Microorganisms

14 pages, 801 KiB

Open AccessArticle

Production of Esters in Escherichia coli Using Citrate Synthase Variants

by Jacoby C. Shipmon, Pasupathi Rathinasabapathi, Michael L. Broich II, Hemansi and Mark A. Eiteman

Microorganisms 2024, 12(7), 1338; https://doi.org/10.3390/microorganisms12071338 (registering DOI) - 29 Jun 2024

Acetate esters comprise a wide range of products including fragrances and industrial solvents. Biosynthesis of esters offers a promising alternative to chemical synthesis because such routes use renewable carbohydrate resources and minimize the generation of waste. One biochemical method for ester formation relies [...] Read more.

Acetate esters comprise a wide range of products including fragrances and industrial solvents. Biosynthesis of esters offers a promising alternative to chemical synthesis because such routes use renewable carbohydrate resources and minimize the generation of waste. One biochemical method for ester formation relies on the ATF1 gene from Saccharomyces cerevisiae, which encodes alcohol-O-acyltransferase (AAT) which converts acetyl-CoA and an exogenously supplied alcohol into the ester. In this study, the formation of several acetate esters via AAT was examined in Escherichia coli chromosomally expressing citrate synthase variants, which create a metabolic bottleneck at acetyl-CoA. In shake flask cultures, variant strains generated more acetate esters than the strains expressing the wild-type citrate synthase. In a controlled bioreactor, E. coli GltA[A267T] generated 3.9 g propyl acetate in 13 h, corresponding to a yield of 0.155 g propyl acetate/g glucose, which is 18% greater than that obtained by the wild-type GltA control. These results demonstrate the ability of citrate synthase variants to redistribute carbon from central metabolism into acetyl-CoA-derived biochemicals. Full article

(This article belongs to the Special Issue Microbial Biotechnology: The Biodiversity, Properties and Benefits of Microorganisms in Medical, Clinical, Food and Environmental Fields)

14 pages, 361 KiB

Open AccessReview

Infective Endocarditis Due to Corynebacterium jeikeium: Four Case Reports and Narrative Review of the Literature

by Daniel Arnés-García, Laura Lucena-Torres, Antonio Bustos-Merlo, Antonio Rosales-Castillo and Carmen Hidalgo-Tenorio

Microorganisms 2024, 12(7), 1337; https://doi.org/10.3390/microorganisms12071337 (registering DOI) - 29 Jun 2024

Abstract

Corynebacterium jeikeium, a pleomorphic Gram-positive bacillus, is a common component of the cutaneous microbiota, usually considered as a contaminant, with little pathogenic potential. However, its role in various types of infections, such as bacteremia, sepsis, endocarditis (IE) and infection of prosthetic material [...] Read more.

Corynebacterium jeikeium, a pleomorphic Gram-positive bacillus, is a common component of the cutaneous microbiota, usually considered as a contaminant, with little pathogenic potential. However, its role in various types of infections, such as bacteremia, sepsis, endocarditis (IE) and infection of prosthetic material is gradually being proven. Few cases of IE due to Corynebacterium jeikeium have been described in the literature. The aim of this article was to describe four cases of IE due to Corynebacterium jeikeium diagnosed in our hospital between May 2021 and April 2022, as well as to conduct a narrative review of the literature on this entity. After analysis, we highlight that 65.6% were men, 81.3% were valve or intravascular device carriers, and IE cases presented early, before one year after surgery. The most affected valve was the aortic valve (68.8%), followed by the mitral valve (21.1%). Valve replacement was performed in 65.6% of cases, and the most commonly used antibiotic was vancomycin (68.8%) at a dose of 15 mg/kg/12 h. With respect to prognosis, the overall mortality rate was 21.9%. The comparative results between our series and the literature review were similar except for a higher mortality rate (50%) and the use of dalbavancin in the treatment. We go on to review previously reported cases, along with four cases described in our hospital, of C. jeikeium endocarditis and will discuss various aspects of C. jeikeium infection, focusing on microbiology, pathophysiology, and treatment. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Multidrug-Resistant Bacteria in Infectious Patients)

15 pages, 7018 KiB

Open AccessArticle

Effect of Trace Element Selenium on the Intestinal Microbial Community in Nude Mice with Colorectal Cancer

by Yintong Su, Xiaohua Cai, Xingxing Fan, Jiayu Ning and Mei Shen

Microorganisms 2024, 12(7), 1336; https://doi.org/10.3390/microorganisms12071336 (registering DOI) - 29 Jun 2024

Abstract

Colorectal cancer (CRC) is the third most common cancer worldwide. The role of intestinal microbiota in carcinogenesis has also become an important research topic, and CRC is closely related to the intestinal microbiota. Selenium-containing compounds have attracted more attention as anticancer drugs as [...] Read more.

Colorectal cancer (CRC) is the third most common cancer worldwide. The role of intestinal microbiota in carcinogenesis has also become an important research topic, and CRC is closely related to the intestinal microbiota. Selenium-containing compounds have attracted more attention as anticancer drugs as they can have minimal side effects. The purpose of this study was to determine and compare the effect of sodium selenite and selenomethionine on the microbial communities of nude mice with CRC. A CRC ectopic tumorigenesis model was established by subcutaneously injecting HCT116 cells into nude mice. The mice were then intraperitoneally injected with sodium selenite and selenomethionine for 24 days to regulate their intestinal microbiota. Compared with sodium selenite, selenomethionine resulted in a greater reduction in the richness and diversity of intestinal microbiota in nude mice with CRC, and the richness and diversity were closer to healthy levels. Selenomethionine also regulated a wider variety of flora. Additionally, sodium selenite and selenomethionine produced different microorganisms, changed function and metabolic pathways in the intestinal microbiota. Both sodium selenite and selenomethionine have certain effects on restoring the intestinal microbial diversity in nude mice with CRC, and the effect of selenomethionine is better than that of sodium selenite. Full article

(This article belongs to the Section Medical Microbiology)

15 pages, 4601 KiB

Open AccessArticle

Selection and Genetic Analysis of High Polysaccharide-Producing Mutants in Inonotus obliquus

by Lanlan Hua, Hongling Shi, Qing Lin, Haozhong Wang, Yan Gao, Jun Zeng, Kai Lou and Xiangdong Huo

Microorganisms 2024, 12(7), 1335; https://doi.org/10.3390/microorganisms12071335 (registering DOI) - 29 Jun 2024

Abstract

Abstract: Inonotus obliquus, a medicinal fungus, has garnered significant attention in scientific research and medical applications. In this study, protoplasts of the I. obliquus HS819 strain were prepared using an enzymatic method and achieved a regeneration rate of 5.83%. To [...] Read more.

Abstract: Inonotus obliquus, a medicinal fungus, has garnered significant attention in scientific research and medical applications. In this study, protoplasts of the I. obliquus HS819 strain were prepared using an enzymatic method and achieved a regeneration rate of 5.83%. To enhance polysaccharide production of I. obliquus HS819, atmospheric and room temperature plasma (ARTP) technology was employed for mutagenesis of the protoplasts. Through liquid fermentation, 32 mutant strains exhibiting diverse characteristics in morphology, color of the fermentation broth, mycelial pellet size, and biomass were screened. Secondary screening identified mutant strain A27, which showed a significant increase in polysaccharide production up to 1.67 g/L and a mycelial dry weight of 17.6 g/L, representing 137.67% and 15% increases compared to the HS819 strain, respectively. Furthermore, the fermentation period was reduced by 2 days, and subsequent subculture cultivation demonstrated stable polysaccharide production and mycelial dry weight. The genome resequencing analysis of the HS819 strain and mutant strain A27 revealed 3790 InDel sites and mutations affecting 612 functional genes associated with polysaccharide synthesis. We predict that our findings will be helpful for high polysaccharide production through genetic engineering of I. obliquus. Full article

(This article belongs to the Section Microbial Biotechnology)

19 pages, 690 KiB

Open AccessArticle

Response of Arugula to Integrated Use of Biological, Inorganic, and Organic Fertilization

by Aleksandra Stanojković-Sebić, Vladimir Miladinović and Radmila Pivić

Microorganisms 2024, 12(7), 1334; https://doi.org/10.3390/microorganisms12071334 (registering DOI) - 29 Jun 2024

Viewed by 128

Abstract

This study evaluated the effects of solely and integrated application of inorganic (NPK), commercial organic (NC), and biological (MIX, mixed strains Ensifer meliloti and Azotobacter chroococcum) fertilizers on the chemical characteristics of arugula biomass and its yield, as well as changes in [...] Read more.

