathogens without irradiating humans. Full article

(This article belongs to the Special Issue The New Advance on Disinfectant of Virus and Microorganisms, 2nd Edition)

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13 pages, 3026 KiB

Open AccessArticle

Antibacterial Effects of Black Cumin Seed Oil on Oral Microcosm Biofilms

by Ahyun Jo and Hee-Eun Kim

Microorganisms 2024, 12(10), 2098; https://doi.org/10.3390/microorganisms12102098 - 20 Oct 2024

Viewed by 640

Abstract

Interest in natural extracts for managing oral biofilms is increasing, with black cumin seed oil (BCSO) demonstrating efficacy against Streptococcus mutans. The effectiveness of antibacterial agents should be evaluated using multi-species oral biofilm models that closely mimic actual conditions. This study aimed [...] Read more.

Interest in natural extracts for managing oral biofilms is increasing, with black cumin seed oil (BCSO) demonstrating efficacy against Streptococcus mutans. The effectiveness of antibacterial agents should be evaluated using multi-species oral biofilm models that closely mimic actual conditions. This study aimed to compare the antibacterial effects of BCSO and chlorhexidine gluconate (CHX) on oral microcosm biofilms. Biofilms using human saliva as the inoculum were cultured for 2 days and subsequently treated with 0.5% dimethyl sulfoxide, 0.5% BCSO, or 0.12% CHX once daily for 6 days. Following treatment, the red fluorescence intensity (Ratio_R/G) of the oral biofilm; biomass, including extracellular polymeric substance (EPS) levels and live bacteria counts; and colony-forming units (CFUs) of aciduric bacteria were evaluated. Ratio_R/G after BCSO treatment (1.26 ± 0.03) was not significantly different from that after CHX treatment (p = 0.552). The EPS levels were also not significantly different between the two groups (p = 0.743). The live bacteria count was 0.55 times lower in the BCSO-treated group than in the CHX-treated group (p = 0.018). No significant between-group difference was observed in the CFUs of aciduric bacteria (p = 0.935). These results suggest that BCSO exhibits antibacterial effects similar to those of CHX, highlighting its potential as an effective alternative. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilm)

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19 pages, 2422 KiB

Open AccessArticle

Study of Different Parameters Affecting Production and Productivity of Polyunsaturated Fatty Acids (PUFAs) and γ-Linolenic Acid (GLA) by Cunninghamella elegans Through Glycerol Conversion in Shake Flasks and Bioreactors

by Gabriel Vasilakis, Christina Roidouli, Dimitris Karayannis, Nikos Giannakis, Emmanuel Rondags, Isabelle Chevalot and Seraphim Papanikolaou

Microorganisms 2024, 12(10), 2097; https://doi.org/10.3390/microorganisms12102097 - 20 Oct 2024

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Abstract

Microbial cultures repurposing organic industrial residues for value-added metabolite production is pivotal for sustainable resource use. Highlighting polyunsaturated fatty acids (PUFAs), particularly gamma-linolenic acid (GLA), renowned for their nutritional and therapeutic value. Notably, Zygomycetes’ filamentous fungi harbor abundant GLA-rich lipid content, furthering their [...] Read more.

Microbial cultures repurposing organic industrial residues for value-added metabolite production is pivotal for sustainable resource use. Highlighting polyunsaturated fatty acids (PUFAs), particularly gamma-linolenic acid (GLA), renowned for their nutritional and therapeutic value. Notably, Zygomycetes’ filamentous fungi harbor abundant GLA-rich lipid content, furthering their relevance in this approach. In this study, the strain C. elegans NRRL Y-1392 was evaluated for its capability to metabolize glycerol and produce lipids rich in GLA under different culture conditions. Various carbon-to-nitrogen ratios (C/N = 11.0, 110.0, and 220.0 mol/mol) were tested in batch-flask cultivations. The highest GLA production of 224.0 mg/L (productivity equal to 2.0 mg/L/h) was observed under nitrogen excess conditions, while low nitrogen content promoted lipid accumulation (0.59 g of lipids per g of dry biomass) without yielding more PUFAs and GLA. After improving the C/N ratio at 18.3 mol/mol, even higher PUFA (600 mg/L) and GLA (243 mg/L) production values were recorded. GLA content increased when the fungus was cultivated at 12 °C (15.5% w/w compared to 12.8% w/w at 28 °C), but productivity values decreased significantly due to prolonged cultivation duration. An attempt to improve productivity by increasing the initial spore population did not yield the expected results. The successful scale-up of fungal cultivations is evidenced by achieving consistent results (compared to flask experiments under corresponding conditions) in both laboratory-scale (Working Volume—Vw = 1.8 L; C/N = 18.3 mol/mol) and semi-pilot-scale (Vw = 15.0 L; C/N = 110.0 mol/mol) bioreactor experiments. To the best of our knowledge, cultivation of the fungus Cunninghamella elegans in glycerol-based substrates, especially in 20 L bioreactor experiments, has never been previously reported in the international literature. The successful scale-up of the process in a semi-pilot-scale bioreactor illustrates the potential for industrializing the bioprocess. Full article

(This article belongs to the Special Issue Bioproduction of Functional and Bioactive Ingredients: State of the Art and Technological Advances)

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15 pages, 2229 KiB

Open AccessArticle

Role of the SaeRS Two-Component Regulatory System in Group B Streptococcus Biofilm Formation on Human Fibrinogen

by Francesco Coppolino, Alessia Berbiglia, Germana Lentini, Agata Famà, Giampiero Pietrocola, Giuseppe Teti, Concetta Beninati and Giuseppe Valerio De Gaetano

Microorganisms 2024, 12(10), 2096; https://doi.org/10.3390/microorganisms12102096 - 20 Oct 2024

Viewed by 818

Abstract

Streptococcus agalactiae, also known as Group B Streptococcus or GBS, is a commensal colonizer of human vaginal and gastrointestinal tracts that can also be a deadly pathogen for newborns, pregnant women, and the elderly. The SaeRS two-component regulatory system (TCS) positively regulates [...] Read more.

Streptococcus agalactiae, also known as Group B Streptococcus or GBS, is a commensal colonizer of human vaginal and gastrointestinal tracts that can also be a deadly pathogen for newborns, pregnant women, and the elderly. The SaeRS two-component regulatory system (TCS) positively regulates the expression of two GBS adhesins genes, but its role in the formation of biofilm, an important step in pathogenesis, has not been investigated. In the present study, we set up a novel model of GBS biofilm formation using surfaces coated with human fibrinogen (hFg). Biofilm mass and structure were analyzed by crystal violet staining and three-dimensional fluorescence microscopy, respectively. GBS growth on hFg resulted in the formation of a mature and abundant biofilm composed of bacterial cells and an extracellular matrix containing polysaccharides, proteins, and extracellular DNA (eDNA). Enzymatic and genetic analysis showed that GBS biofilm formation on hFg is dependent on proteins and eDNA in the extracellular matrix and on the presence of covalently linked cell wall proteins on the bacterial surface but not on the type-specific capsular polysaccharide. In the absence of the SaeR regulator of the SaeRS TCS, there was a significant reduction in biomass formation, with reduced numbers of bacterial cells, reduced eDNA content, and disruption of the biofilm architecture. Overall, our data suggest that GBS binding to hFg contributes to biofilm formation and that the SaeRS TCS plays an important role in this process. Full article

(This article belongs to the Special Issue Advanced Research on Microbial Biofilms—a Themed Issue in Honor of Professor Gianfranco Donelli)

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14 pages, 2386 KiB

Open AccessArticle

Optimization of Citrus Pulp Waste-Based Medium for Improved Bacterial Nanocellulose Production

by Carlotta Minardi, Davide Bersanetti, Essi Sarlin, Ville Santala and Rahul Mangayil

Microorganisms 2024, 12(10), 2095; https://doi.org/10.3390/microorganisms12102095 - 20 Oct 2024

Viewed by 566

Abstract

Bacterial nanocellulose (BC) has attracted significant attention across a wide array of applications due to its distinctive characteristics. Recently, there has been increasing interest in leveraging waste biomass to improve sustainability in BC biogenesis processes. This study focuses on optimizing the citrus pulp [...] Read more.

Bacterial nanocellulose (BC) has attracted significant attention across a wide array of applications due to its distinctive characteristics. Recently, there has been increasing interest in leveraging waste biomass to improve sustainability in BC biogenesis processes. This study focuses on optimizing the citrus pulp waste (CPW) medium to enhance BC production using Komagataeibacter sucrofermentans. The screening of initial medium pH, yeast extract, CPW sugar and inoculum concentrations was conducted using the Plackett–Burman design, with BC yield (mgDW/gCPW) as the model response. The significant parameters, i.e., CPW sugars and yeast extract concentrations, were optimized using response surface methodology, employing a five-level, two-factor central composite design. The optimized CPW-based growth medium resulted in a final yield of 66.7 ± 5.1 mgDW/gCPW, representing a 14-fold increase compared to non-optimized conditions (4.3 ± 0.4 mgBC/gCPW). Material characterization analysis indicated that the produced BC showed high thermal stability (30% mass retained at 600 °C) and a crystallinity index value of 71%. Additionally, to enhance process sustainability, spent baker’s yeast hydrolysate (BYH) was assessed as a substitute for yeast extract, leading to a final BC titer of 9.3 ± 0.6 g/L. Full article