This study evaluated the effects of solely and integrated application of inorganic (NPK), commercial organic (NC), and biological (MIX, mixed strains Ensifer meliloti and Azotobacter chroococcum) fertilizers on the chemical characteristics of arugula biomass and its yield, as well as changes in soil microbiological parameters after the experiment in relation to the control treatment (Ø). The experiment was performed in semi-controlled greenhouse conditions, in pots, from the 4th decade of March to the 2nd decade of September, in 2023, at three cutting times/swaths, during one agricultural season, with Vertisol soil. For soil characterization, the following parameters were analysed: granulometric composition using sieving and sedimentation procedure; soil acidity—potentiometrically; SOM—soil organic matter by Kotzmann method; total N using CNS analyser; available P—spectrophotometrically; available K—flame photometrically; total number of microorganisms on an agarized soil extract medium; fungi on a solid Czapek agar; actinomycetes on a solid Krasiljnikov agar with saccharose; Azotobacter spp. on a liquid Fyodorov medium with mannitol; ammonifiers on a liquid medium with asparagine; and dehydrogenase activity—spectrophotometrically. For plant characterization, the following parameters were determined: N and C, both on CNS analyser; P on spectrophotometer; K on flame photometer; air-dried yield biomass. A stimulative effect on all microbiological parameters was found in the treatment with integrated use of organic and biological fertilizer, except for fungi, which grew better in the treatments with separate inorganic and organic fertilizers. Generally, the stimulative impact on plant chemical parameters manifested in combined inorganic and biological, organic and biological, and inorganic and organic fertilization treatments, and was inhibited in treatment without fertilization, in all three swaths, which could also be stated for the plant yield. Positive influence of all fertilization treatments on chemical parameters was observed for the second swath in relation to the first and the third. The total yield in the NPK+MIX treatment was 121%, and in the NC+MIX treatment, it was 87% higher compared to the control (Ø). In general, integrated use of inorganic and biological, organic and biological, and inorganic and organic fertilizers, respectively, could be proposed as an optimal fertilization treatment in arugula cultivation. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

► Show Figures

Figure 1

17 pages, 9029 KiB

Open AccessArticle

The Cellular Microbiome of Visceral Organs: An Inherent Inhabitant of Parenchymal Cells

by Xiaowei Sun, Hua Zhang, Xiao Zhang, Wenmin Gao, Caiyun Zhou, Xuanxuan Kou, Jingxin Deng and Jiangang Zhang

Microorganisms 2024, 12(7), 1333; https://doi.org/10.3390/microorganisms12071333 (registering DOI) - 29 Jun 2024

Viewed by 151

Abstract

The cell is the basic unit of life. It is composed of organelles and various organic and inorganic biomolecules. Recent 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing studies have revealed the presence of tissue bacteria in both tumor and normal tissues. Recently, [...] Read more.

The cell is the basic unit of life. It is composed of organelles and various organic and inorganic biomolecules. Recent 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing studies have revealed the presence of tissue bacteria in both tumor and normal tissues. Recently, we found that the liver microbiome resided in hepatocytes. Here, we further report on the cellular microbiome in the parenchymal cells of visceral organs as inherent inhabitants. We performed 16S rRNA gene sequencing on visceral organs of male adult Sprague Dawley (SD) rats, pregnant rats, newborn rats, and fetuses and placentas; then, we performed fluorescence in situ hybridization and immunofluorescence in visceral organs. Furthermore, we performed Western blotting on nuclear and cytoplasmic extractions of visceral organs of SD rats and cell lines HepG2, Huh-7, Hepa1-6, and HSC-T6. A high abundance of 16S rRNA gene was detected in the visceral organs of male adult, pregnant, newborn, and fetal rats as well as their placentas. The number of operational taxonomic units (OTUs) of visceral bacteria was higher than that of the feces and ileum bacteria. Bacterial 16S rRNA, lipopolysaccharide (LPS), and lipoteichoic acid (LTA) were found in the parenchymal cells of visceral organs, as well as in HepG2, Huh-7, HSC-T6, and Hepa1-6 cells. LPS consistently appeared in the nucleus of cells, while LTA was mainly found in the cytoplasm. In conclusion, the cellular microbiome is an intrinsic component of cells. Gram-negative bacteria are located in the nucleus, and Gram-positive bacteria are located in the cytoplasm. This differs from the gut microbiome and may be inherited. Full article

(This article belongs to the Section Medical Microbiology)

► Show Figures

Figure 1

13 pages, 1415 KiB

Open AccessArticle

Application of MALDI-TOF MS to Identify and Detect Antimicrobial-Resistant Streptococcus uberis Associated with Bovine Mastitis

by Tingrui Zhang, Duangporn Pichpol and Sukolrat Boonyayatra

Microorganisms 2024, 12(7), 1332; https://doi.org/10.3390/microorganisms12071332 (registering DOI) - 29 Jun 2024

Viewed by 101

Abstract

Streptococcus uberis is a common bovine mastitis pathogen in dairy cattle. The rapid identification and characterization of antimicrobial resistance (AMR) in S. uberis plays an important role in its diagnosis, treatment, and prevention. In this study, matrix-assisted laser desorption ionization time-of-flight mass spectrometry [...] Read more.

Streptococcus uberis is a common bovine mastitis pathogen in dairy cattle. The rapid identification and characterization of antimicrobial resistance (AMR) in S. uberis plays an important role in its diagnosis, treatment, and prevention. In this study, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify S. uberis and screen for potential AMR biomarkers. Streptococcus uberis strains (n = 220) associated with bovine mastitis in northern Thailand were identified using the conventional microbiological methods and compared with the results obtained from MALDI-TOF MS. Streptococcus uberis isolates were also examined for antimicrobial susceptibility using a microdilution method. Principal component analysis (PCA) and the Mann–Whitney U test were used to analyze the MALDI-TOF mass spectrum of S. uberis and determine the difference between antimicrobial-resistant and -susceptible strains. Using MALDI-TOF MS, 73.18% (161/220) of the sampled isolates were identified as S. uberis, which conformed to the identifications obtained using conventional microbiological methods and PCR. Using PCR, antimicrobial-resistant strains could not be distinguished from antimicrobial-susceptible strains for all three antimicrobial agents, i.e., tetracycline, ceftiofur, and erythromycin. The detection of spectral peaks at 7531.20 m/z and 6804.74 m/z was statistically different between tetracycline- and erythromycin-resistant and susceptible strains, respectively. This study demonstrates a proteomic approach for the diagnosis of bovine mastitis and potentially for the surveillance of AMR among bovine mastitis pathogens. Full article

(This article belongs to the Special Issue Research on Infections and Veterinary Medicine)

18 pages, 2256 KiB

Open AccessArticle

Effects of Age in Fecal Microbiota and Correlations with Blood Parameters in Genetic Nucleus of Cattle

by Richard Estrada, Yolanda Romero, Deyanira Figueroa, Pedro Coila, Renán Dilton Hañari-Quispe, Mery Aliaga, Walter Galindo, Wigoberto Alvarado, David Casanova and Carlos Quilcate

Microorganisms 2024, 12(7), 1331; https://doi.org/10.3390/microorganisms12071331 (registering DOI) - 29 Jun 2024

Viewed by 99

Abstract

This study aimed to determine the impact of age on the fecal microbiota in the genetic nucleus of cattle, with a focus on microbial richness, composition, functional diversity, and correlations with blood parameters. Fecal and blood samples from 21 cattle were analyzed using [...] Read more.