(This article belongs to the Special Issue The Role of Microbial Biotechnology in the Development of Sustainable Biopolymers)

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16 pages, 10295 KiB

Open AccessArticle

Taxonomic Diversity, Predicted Metabolic Pathway, and Interaction Pattern of Bacterial Community in Sea Urchin Anthocidaris crassispina

by Xinye Chen, Li Mo, Lin Zhang, Liyu Huang, Ziqing Gao, Jingjing Peng, Zonghe Yu and Xiaoyong Zhang

Microorganisms 2024, 12(10), 2094; https://doi.org/10.3390/microorganisms12102094 - 20 Oct 2024

Viewed by 563

Abstract

Bacterial assemblages associated with sea urchin are critical to their physiology and ecology within marine ecosystems. In this study, we characterized the bacterial communities in wild sea urchin Anthocidaris crassispina captured in Daya Bay, South China Sea. A total of 363 amplicon sequence [...] Read more.

Bacterial assemblages associated with sea urchin are critical to their physiology and ecology within marine ecosystems. In this study, we characterized the bacterial communities in wild sea urchin Anthocidaris crassispina captured in Daya Bay, South China Sea. A total of 363 amplicon sequence variants belonging to nine phyla and 141 genera were classified from intestine, body surface, and surrounding seawater samples. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacteria phyla found in this study. A network analysis of bacterial interspecies interactions revealed varying complexity, stability, connectivity, and relationship patterns across the samples, with the most intricate network observed in the surrounding seawater. Metagenomic predictions highlighted the distinct bacterial metabolic pathways, with significant differences between intestine and seawater samples. Notably, pathways associated with polysaccharide degradation, including chitin derivatives, starch, and CoM biosynthesis, were markedly abundant, underscoring the gut microbiota’s key role in digesting algae. In addition, other metabolic pathways in intestine samples were linked to immune response regulation of sea urchins. Overall, this study provides a comprehensive overview of the bacterial community structure and potential functional roles in A. crassispina. Full article

(This article belongs to the Special Issue Bacterial Infections in Aquaculture of Farmed Fish: Pathogenesis, Pathophysiology, Molecular Diagnosis, and Control)

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20 pages, 6293 KiB

Open AccessArticle

FgUbiH Is Essential for Vegetative Development, Energy Metabolism, and Antioxidant Activity in Fusarium graminearum

by Jinwen Ge, Huanchen Zhai, Lei Tang, Shuaibing Zhang, Yangyong Lv, Pingan Ma, Shan Wei, Yu Zhou, Xiaofu Wu, Yang Lei, Fengguang Zhao and Yuansen Hu

Microorganisms 2024, 12(10), 2093; https://doi.org/10.3390/microorganisms12102093 - 20 Oct 2024

Viewed by 654

Abstract

Fusarium head blight in wheat is mainly caused by Fusarium graminearum and results in significant economic losses. Coenzyme Q (CoQ) is ubiquitously produced across organisms and functions as a hydrogen carrier in energy metabolism. While UbiH in Escherichia coli serves as a hydroxylase [...] Read more.

Fusarium head blight in wheat is mainly caused by Fusarium graminearum and results in significant economic losses. Coenzyme Q (CoQ) is ubiquitously produced across organisms and functions as a hydrogen carrier in energy metabolism. While UbiH in Escherichia coli serves as a hydroxylase in CoQ biosynthesis, its role in phytopathogenic fungi is not well understood. This study explored the role of the hydroxylase FgUbiH in F. graminearum. Using a FgUbiH deletion mutant, we observed reduced hyphal growth, conidial production, germination, toxin synthesis, and pathogenicity compared to the wild-type. A transcriptome analysis indicated FgUbiH’s involvement in regulating carbohydrate and amino acid metabolism. Deletion of FgUbiH impaired mitochondrial function, reducing adenosine triphosphate synthesis and increasing reactive oxygen species. Additionally, genes related to terpene skeleton synthesis and aldehyde dehydrogenase were downregulated. Our results underscore the importance of FgUbiH in F. graminearum’s growth, toxin production, and energy metabolism, aiding in the development of strategies for disease management. Full article

(This article belongs to the Special Issue Plant Pathogens: Monitoring, Identification and Biological Control)

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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 - 19 Oct 2024

Viewed by 584

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 - 19 Oct 2024

Viewed by 529

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 - 18 Oct 2024

Viewed by 604

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 561

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 463

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 855

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 561

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 599

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

Viewed by 664

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

Viewed by 571

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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Microorganisms, Volume 12, Issue 10 (October 2024) – 181 articles

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