This study aimed to determine the impact of age on the fecal microbiota in the genetic nucleus of cattle, with a focus on microbial richness, composition, functional diversity, and correlations with blood parameters. Fecal and blood samples from 21 cattle were analyzed using 16S rRNA gene sequencing. Older cattle exhibited greater bacterial diversity and abundance, with significant changes in alpha diversity indices (p < 0.05). Beta diversity analysis revealed significant variations in microbial composition between age groups and the interaction of age and sex (p < 0.05). Correlations between alpha diversity, community composition, and hematological values highlighted the influence of microbiota on bovine health. Beneficial butyrate-producing bacteria, such as Ruminococcaceae, were more abundant in older cattle, suggesting a role in gut health. Functional diversity analysis indicated that younger cattle had significantly more abundant metabolic pathways in fermentation and anaerobic chemoheterotrophy. These findings suggest management strategies including tailored probiotic therapies, dietary adjustments, and targeted health monitoring to enhance livestock health and performance. Further research should include comprehensive metabolic analyses to better correlate microbiota changes with age-related variations, enhancing understanding of the complex interactions between microbiota, age, and reproductive status. Full article

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

15 pages, 9261 KiB

Open AccessArticle

SARS-CoV-2 Molecular Evolution: A Focus on Omicron Variants in Umbria, Italy

by Giulia Bicchieraro, Raffaella Ciurnelli, Alessandro Graziani, Alicia Yoke Wei Wong, Barbara Camilloni, Antonella Mencacci and Roberta Spaccapelo

Microorganisms 2024, 12(7), 1330; https://doi.org/10.3390/microorganisms12071330 (registering DOI) - 29 Jun 2024

Viewed by 123

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 6 million deaths worldwide, and the spread of new variants over time increased the ability of this virus to cause infection. The Omicron variant was detected for the first time in Umbria, [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 6 million deaths worldwide, and the spread of new variants over time increased the ability of this virus to cause infection. The Omicron variant was detected for the first time in Umbria, a region of central Italy, in November 2021 and it induced an unprecedented increase in the number of infection cases. Here, we analysed 3300 SARS-CoV-2 positive samples collected in Umbria between April 2022 and December 2023. We traced the molecular evolution of SARS-CoV-2 variants over time through the Next-Generation Sequencing (NGS) approach. We assessed correlation between SARS-CoV-2 infection and patients’ health status. In total, 17.3% of our samples came from patients hospitalised as a consequence of COVID-19 infection even though 81.4% of them received at least three vaccine doses. We identified only Omicron variants, and the BA.5 lineage was detected in the majority of our samples (49.2%). Omicron variants outcompeted each other through the acquisition of mutations especially in Spike glycoprotein that are fingerprints of each variant. Viral antigenic evolution confers higher immunological escape and makes a continuous improvement of vaccine formulation necessary. The continuous update of international genomic databases with sequencing results obtained by emergent pathogens is essential to manage a possible future pandemic. Full article

(This article belongs to the Special Issue The Evolution of SARS-CoV-2: Molecular Properties, Virulence and Epidemiology)

► Show Figures

Figure 1

17 pages, 4412 KiB

Open AccessArticle

Comparison of Bacterial Communities in Five Ectomycorrhizal Fungi Mycosphere Soil

by Pi Chen, Zhen Li, Ning Cao, Ruixuan Wu, Zhaoren Kuang and Fei Yu

Microorganisms 2024, 12(7), 1329; https://doi.org/10.3390/microorganisms12071329 (registering DOI) - 29 Jun 2024

Viewed by 124

Abstract

Ectomycorrhizal fungi have huge potential value, both nutritionally and economically, but most of them cannot be cultivated artificially. To better understand the influence of abiotic and biotic factors upon the growth of ectomycorrhizal fungi, mycosphere soil and bulk soil of five ectomycorrhizal fungi [...] Read more.

Ectomycorrhizal fungi have huge potential value, both nutritionally and economically, but most of them cannot be cultivated artificially. To better understand the influence of abiotic and biotic factors upon the growth of ectomycorrhizal fungi, mycosphere soil and bulk soil of five ectomycorrhizal fungi (Calvatia candida, Russula brevipes, Leucopaxillus laterarius, Leucopaxillus giganteus, and Lepista panaeola) were used as research objects for this study. Illumina MiSeq sequencing technology was used to analyze the community structure of the mycosphere and bulk soil bacteria of the five ectomycorrhizal fungi, and a comprehensive analysis was conducted based on soil physicochemical properties. Our results show that the mycosphere soil bacteria of the five ectomycorrhizal fungi are slightly different. Escherichia, Usitatibacter, and Bradyrhizobium are potential mycorrhizal-helper bacteria of distinct ectomycorrhizal fungi. Soil water content, soil pH, and available potassium are the main factors shaping the soil bacterial community of the studied ectomycorrhizal fungi. Moreover, from the KEGG functional prediction and LEfSe analysis, there are significant functional differences not only between the mycosphere soil and bulk soil. ‘Biosynthesis of terpenoidsand steroids’, ‘alpha-Linolenic acid metabolism’, ‘Longevity regulating pathway-multiple species’, ‘D-Arginine and D-ornithine metabolism’, ‘Nitrotoluene degradation’ and other functions were significantly different in mycosphere soil. These findings have pivotal implications for the sustainable utilization of ectomycorrhizal fungi, the expansion of edible fungus cultivation in forest environments, and the enhancement of derived economic benefits. Full article

(This article belongs to the Special Issue Soil Microbial Communities and Ecosystem Functions 2.0)

► Show Figures

Figure 1

22 pages, 1768 KiB

Open AccessArticle

A Photonic Immunosensor Detection Method for Viable and Non-Viable E. coli in Water Samples

by Ana Fernández Blanco, Yolanda Moreno, Jorge García-Hernández and Manuel Hernández

Microorganisms 2024, 12(7), 1328; https://doi.org/10.3390/microorganisms12071328 (registering DOI) - 29 Jun 2024

Viewed by 174

Abstract

Detection and enumeration of coliform bacteria using traditional methods and current molecular techniques against E. coli usually involve long processes with less sensitivity and specificity to distinguish between viable and non-viable bacteria for microbiological water analysis. This approach involves developing and validating an [...] Read more.

Detection and enumeration of coliform bacteria using traditional methods and current molecular techniques against E. coli usually involve long processes with less sensitivity and specificity to distinguish between viable and non-viable bacteria for microbiological water analysis. This approach involves developing and validating an immunosensor comprising ring resonators functionalized with specific antibodies surrounded by a network of microchannels as an alternative method for detecting and indirectly enumerating Escherichia coli in samples of water for consumption. Different ELISA assays were conducted to characterize monoclonal and polyclonal antibodies selected as detection probes for specific B-galactosidase enzymes and membrane LPS antigens of E. coli. An immobilization control study was performed on silicon nitride surfaces used in the immunosensor, immobilized with the selected antibodies from the ELISA assays. The specificity of this method was confirmed by detecting as few as 10 CFU/mL of E. coli from viable and non-viable target bacteria after applying various disinfection methods to water samples intended for human consumption. The 100% detection rate and a 100 CFU/mL Limit of Quantification of the proposed method were validated through a comprehensive assessment of the immunosensor-coupled microfluidic system, involving at least 50 replicates with a concentration range of 10 to 10⁶ CFU/mL of the target bacteria and 50 real samples contaminated with and without disinfection treatment. The correlation coefficient of around one calculated for each calibration curve obtained from the results demonstrated sensitive and rapid detection capabilities suitable for application in water resources intended for human consumption within the food industry. The biosensor was shown to provide results in less than 4 h, allowing for rapid identification of microbial contamination crucial for ensuring water monitoring related to food safety or environmental diagnosis and allowing for timely interventions to mitigate contamination risks. Indeed, the achieved setup facilitates the in situ execution of laboratory processes, allowing for the detection of both viable and non-viable bacteria, and it implies future developments of simultaneous detection of pathogens in the same contaminated sample. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0)

► Show Figures

Figure 1

12 pages, 877 KiB

Open AccessArticle

Clinically Defined Lymphogranuloma Venereum among US Veterans with Human Immunodeficiency Virus, 2016–2023

by Gina Oda, Joyce Chung, Cynthia Lucero-Obusan and Mark Holodniy

Microorganisms 2024, 12(7), 1327; https://doi.org/10.3390/microorganisms12071327 (registering DOI) - 29 Jun 2024

Viewed by 154

Abstract

We applied lymphogranuloma venereum (LGV) clinical case criteria to a cohort of 1381 Veterans positive for HIV and Chlamydia trachomatis (CT) from 2016 from 2023 and analyzed variables to ascertain risk factors for LGV and factors associated with the use of standard treatment [...] Read more.

We applied lymphogranuloma venereum (LGV) clinical case criteria to a cohort of 1381 Veterans positive for HIV and Chlamydia trachomatis (CT) from 2016 from 2023 and analyzed variables to ascertain risk factors for LGV and factors associated with the use of standard treatment regimens. In total, 284/1381 (20.6%) met the criteria for LGV. A total of 179/284 (63%) were probable cases, and 105/284 (37%) were possible cases (those meeting clinical criteria but with concurrent sexually transmitted infections (STI) associated with LGV-like symptoms). None had confirmatory CT L1–L3 testing. A total of 230 LGV cases (81%) presented with proctitis, 71 (25%) with ulcers, and 57 (20.1%) with lymphadenopathy. In total, 66 (23.2%) patients had >1 symptom of LGV. A total of 43 (15%) LGV cases were hospitalized. Primary risk factors for LGV were male birth sex (p = 0.004), men who have sex with men (p < 0.001), and the presence of STIs other than gonorrhea or syphilis (p = 0.011). In total, 124/284 (43.7%) LGV cases received standard recommended treatment regimens. Probable cases were more likely to receive standard treatment than possible cases (p = 0.003). We report that 20.6% of CT cases met clinical criteria for LGV among HIV-infected Veterans and that less than half of cases received recommended treatment regimens, indicating that LGV is likely underestimated and inadequately treated among this US population. Full article

(This article belongs to the Special Issue Chlamydiae and Chlamydia-Like Infections)

► Show Figures

Figure 1

2 pages, 194 KiB

Open AccessCorrection

Correction: Mongruel et al. Expanding the Universe of Hemoplasmas: Multi-Locus Sequencing Reveals Putative Novel Hemoplasmas in Lowland Tapirs (Tapirus terrestris), the Largest Land Mammals in Brazil. Microorganisms 2022, 10, 614

by Anna Claudia Baumel Mongruel, Emília Patrícia Medici, Ariel da Costa Canena, Ana Cláudia Calchi, Rosangela Zacarias Machado and Marcos Rogério André

Microorganisms 2024, 12(7), 1326; https://doi.org/10.3390/microorganisms12071326 (registering DOI) - 28 Jun 2024

Viewed by 99

Abstract

In the original publication [...] Full article

11 pages, 2128 KiB

Open AccessArticle

Development and Comparison of Visual LAMP and LAMP-TaqMan Assays for Colletotrichum siamense

by Shuning Cui, Haoze Ma, Xinyue Wang, Han Yang, Yuanzheng Wu, Yanli Wei, Jishun Li and Jindong Hu

Microorganisms 2024, 12(7), 1325; https://doi.org/10.3390/microorganisms12071325 (registering DOI) - 28 Jun 2024

Viewed by 210

Abstract

Strawberry anthracnose caused by Colletotrichum spp. has resulted in significant losses in strawberry production worldwide. Strawberry anthracnose occurs mainly at the seedling and early planting stages, and Colletotrichum siamense is the main pathogen in North China, where mycelia, anamorphic nuclei, and conidia produced [...] Read more.

Strawberry anthracnose caused by Colletotrichum spp. has resulted in significant losses in strawberry production worldwide. Strawberry anthracnose occurs mainly at the seedling and early planting stages, and Colletotrichum siamense is the main pathogen in North China, where mycelia, anamorphic nuclei, and conidia produced in the soil are the main sources of infection. The detection of pathogens in soil is crucial for predicting the prevalence of anthracnose. In this study, a visualized loop-mediated isothermal amplification (LAMP) assay and a loop-mediated isothermal amplification method combined with a TaqMan probe (LAMP-TaqMan) assay were developed for the β-tubulin sequence of C. siamense. Both methods can detect Colletotrichum siamense genomic DNA at very low concentrations (10⁴ copies/g) in soil, while both the visualized LAMP and LAMP-TaqMan assays exhibited a detection limit of 50 copies/μL, surpassing the sensitivity of conventional PCR and qPCR techniques, and both methods showed high specificity for C. siamense. The two methods were compared: LAMP-TaqMan exhibited enhanced specificity due to the incorporation of fluorescent molecular beacons, while visualized LAMP solely necessitated uncomplicated incubation at a constant temperature, with the results determined by the color change; therefore, the requirements for the instrument are relatively straightforward and user-friendly. In conclusion, both assays will help monitor populations of C. siamense in China and control strawberry anthracnose in the field. Full article

(This article belongs to the Section Plant Microbe Interactions)

15 pages, 1221 KiB

Open AccessArticle

Sequential Sampling of the Gastrointestinal Tract to Characterize the Entire Digestive Microbiome in Japanese Subjects

by Kota Ishizawa, Toru Tamahara, Suguo Suzuki, Yutaka Hatayama, Bin Li, Michiaki Abe, Yuichi Aoki, Ryutaro Arita, Natsumi Saito, Minoru Ohsawa, Soichiro Kaneko, Rie Ono, Shin Takayama, Muneaki Shimada, Kazuki Kumada, Tomoyuki Koike, Atsushi Masamune, Ko Onodera, Tadashi Ishii, Ritsuko Shimizu and Takeshi Kanno Show full author list Hide full author list

Microorganisms 2024, 12(7), 1324; https://doi.org/10.3390/microorganisms12071324 (registering DOI) - 28 Jun 2024

Viewed by 252

Abstract

The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive [...] Read more.

The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive metagenomic datasets covering the entire tract are scarce due to cost and technical challenges. Despite the widespread use of fecal samples, integrated datasets encompassing the entire digestive process, beginning at the mouth and ending with feces, are lacking. With this study, we aimed to fill this gap by analyzing the complete metagenome of the GI tract, providing insights into the dynamics of the microbiota and potential therapeutic avenues. In this study, we delved into the complex world of the GI microbiota, which we examined in five healthy Japanese subjects. While samples from the whole GI flora and fecal samples provided sufficient bacteria, samples obtained from the stomach and duodenum posed a challenge. Using a principal coordinate analysis (PCoA), clear clustering patterns were identified; these revealed significant diversity in the duodenum. Although this study was limited by its small sample size, the flora in the overall GI tract showed unwavering consistency, while the duodenum exhibited unprecedented phylogenetic diversity. A visual heat map illustrates the discrepancy in abundance, with Fusobacteria and Bacilli dominating the upper GI tract and Clostridia and Bacteroidia dominating the fecal samples. Negativicutes and Actinobacteria were found throughout the digestive tract. This study demonstrates that it is possible to continuously collect microbiome samples throughout the human digestive tract. These findings not only shed light on the complexity of GI microbiota but also provide a basis for future research. Full article

(This article belongs to the Topic High-Throughput Analyses as a Multi-Faceted Approach for Characterizing the Human Microbiota)

13 pages, 3902 KiB

Open AccessArticle

Multiple Chitin- or Avirulent Strain-Triggered Immunity Induces Microbiome Reassembly in Rice

by Sauban Musa Jibril, Chun Wang, Chao Yang, Hao Qu, Xinyun Yang, Kexin Yang, Chengyun Li and Yi Wang

Microorganisms 2024, 12(7), 1323; https://doi.org/10.3390/microorganisms12071323 (registering DOI) - 28 Jun 2024

Viewed by 266

Abstract

Magnaporthe oryzae is one of the most important fungal pathogens of rice. Chitin and avirulent strains can induce two layers of immunity response, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI), in rice with cognate R genes. However, little is known [...] Read more.

Magnaporthe oryzae is one of the most important fungal pathogens of rice. Chitin and avirulent strains can induce two layers of immunity response, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI), in rice with cognate R genes. However, little is known about the assembly of the rice microbiome induced by PTI and ETI in rice. In this study, we investigate the impact of continuous treatment of the avirulent M. oryzae strain with AvrPi9 and chitin on the bacterial endophytic community of rice varieties harboring resistant gene Pi9 and their antagonistic activity against rice blast fungus. Analysis of the 16S rRNA showed a significant increase in the diversity and microbial co-occurrence network complexity and the number of beneficial taxa—Bacillus, Pseudomonas, Microbacterium, and Stenotrophomonas spp.—following the chitin and avirulent strain treatments. The antifungal assay with bacterial endophytes recovered from the leaves showed few bacteria with antagonistic potential in rice treated with avirulent strains, suggesting that the sequential treatment of the avirulent strain decreased the antagonistic bacteria against M. oryzae. Moreover, we identified Bacillus safensis Ch_66 and Bacillus altitudinis Nc_68 with overall antagonistic activities in vivo and in vitro. Our findings provide a novel insight into rice microbiome assembly in response to different innate immunity reactions. Full article

(This article belongs to the Section Plant Microbe Interactions)

► Show Figures

Figure 1

22 pages, 1955 KiB

Open AccessArticle

Soil Fungal Community Differences in Manual Plantation Larch Forest and Natural Larch Forest in Northeast China

by Mingyu Wang, Xin Sui, Xin Wang, Xianbang Zhang and Xiannan Zeng

Microorganisms 2024, 12(7), 1322; https://doi.org/10.3390/microorganisms12071322 (registering DOI) - 28 Jun 2024

Viewed by 132

Abstract

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve [...] Read more.

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve and Gala Mountain Forest using high-throughput sequencing. The interactions between soil fungal communities were analysed utilising a co-occurrence network. The relationship between soil nutrients and soil fungal communities was determined with the help of Mantel analysis and a correlation heatmap. The Kruskal–Wallis test indicated that different genera of fungi differed in the two forest types. The results show that there was a significant change in the alpha diversity of soil fungal communities in both forests. In contrast, nonmetric multidimensional scaling (NMDS) analysis showed significant differences in the soil fungal community structures between the manual plantation larch forest and the natural larch forest. The soil fungal co-occurrence network showed that the complexity of the soil fungal communities in the manual plantation larch forest decreased significantly compared to those in the natural larch forest. A Mantel analysis revealed a correlation between the soil fungal co-occurrence network, the composition of soil fungi, and soil nutrients. The RDA analysis also showed that AN, TK, and pH mainly influenced the soil fungal community. The null model test results showed the importance of stochastic processes in soil fungal community assembly in manual plantation larch forests. Overall, this study enhances our understanding of the differences in soil fungal communities in manual plantation larch forests and natural larch forests, providing insights into their sustainable management. It also serves as a reminder that the ecological balance of natural ecosystems is difficult to restore through human intervention, so we need to protect natural ecosystems. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System)

23 pages, 4244 KiB

Open AccessArticle

Pangenome Analysis Reveals Novel Contact-Dependent Growth Inhibition System and Phenazine Biosynthesis Operons in Proteus mirabilis BL95 That Are Located in an Integrative and Conjugative Element

by Andrey Tatarenkov, Iván Muñoz-Gutiérrez, Isabel Vargas, Judith Behnsen and Luis Mota-Bravo

Microorganisms 2024, 12(7), 1321; https://doi.org/10.3390/microorganisms12071321 (registering DOI) - 28 Jun 2024

Viewed by 154

Abstract

Proteus mirabilis is a leading cause of urinary tract infections and a common commensal of the gastrointestinal tract. Our recent study (JB) showed that P. mirabilis strain BL95 employs a novel contact-dependent killing system against enteric bacteria in the mouse gut and in [...] Read more.

Proteus mirabilis is a leading cause of urinary tract infections and a common commensal of the gastrointestinal tract. Our recent study (JB) showed that P. mirabilis strain BL95 employs a novel contact-dependent killing system against enteric bacteria in the mouse gut and in vitro. To uncover the genetic determinants of this system, we performed whole-genome sequencing of BL95 and compared it with 98 complete genomes of P. mirabilis. BL95 carries 56 coding sequences (CDSs) not found in other P. mirabilis. Over half of these unique genes are located on a novel integrative conjugative element (ICE) named ICEPm2, inserted in tRNA-Phe and exclusive to BL95. ICEPm2 has integration, conjugation, and DNA replication modules nearly identical to ICEPm1 (common in P. mirabilis), but ICEPm2 of BL95 carries two unique operons for P. mirabilis—a phenazine biosynthesis and a contact-dependent growth inhibition (CDI) system. ICEPm2 is absent in the P. mirabilis (AR_0156) closest to BL95 and it is present in the genomes of several Escherichia coli from mouse intestines, indicating its recent horizontal mobilization. BL95 shares over 100 genes of five different secretion systems with other P. mirabilis, mostly poorly studied, making a large pool of candidate genes for the contact-dependent growth inhibition. Full article

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

11 pages, 1170 KiB

Open AccessArticle

The Role of Microbes in Surgical Decision Making for Infective Endocarditis: Mitral Valve Repair or Replacement?

by Elisa Mikus, Mariafrancesca Fiorentino, Diego Sangiorgi, Renato Pascale, Antonino Costantino, Chiara Nocera, Simone Calvi, Elena Tenti, Elena Tremoli, Alberto Tripodi and Carlo Savini

Microorganisms 2024, 12(7), 1320; https://doi.org/10.3390/microorganisms12071320 - 28 Jun 2024

Viewed by 146

Abstract

Background: The benefits of mitral repair versus replacement for endocarditis are inconclusive. This study compares outcomes of patients with infective endocarditis undergoing mitral valve repair versus replacement and investigates the impact of microbial etiology. Methods: All 251 patients undergoing mitral valve surgery for [...] Read more.

Background: The benefits of mitral repair versus replacement for endocarditis are inconclusive. This study compares outcomes of patients with infective endocarditis undergoing mitral valve repair versus replacement and investigates the impact of microbial etiology. Methods: All 251 patients undergoing mitral valve surgery for active endocarditis between 2010 and 2023 were enrolled, 180 (71.7%) replacement and 71 (28.3%) repair. To adjust for imbalances, inverse probability of treatment weighting was applied and 187 patients were obtained. Results: The analysis between groups, following the application of inverse probability of treatment weighting, showed no statistically significant differences across all considered outcomes. Early and late death was observed respectively in 6 (8.5%) and 11 (15.5%) patients in the repair group versus 24 (13.3%) and 45 (25.0%) in the replacement group without statistical significance (p = 0.221 and p = 0.446). Relapse occurred in six patients (8.5%) in the repair group after a median time of 4.0 months and in six (3.3%) in the replacement after 6.9 months (p = 0.071). Conclusions: Surgical strategy in mitral endocarditis has no effect on major postoperative complications, mortality, or medium/long-term survival. Staphylococcus aureus and Coagulase-negative Staphylococci represent a risk for early mortality and relapse. However, mitral valve repair for endocarditis can be pursued when it ensures the complete eradication of all infected tissue, particularly in cases caused by Streptococcus infection, in young patients, and after a minimum of 18 days of antibiotic therapy. Full article

(This article belongs to the Special Issue The Infective Endocarditis)

► Show Figures

Figure 1

21 pages, 7372 KiB

Open AccessArticle

Characteristics of Gut Microbiota and Fecal Metabolites in Patients with Colorectal Cancer-Associated Iron Deficiency Anemia

by Qinyuan Zhang, Wen Wu, Fanying Guo, Jinming Li, Yutao Jin, Guoxiang Cai and Yongzhi Yang

Microorganisms 2024, 12(7), 1319; https://doi.org/10.3390/microorganisms12071319 - 28 Jun 2024

Viewed by 193

Abstract

Patients with colorectal cancer (CRC) have a high prevalence of iron deficiency anemia (IDA), and the gut microbiota is closely related to iron metabolism. We performed metagenomic and metabolomic analyses of stool samples from 558 eligible samples, including IDA CRC patients (IDA, n [...] Read more.

Patients with colorectal cancer (CRC) have a high prevalence of iron deficiency anemia (IDA), and the gut microbiota is closely related to iron metabolism. We performed metagenomic and metabolomic analyses of stool samples from 558 eligible samples, including IDA CRC patients (IDA, n = 69), non-anemia CRC patients (Non-Anemia, n = 245), and healthy controls (CTRL, n = 244), to explore the dynamically altered gut microbes and their metabolites. Compared with the CTRL group, fecal bacteria in both the IDA group and the Non-Anemia group showed a decrease in alpha diversity and changes in microbial communities. Flavonifractor plautii (F. plautii) increases progressively from CTRL to Non-Anemia to IDA, accompanied by decreased trimethoxyflavanone and a downregulated KO gene, megDIII. In the Non-Anemia group, Parabacteroides showed a specifically elevated abundance positively correlated with enriched 1,25-dihydroxyvitamin D3. The intricate correlations among gut microbiota, metabolites, and KO genes were uncovered and highlighted, implicating an aberrant iron metabolism vulnerable to chronic inflammation during the deterioration of the anemic condition. Furthermore, the amount of F. plautii in feces achieved independent and effective prediction performance for the poor outcome of CRC. Perturbed host-microbe interplays represent a novel prospect for explaining the pathogenesis of CRC-associated IDA. The fecal microbial features also reflect the associations between IDA and elevated CRC recurrence risk. Full article

(This article belongs to the Special Issue Gut Microbiota in Disease—Third Edition)

► Show Figures

Figure 1

21 pages, 4999 KiB

Open AccessArticle

Evaluation of Chemical and Physical Triggers for Enhanced Photosynthetic Glycerol Production in Different Dunaliella Isolates

by Linda Keil, Farah Mitry Qoura, Jonas Martin Breitsameter, Bernhard Rieger, Daniel Garbe and Thomas Bartholomäus Brück

Microorganisms 2024, 12(7), 1318; https://doi.org/10.3390/microorganisms12071318 - 28 Jun 2024

Viewed by 179

Abstract

The salt-tolerant marine microalgae Dunaliella tertiolecta is reported to generate significant amounts of intracellular glycerol as an osmoprotectant under high salt conditions. This study highlights the phylogenetic distribution and comparative glycerol biosynthesis of seven new Dunaliella isolates compared to a D. tertiolecta reference [...] Read more.

The salt-tolerant marine microalgae Dunaliella tertiolecta is reported to generate significant amounts of intracellular glycerol as an osmoprotectant under high salt conditions. This study highlights the phylogenetic distribution and comparative glycerol biosynthesis of seven new Dunaliella isolates compared to a D. tertiolecta reference strain. Phylogenetic analysis indicates that all Dunaliella isolates are newly discovered and do not relate to the D. tertiolecta reference. Several studies have identified light color and intensity and salt concentration alone as the most inducing factors impacting glycerol productivity. This study aims to optimize glycerol production by investigating these described factors singularly and in combination to improve the glycerol product titer. Glycerol production data indicate that cultivation with white light of an intensity between 500 and 2000 μmol m⁻² s⁻¹ as opposed to 100 μmol m⁻² s⁻¹ achieves higher biomass and thereby higher glycerol titers for all our tested Dunaliella strains. Moreover, applying higher light intensity in a cultivation of 1.5 M NaCl and an increase to 3 M NaCl resulted in hyperosmotic stress conditions, providing the highest glycerol titer. Under these optimal light intensity and salt conditions, the glycerol titer of D. tertiolecta could be doubled to 0.79 mg mL⁻¹ in comparison to 100 μmol m⁻² s⁻¹ and salt stress to 2 M NaCl, and was higher compared to singularly optimized conditions. Furthermore, under the same conditions, glycerol extracts from new Dunaliella isolates did provide up to 0.94 mg mL⁻¹. This highly pure algae-glycerol obtained under optimal production conditions can find widespread applications, e.g., in the pharmaceutical industry or the production of sustainable carbon fibers. Full article

(This article belongs to the Special Issue Advances in Microbial Cell Factories, 2nd Edition)

► Show Figures

Figure 1

11 pages, 978 KiB

Open AccessArticle

Epidemiology and Genetic Characterization of Leishmania RNA Virus in Leishmania (Viannia) spp. Isolates from Cutaneous Leishmaniasis Endemic Areas in Panama

by Armando Assair Bonilla, Vanessa Pineda, José Eduardo Calzada, Azael Saldaña, Marcia Dalastra Laurenti, Stephanie Goya, Leyda Abrego and Kadir González

Microorganisms 2024, 12(7), 1317; https://doi.org/10.3390/microorganisms12071317 - 27 Jun 2024

Viewed by 314

Abstract

Leishmania (Viannia) spp. can harbor a double-stranded RNA virus known as Leishmania RNA virus 1 (LRV-1), whose presence has been reported in nine countries across the Americas and seven Leishmania species. Here, we studied 100 Leishmania (Viannia) isolates from patients with cutaneous leishmaniasis [...] Read more.

Leishmania (Viannia) spp. can harbor a double-stranded RNA virus known as Leishmania RNA virus 1 (LRV-1), whose presence has been reported in nine countries across the Americas and seven Leishmania species. Here, we studied 100 Leishmania (Viannia) isolates from patients with cutaneous leishmaniasis collected from different endemic areas in Panama from 2016 to 2022. We identified L. (V.) panamensis, L. (V.) guyanensis, L. (V.) braziliensis/guyanensis hybrid, and L. (V.) panamensis sp.1. (genetic variant). LRV-1 was detected by RT-PCR in 9% of L. (Viannia) isolates (eight cases in L. (V.) panamensis, and one in L. (V.) guyanensis). Phylogenetic analysis based on sequencing data classified all LRV-1 isolates within genotype A, suggesting that LRV phylogenetic proximity is closely aligned with geographical distribution or to the phylogenetic proximity of the Leishmania host in the case of the L. (V.) panamensis and L. (V.) guyanensis in Panama. Full article

(This article belongs to the Special Issue Research on Leishmania and Leishmaniasis)

10 pages, 832 KiB

Open AccessArticle

First Insight into the Whole Genome Sequencing Whole Variations in Mycobacterium bovis from Cattle in Morocco

by Mohammed Khoulane, Siham Fellahi, Slimane Khayi, Mohammed Bouslikhane, Hassan Lakhdissi and Jaouad Berrada

Microorganisms 2024, 12(7), 1316; https://doi.org/10.3390/microorganisms12071316 - 27 Jun 2024

Viewed by 219

Abstract

Six cattle heads which tested positive against bovine tuberculosis (bTB) in Morocco were investigated to confirm the disease and to determine the source(s) of infection. Polymerase Chain Reaction (PCR) was directly performed on tissue samples collected from slaughtered animals. All investigated animals tested [...] Read more.

Six cattle heads which tested positive against bovine tuberculosis (bTB) in Morocco were investigated to confirm the disease and to determine the source(s) of infection. Polymerase Chain Reaction (PCR) was directly performed on tissue samples collected from slaughtered animals. All investigated animals tested positive to PCR for the Mycobacterium bovis sub-type. Bacteriological isolation was conducted according to the technique recommended by WOAH for the cultivation of the Mycobacterium tuberculosis Complex (MBTC). Whole genome sequencing (WGS) was carried out on six mycobacterial isolates and the phylogenic tree was constructed. The six Moroccan isolates fit with clades II, III, IV, V and VII and were confirmed to belong to the clonal complexes Eu2, Unknown 2 and 7 as well as to sublineages La1.7.1, La1.2 and La1.8.2. The significant Single Nucleotide Polymorphism (SNPs) ranged from 84 to 117 between the isolates and the reference M. bovis strain and from 17 to 212 between the six isolates. Considering the high resolution of WGS, these results suggests that the source of infection of the bTB could be linked to imported animals as five of the investigated reactor animals were imported a few months prior. WGS can be a useful component to the Moroccan strategy to control bTB. Full article

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

16 pages, 1830 KiB

Open AccessArticle

A New Dual Fluorescence Method for Rapid Detection of Infectious Bronchitis Virus at Constant Temperature

by Xinheng Zhang, Xiuhong Wu, Keyu Feng, Qian Wang and Qingmei Xie

Microorganisms 2024, 12(7), 1315; https://doi.org/10.3390/microorganisms12071315 - 27 Jun 2024

Viewed by 187

Abstract

Infectious bronchitis virus (IBV) causes infectious bronchitis in chicken, an acute, highly contagious respiratory infection. Because of genetic mutations and recombination, IBV forms many subtypes, which makes it difficult to treat the disease and apply commercial vaccines. Therefore, to detect IBV in time [...] Read more.

Infectious bronchitis virus (IBV) causes infectious bronchitis in chicken, an acute, highly contagious respiratory infection. Because of genetic mutations and recombination, IBV forms many subtypes, which makes it difficult to treat the disease and apply commercial vaccines. Therefore, to detect IBV in time and stop the virus from spreading, a novel and convenient IBV detection technology based on reverse transcription recombinase-aided amplification (RT-RAA) was established in this study. According to the S1 gene of IBV CH Ⅰ–Ⅴ and Mass genotypes and S1 gene of IBV CH Ⅵ genotype, a set of optimal primers were designed and selected to establish a real-time dual fluorescence RT-RAA method. The lowest detection line was 10 copies/μL of RNA molecules and the method exhibited no cross-reactivity with avian reticuloendotheliosis virus (REV), infectious bursal disease virus (IBDV), avian leukosis virus (ALV), Newcastle disease virus (NDV), chicken infectious anemia virus (CIAV), infectious laryngotracheitis virus (ILTV), Marek’s disease virus (MDV), and H9N2 avian influenza virus (H9N2), demonstrating high specificity. When compared to qPCR detection results, our method achieved a sensitivity of 96.67%, a specificity of 90%, and a Kappa value of 0.87 for the IBV CH Ⅰ–Ⅴ and Mass genotypes, and achieved a sensitivity of 100%, a specificity of 97.73%, and a Kappa value of 0.91 for the IBV CH Ⅵ genotype. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases)

14 pages, 1403 KiB

Open AccessArticle

Investigating the Impact That Diagnostic Screening with Lateral Flow Devices Had on the Rabies Surveillance Program in Zanzibar, Tanzania

by Ali Z. Moh’d, Andre Coetzer, Ayla J. Malan, Terence P. Scott, Ramadhan J. Ramadhan, Nicolette Wright and Louis H. Nel

Microorganisms 2024, 12(7), 1314; https://doi.org/10.3390/microorganisms12071314 - 27 Jun 2024

Viewed by 154

Abstract

With the global impetus for the elimination of canine-mediated human rabies, the need for robust rabies surveillance systems has become ever more important. Many countries are working to improve their rabies surveillance programs and, as a result, the reported use of lateral flow [...] Read more.

With the global impetus for the elimination of canine-mediated human rabies, the need for robust rabies surveillance systems has become ever more important. Many countries are working to improve their rabies surveillance programs and, as a result, the reported use of lateral flow devices (LFDs) is increasing. Despite their known diagnostic limitations, previous studies have hypothesised that the benefits associated with LFDs could make them potentially quite useful towards improving the overall robustness of surveillance programs. To test this, a best practice standard operating procedure was developed which was used to guide the implementation of the ADTEC LFD as a diagnostic screening tool in Zanzibar. Over the course of the first 22 months of this investigation, 83 samples were subjected to in-field diagnostic screening, coupled with subsequent laboratory confirmation, and only one false-negative result was detected. Furthermore, the findings of our investigation indicated that the routine use of LFDs as a diagnostic screening tool resulted in a four-fold increase in the number of samples subjected to rabies diagnosis per month and a three-fold increase in the number of wards where samples were collected per year. Our findings suggest that LFDs could play a noteworthy role in improving the robustness of surveillance systems by increasing the number of samples tested and promoting diagnostic screening in areas distant from laboratories. Their implementation would, however, need to be carefully controlled through standardised protocols that align with the international best practices to ensure their judicious use. Full article

(This article belongs to the Special Issue Prevention and Control of Zoonotic Pathogen Infection)

21 pages, 5907 KiB

Open AccessArticle

A Comparative Analysis of Bacterial and Fungal Communities in Coastal and Inland Pecan Plantations

by Shijie Zhang, Ting Chen, Yu Chen, Shucheng Li, Wu Wang, Yuqiang Zhao and Cancan Zhu

Microorganisms 2024, 12(7), 1313; https://doi.org/10.3390/microorganisms12071313 - 27 Jun 2024

Viewed by 166

Abstract

Pecan forests (Carya illinoinensis) are significant contributors to both food and oil production, and thrive in diverse soil environments, including coastal regions. However, the interplay between soil microbes and pecan forest health in coastal environments remains understudied. Therefore, we investigated soil [...] Read more.

Pecan forests (Carya illinoinensis) are significant contributors to both food and oil production, and thrive in diverse soil environments, including coastal regions. However, the interplay between soil microbes and pecan forest health in coastal environments remains understudied. Therefore, we investigated soil bacterial and fungal diversity in coastal (Dafeng, DF) and inland (Guomei, GM) pecan plantations using high-throughput sequencing. The results revealed a higher microbial diversity in the DF plantation than in the GM plantation, significantly influenced by pH and edaphic factors. The dominant bacterial phyla were Proteobacteria, Acidobacteriota and Bacteroidota in the DF plantation, and Acidobacteriota, Proteobacteria, and Verrucomicrobiota in the GM plantation. Bacillus, Nitrospira and UTCFX1 were significantly more abundant bacterial genera in DF soil, whereas Candidatus Udaeobacter, HSB_OF53-F07 and ADurbBin063-1 were more prevalent in GM soil. Basidiomycota dominated fungal sequences in the GM plantation, with a higher relative abundance of Ascomycota in the DF plantation. Significant differences in fungal genus composition were observed between plantations, with Scleroderma, Hebeloma, and Naucoria being more abundant in DF soil, and Clavulina, Russula, and Inocybe in GM soil. A functional analysis revealed greater carbohydrate metabolism potential in GM plantation bacteria and a higher ectomycorrhizal fungi abundance in DF soil. Significantly positive correlations were detected between certain bacterial and fungal genera and pH and total soluble salt content, suggesting their role in pecan adaptation to coastal environments and saline–alkali stress mitigation. These findings enhance our understanding of soil microbiomes in coastal pecan plantations, and are anticipated to foster ecologically sustainable agroforestry practices and contribute to coastal marshland ecosystem management. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition)

► Show Figures

Figure 1

12 pages, 3499 KiB

Open AccessArticle

Fourier Transform Infrared Spectroscopy Application for Candida auris Outbreak Typing in a Referral Intensive Care Unit: Phylogenetic Analysis and Clustering Cut-Off Definition

by Antonio Curtoni, Lisa Pastrone, Miriam Cordovana, Alessandro Bondi, Giorgia Piccinini, Mattia Genco, Paolo Bottino, Carlotta Polizzi, Lorenza Cavallo, Narcisa Mandras, Silvia Corcione, Giorgia Montrucchio, Luca Brazzi and Cristina Costa

Microorganisms 2024, 12(7), 1312; https://doi.org/10.3390/microorganisms12071312 - 27 Jun 2024

Viewed by 161

Abstract

Recently Candida auris has emerged as a multi-resistant fungal pathogen, with a significant clinical impact, and is able to persist for a long time on human skin and hospital environments. It is a critical issue on the WHO fungal priority list and therefore [...] Read more.

Recently Candida auris has emerged as a multi-resistant fungal pathogen, with a significant clinical impact, and is able to persist for a long time on human skin and hospital environments. It is a critical issue on the WHO fungal priority list and therefore it is fundamental to reinforce hospital surveillance protocols to limit nosocomial outbreaks. The purpose of this study was to apply Fourier transform infrared spectroscopy (FT-IR) to investigate the phylogenetic relationships among isolated strains from a C. auris outbreak at the University Intensive Care Unit of a Tertiary University hospital in Turin (Italy). To calculate a clustering cut-off, intra- and inter-isolate, distance values were analysed. The data showed the presence of a major Alfa cluster and a minor Beta cluster with a defined C. auris clustering cut-off. The results were validated by an external C. auris strain and Principal Component and Linear Discriminant Analyses. The application of FT-IR technology allowed to obtain important information about the phylogenetic relationships between the analysed strains, defining for the first time a “not WGS-based” clustering cut-off with a statistical–mathematical approach. FT-IR could represent a valid alternative to molecular methods for the rapid and cost-saving typing of C. auris strains with important clinical implications. Full article

(This article belongs to the Collection Advances in Public Health Microbiology)

► Show Figures

Figure 1

27 pages, 5346 KiB

Open AccessReview

Phytoplasma-Associated Diseases in South America: Thirty Years of Research

by Helena Guglielmi Montano, Assunta Bertaccini and Nicola Fiore

Microorganisms 2024, 12(7), 1311; https://doi.org/10.3390/microorganisms12071311 - 27 Jun 2024

Viewed by 201

Abstract

Phytoplasma-associated diseases are mainly insect-transmitted and are present worldwide. Considering that disease detection is a relevant environmental factor that may elucidate the presence of these diseases, a review reporting the geographic distribution of phytoplasma taxa in geographically consistent areas helps manage diseases appropriately [...] Read more.

Phytoplasma-associated diseases are mainly insect-transmitted and are present worldwide. Considering that disease detection is a relevant environmental factor that may elucidate the presence of these diseases, a review reporting the geographic distribution of phytoplasma taxa in geographically consistent areas helps manage diseases appropriately and reduce their spreading. This work summarizes the data available about the identification of the phytoplasma associated with several diverse diseases in South America in the last decades. The insect vectors and putative vectors together with the plant host range of these phytoplasmas are also summarized. Overall, 16 ‘Candidatus Phytoplasma’ species were detected, and those most frequently detected in agricultural-relevant crops such as corn, alfalfa, grapevine, and other horticultural species are ‘Ca. P. pruni’, ‘Ca. P. asteris’, and ‘Ca. P. fraxini’. Full article

(This article belongs to the Special Issue Phloem Localized Insect Transmitted Bacteria Associated with Plant Diseases)

► Show Figures

Figure 1

21 pages, 3590 KiB

Open AccessArticle

Effects of Fungal Solid-State Fermentation on the Profile of Phenolic Compounds and on the Nutritional Properties of Grape Pomace

by Gordana Šelo, Mirela Planinić, Marina Tišma, Ana-Marija Klarić and Ana Bucić-Kojić

Microorganisms 2024, 12(7), 1310; https://doi.org/10.3390/microorganisms12071310 - 27 Jun 2024

Viewed by 198

Abstract

Grape pomace (GP) is considered a natural source of bioactive compounds. To improve the extractability of bioactive compounds, in this work, GP was biologically treated for 15 days with the white-rot fungus Trametes versicolor in laboratory jars and a tray bioreactor under solid-state [...] Read more.

Grape pomace (GP) is considered a natural source of bioactive compounds. To improve the extractability of bioactive compounds, in this work, GP was biologically treated for 15 days with the white-rot fungus Trametes versicolor in laboratory jars and a tray bioreactor under solid-state fermentation (SSF) conditions. During SSF, the activity of lignolytic (laccase and manganese peroxidase) and hydrolytic (xylanase, cellulase, β-glucosidase, and invertase) enzymes was measured, with the activities of laccase (2.66 U/g_db in jars and 0.96 U/g_db in the bioreactor) and xylanase (346.04 U/g_db in jars and 200.65 U/g_db in the bioreactor) being the highest. The effect of the complex enzyme system was reflected in the changes in the chemical composition of GP with increasing ash, crude protein, and free fat content: 28%, 10%, and 17% in the laboratory jars, and 29%, 11%, and 7% in the bioreactor, respectively. In addition, the biological treatment improved the extractability of 13 individual phenolic compounds. Therefore, the applied SSF technique represents an effective strategy to improve the profile of phenolic compounds and the nutritional composition of GP, promoting their valorization and opening the door for potential applications in the food industry and other sectors. Full article

(This article belongs to the Section Microbial Biotechnology)

► Show Figures

Figure 1

18 pages, 5094 KiB

Open AccessArticle

Adaptation of Bacillus subtilis MreB Filaments to Osmotic Stress Depends on Influx of Potassium Ions

by Simon Dersch and Peter L. Graumann

Microorganisms 2024, 12(7), 1309; https://doi.org/10.3390/microorganisms12071309 - 27 Jun 2024

Viewed by 172

Abstract

The circumferential motion of MreB filaments plays a key role in cell shape maintenance in many bacteria. It has recently been shown that filament formation of MreB filaments in Bacillus subtilis is influenced by stress conditions. In response to osmotic upshift, MreB molecules [...] Read more.

The circumferential motion of MreB filaments plays a key role in cell shape maintenance in many bacteria. It has recently been shown that filament formation of MreB filaments in Bacillus subtilis is influenced by stress conditions. In response to osmotic upshift, MreB molecules were released from filaments, as seen by an increase in freely diffusive molecules, and the peptidoglycan synthesis pattern became less organized, concomitant with slowed-down cell extension. In this study, biotic and abiotic factors were analysed with respect to a possible function in the adaptation of MreB filaments to stress conditions. We show that parallel to MreB, its interactor RodZ becomes more diffusive following osmotic stress, but the remodeling of MreB filaments is not affected by a lack of RodZ. Conversely, mutant strains that prevent efficient potassium influx into cells following osmotic shock show a failure to disassemble MreB filaments, accompanied by less perturbed cell wall extension than is observed in wild type cells. Because potassium ions are known to negatively affect MreB polymerization in vitro, our data indicate that polymer disassembly is directly mediated by the physical consequences of the osmotic stress response. The lack of an early potassium influx response strongly decreases cell survival following stress application, suggesting that the disassembly of MreB filaments may ensure slowed-down cell wall extension to allow for efficient adaptation to new osmotic conditions. Full article

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

► Show Figures

Figure 1

Journal Menu

Journal Browser

Microorganisms, Volume 12, Issue 7 (July 2024) – 86 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI