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Microbiol. Res., Volume 15, Issue 2 (June 2024) – 40 articles

Cover Story (view full-size image): The gut–brain axis (GBA) is a complex network connecting the gastrointestinal tract and brain which comprises the vagus nerve, enteric nervous system, immune signals, microbial metabolites, etc. Recent advances in microbiome research have indicated the role of gut bacteria in influencing brain function through neurotransmitters such as serotonin and dopamine, thereby affecting mood, cognition, and behaviour. Disruptions in the GBA are linked to neurodegenerative diseases such as Alzheimer’s, Parkinson’s, Huntington’s, and Amyotrophic Lateral Sclerosis. The evolving understanding of the GBA underscores the need for novel therapeutic approaches targeting gut microbiota. This review explores the mechanisms through which gut microbiota influence brain health and potential therapeutic interventions aiming to modulate the gut microbiome. View this paper
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22 pages, 1015 KiB  
Review
Green Microbe Profile: Rhizophagus intraradices—A Review of Benevolent Fungi Promoting Plant Health and Sustainability
by Helen N. Onyeaka, Adenike A. Akinsemolu, Kehinde Favour Siyanbola and Victoria Ademide Adetunji
Microbiol. Res. 2024, 15(2), 1028-1049; https://doi.org/10.3390/microbiolres15020068 - 18 Jun 2024
Viewed by 804
Abstract
Arbuscular mycorrhizal fungi (AMF) such as Rhizophagus intraradices (formerly known as Glomus intraradices) are of great importance to maintaining the soil ecosystem while supporting sustainable agriculture and practices. This review explores the taxonomy of Rhizophagus intraradices, their attributes, mycorrhizal symbiosis, plant [...] Read more.
Arbuscular mycorrhizal fungi (AMF) such as Rhizophagus intraradices (formerly known as Glomus intraradices) are of great importance to maintaining the soil ecosystem while supporting sustainable agriculture and practices. This review explores the taxonomy of Rhizophagus intraradices, their attributes, mycorrhizal symbiosis, plant growth improvement, nutrient recycling in the soil, soil health and environmental rehabilitation, and challenges that impede the effective use of AMF in agriculture. AMF impacts soil structure by releasing organic compounds like glomalin, improving total organic carbon and water-holding capacity, and reducing water scarcity. AMF, in sustainable agriculture, not only improves crop productivity through nutrient uptake but also enhances soil fertility and plants’ resistance to so-called stress from abiotic factors as well. The integration of AMF with other beneficial microorganisms in organic farming will be powerful both to ensure long-term soil output and to protect food from bacteria. Nevertheless, chemical inputs and spatial biases of the researchers remain matters to be solved in connection with the broad feasibility of AMF use. Full article
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12 pages, 3722 KiB  
Case Report
The First Report on Saprolegnia parasitica and Neoparamoeba perurans Isolated from Atlantic Salmon (Salmo salar) Reared in Korea
by Dong-Hwi Kim, Min-Soo Joo, Soo-Ji Woo, Kwang-Tae Son, Woo-Seok Hong, Mun-Chang Park, Jin-Chul Park and Sung-Oh Park
Microbiol. Res. 2024, 15(2), 1016-1027; https://doi.org/10.3390/microbiolres15020067 - 18 Jun 2024
Viewed by 499
Abstract
This study is the first report of parasite and fungal disease separated from domestically reared Atlantic salmon in Korea; the characteristics of the pathogens were identified, and histopathological analysis was conducted. Fungal and parasitic diseases were detected in Atlantic salmon and were isolated [...] Read more.
This study is the first report of parasite and fungal disease separated from domestically reared Atlantic salmon in Korea; the characteristics of the pathogens were identified, and histopathological analysis was conducted. Fungal and parasitic diseases were detected in Atlantic salmon and were isolated as Saprolegnia parasitica and Neoparamoeba perurans based on morphological and genetic analysis. External symptoms observed in Atlantic salmon infected with S. parasitica include fin ulcers and hemorrhage, abdominal hemorrhage, and necrosis of the gills and gill covers. The histopathological analysis results showed necrosis, hemorrhaging, and inflammatory cell infiltration in the abdominal muscles, while only inflammatory cell infiltration was observed in the gill covers. The clinical symptoms observed in Atlantic salmon infected with N. perurans included excessive mucus secretion in the gills, a dense amoebic presence on the gill filaments, respiratory distress, and opening of the mouth and gill covers after death. Through histopathological analysis, we observed lesions in epithelial cells, characterized by the proliferation of epithelial cells and the fusion of secondary lamellae. Numerous lamellae were observed to be attached or fused with each other. To ensure the successful establishment of the Atlantic salmon aquaculture industry in Korea, it is essential to swiftly quarantine infected fish based on the morphological characteristics of S. parasitica and N. perurans revealed in this study, along with the external symptoms of Atlantic salmon infected with these pathogens. Developing disease control strategies based on the findings of this research is imperative. Full article
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9 pages, 564 KiB  
Brief Report
Gender, Immunological Response, and COVID-19: An Assessment of Vaccine Strategies in a Pandemic Region of Oaxaca, México
by Luis M. Rodríguez-Martínez, José L. Chavelas-Reyes, Carlo F. Medina-Ramírez, Francisco J. Cabrera-Santos, Nadia A. Fernández-Santos, Jesús A. Aguilar-Durán, Sonia M. Pérez-Tapia, Josefina G. Rodríguez-González and Mario A. Rodríguez Pérez
Microbiol. Res. 2024, 15(2), 1007-1015; https://doi.org/10.3390/microbiolres15020066 - 17 Jun 2024
Viewed by 537
Abstract
COVID-19 is no longer a public health emergency of international concern, but long COVID’s effects are yet to be fully understood. Hence, globally, SARS-CoV-2 is still a profound threat to public health and of perilous nature as a zoonotic disease. Timely vaccination provided [...] Read more.
COVID-19 is no longer a public health emergency of international concern, but long COVID’s effects are yet to be fully understood. Hence, globally, SARS-CoV-2 is still a profound threat to public health and of perilous nature as a zoonotic disease. Timely vaccination provided to individuals worldwide during the pandemic phase was under a certain degree of control; however, few studies have reported the effectiveness of vaccines administered in Mexico, and its surveillance is paramount. Furthermore, an unknown proportion of Mexican individuals have not yet received any vaccine, and the circulation of the Omicron, Pirola, and FLiRT variants is ongoing. A cross-sectional serology survey study design was employed, involving 150 individuals from Southern Mexico (Oaxaca) whose humoral immune responses after vaccination were tested by an ELISA; the receptor-binding domain of the SARS-CoV-2 spike protein served as a recombinant antigen in the ELISA. One hundred thirty-nine out of 150 individuals (92.6%; 95%-CI = 87–95%) examined were positive for the ELISA, but in 11 individuals, the vaccines did not induce any immune response. Interestingly, the immune responses (antibody prevalence and levels) of females (58%) were higher (T= −2.21; p-value = 0.02) than those of males (41%). However, in this sample population of Southern Mexico, age, vaccine type, comorbidity, and body mass index did not have any effect (p > 0.05) after COVID-19 vaccination. Taking all results together, here, we present factors that affected immune responses of individuals during the first vaccination campaign in Oaxaca, Mexico; however, vaccine surveillance during the post-pandemic phase needs further investigation. Full article
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13 pages, 4083 KiB  
Article
Etiology of Four Waves of the COVID-19 Pandemic in Ukraine according to the SARS-CoV-2 Virus Genome Sequencing Data: A Pilot Study
by Alla Mironenko, Ihor Kravchuk, Larysa Radchenko, Nataliia Teteriuk, Olha Holubka, Liudmyla Bolotova, Mykola Pydiura and Andriy Goy
Microbiol. Res. 2024, 15(2), 994-1006; https://doi.org/10.3390/microbiolres15020065 - 13 Jun 2024
Viewed by 354
Abstract
The COVID-19 pandemic in Ukraine, from March 2020 to June 2022, witnessed distinct waves, each characterized by an increase in cases and fatalities. Next-generation sequencing has been used to understand the impact of viral variants on the pandemic situation in Ukraine. We analyzed [...] Read more.
The COVID-19 pandemic in Ukraine, from March 2020 to June 2022, witnessed distinct waves, each characterized by an increase in cases and fatalities. Next-generation sequencing has been used to understand the impact of viral variants on the pandemic situation in Ukraine. We analyzed SARS-CoV-2 genome sequencing data to identify viral variants circulating during each wave. By integrating epidemiological information, we established associations between viral variants and disease spread. The adoption of next-generation sequencing for SARS-CoV-2 surveillance in Ukraine, despite limited resources, yielded adequate and trustworthy results, reflecting the pandemic situation. After the Russian military invasion of Ukraine in February 2022, a large number of refugees crossed the border with neighboring countries. Mutation analysis on sequencing data from Ukraine and Poland was used to estimate the exchange of SARS-CoV-2 variants between the countries during this period. Omicron subvariants detected in both countries were similar. The analysis of SARS-CoV-2 sequences from Poland and Ukraine revealed shared nucleotide mutations that can be used to identify the directions of spreading. Full article
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22 pages, 4790 KiB  
Review
Endophytic Fungi in Rice Plants and Their Prospective Uses
by Yingping Hu, Guodong Lu, Dongmei Lin, Hailin Luo, Mediatrice Hatungimana, Bin Liu and Zhanxi Lin
Microbiol. Res. 2024, 15(2), 972-993; https://doi.org/10.3390/microbiolres15020064 - 12 Jun 2024
Viewed by 432
Abstract
In a long-term evolution, fungal endophytes have formed a mutually beneficial relationship with host plants. Therefore, what roles do fungal endophytes play in the growth and development of rice, one of the major food crops in the world, and agricultural production? This mini-review [...] Read more.
In a long-term evolution, fungal endophytes have formed a mutually beneficial relationship with host plants. Therefore, what roles do fungal endophytes play in the growth and development of rice, one of the major food crops in the world, and agricultural production? This mini-review aims to highlight the diversity, identification, colonization, function, and mechanism of action of endophytic fungi isolated from rice tissues through a literature review; comprehensively expound the interaction mechanism between rice fungal endophytes and their hosts in stimulating the growth of rice plants and alleviating biological and abiotic stresses on plants; and contribute new ideas for rice production and a sustainable rice industry. Additionally, rice fungal endophytes, as a new resource, have broad prospects in the development of biopesticides, biocontrol agents, and new medicine. Full article
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10 pages, 9130 KiB  
Review
Outcomes of Microbiological Challenges in Poultry Transport: A Mini Review of the Reasons for Effective Bacterial Control
by Vinícius Machado dos Santos, Gabriel da Silva Oliveira, Cristiane Batista Salgado, Paula Gabriela da Silva Pires, Pedro Henrique Gomes de Sá Santos and Concepta McManus
Microbiol. Res. 2024, 15(2), 962-971; https://doi.org/10.3390/microbiolres15020063 - 7 Jun 2024
Viewed by 685
Abstract
This review aims to highlight the main microbiological challenges faced in poultry transport and show the role of effective bacterial control during this process to ensure poultry health and meat safety and to reduce economic losses. Poultry infections are among the most frequent [...] Read more.
This review aims to highlight the main microbiological challenges faced in poultry transport and show the role of effective bacterial control during this process to ensure poultry health and meat safety and to reduce economic losses. Poultry infections are among the most frequent infections in production systems, manifesting themselves in hatcheries, farms, slaughterhouses, and during transport between these integration centers. Although the clinical symptoms of these infections can range from mild to severe, many of them can lead to irreversible conditions, resulting in death and compromising productive results. Bacteria are the main causative agents of these infections, although fungi, viruses, and protozoa may also be involved. During the transport of poultry from farms to slaughterhouses, poultry are very vulnerable to infectious conditions. Therefore, implementing effective antibacterial management, focused on professionals, transport crates, and transport vehicles, is essential to guarantee the survival and quality of poultry until the moment of slaughter. Full article
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19 pages, 2129 KiB  
Article
Biochemical and Molecular Analysis of Gut Microbial Changes in Spodoptera littoralis (Lepidoptera: Noctuidae) to Counteract Cry1c Toxicity
by Abeer Abd El Aziz, Saad Moussa, Mohamed T. Yassin, Iman El Husseiny and Samar El Kholy
Microbiol. Res. 2024, 15(2), 943-961; https://doi.org/10.3390/microbiolres15020062 - 6 Jun 2024
Viewed by 534
Abstract
Bacillus thuringiensis (Bt) represents one of the most economical biopesticides to date. It produces toxins with insecticidal activity against many agricultural pests, including members of the genus Spodoptera. However, Bt tolerance leads to inefficiency in biological control. To overcome this [...] Read more.
Bacillus thuringiensis (Bt) represents one of the most economical biopesticides to date. It produces toxins with insecticidal activity against many agricultural pests, including members of the genus Spodoptera. However, Bt tolerance leads to inefficiency in biological control. To overcome this problem, discovering the hidden cause(s) for the evolution of insect tolerance against Bt is of great importance. We hypothesized that changes in the gut microbiota due to the frequent application of Bt is one of those hidden causes. To investigate this hypothesis, we studied the effect of Bt Cry1c application on the Spodoptera littoralis larval gut microbiota in both Bt-susceptible and Bt-tolerant populations. The results revealed changes in the diversity and abundance of gut bacterial composition between the susceptible and tolerant populations. A high abundance of Enterococcaceae was detected in the tolerant population. Interestingly, Cry1c tolerance eliminates the bacterial genera Klebsiella and Serratia from the larval midgut. These changes may confirm the mechanism developed by Spodoptera larvae to counteract Bt Cry1c toxicity. Understanding the B. thuringiensis–gut microbiota interaction may help in improving biocontrol strategies against agricultural pests to overcome the evolution of tolerance. Full article
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17 pages, 3339 KiB  
Article
New Insights into the Potential Inhibitory Effects of Native Plants from Cyprus on Pathogenic Bacteria and Diabetes-Related Enzymes
by Atalanti Christou, Constantina Stavrou, Christodoulos Michael, George Botsaris and Vlasios Goulas
Microbiol. Res. 2024, 15(2), 926-942; https://doi.org/10.3390/microbiolres15020061 - 29 May 2024
Viewed by 685
Abstract
Plants possess endless structural and chemical diversity, which is peerless with any synthetic library of small biomolecules, inspiring novel drug discovery. Plants are widely applied to encounter global health challenges such as antimicrobial resistance and diabetes. The objective of this work was to [...] Read more.
Plants possess endless structural and chemical diversity, which is peerless with any synthetic library of small biomolecules, inspiring novel drug discovery. Plants are widely applied to encounter global health challenges such as antimicrobial resistance and diabetes. The objective of this work was to evaluate the antibacterial and antidiabetic potency of native plants grown in Cyprus. All plants were sequentially extracted with solvents of increasing polarity, namely hexane, acetone, methanol, and water. First, the phenolic and flavonoid contents of the extracts were assessed. Afterwards, the bacteriostatic and bactericidal potency of plant extracts were tested against a panel of six bacteria using the broth microdilution method, whereas the inhibitory effects on alpha-glucosidase and alpha-amylase enzymes were also determined with the employment of microplate assays. The results highlighted the superiority of Sarcopoterium spinosum as a potential enzyme inhibitor, while a knowledge base was also acquired for the inhibitory potential of all plants. Daucus carota, Ferula communis, and Tordylium.aegyptiacum displayed additionally outstanding bacteriostatic and bactericidal effects on Gram-positive bacteria at concentrations of 250 µg mL−1 and 500 µg mL−1. Overall, the present study describes the antibacterial and inhibitory activity against carbohydrate digestive enzymes of native plants grown in Cyprus delivering the first reports for many plant species. Full article
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12 pages, 270 KiB  
Article
Are Mouse Mammary Tumor Virus and Bovine Leukemia Virus Linked to Breast Cancer among Jordanian Women?
by Ashraf I. Khasawneh, Nisreen Himsawi, Ashraf Sammour, Mohammed Alorjani, Hadeel Al-Momani, Uruk Shahin, Moureq R. Alotaibi, Sofian Al Shboul and Tareq Saleh
Microbiol. Res. 2024, 15(2), 914-925; https://doi.org/10.3390/microbiolres15020060 - 27 May 2024
Viewed by 437
Abstract
The investigation into the potential association between retroviruses and breast cancer (BC) presents a fascinating area of research. In this study, the focus was on assessing the presence of two retroviruses, Mouse Mammary Tumor Virus (MMTV) and Bovine Leukemia Virus (BLV), in BC [...] Read more.
The investigation into the potential association between retroviruses and breast cancer (BC) presents a fascinating area of research. In this study, the focus was on assessing the presence of two retroviruses, Mouse Mammary Tumor Virus (MMTV) and Bovine Leukemia Virus (BLV), in BC samples and exploring their relationship with relevant clinicopathological variables. The study involved analyzing BC samples from 103 Jordanian female patients diagnosed with BC, as well as breast tissue samples from 25 control patients without evidence of breast malignancy. Real-time PCR was used to investigate the evidence of MMTV and BLV infection in these samples, and the findings were then correlated with various clinicopathological characteristics of BC. The results showed that BLV was detected in 19 (18.4%) of the BC samples, while MMTV was detected in only seven (6.8%). Importantly, none of the control samples tested positive for MMTV or BLV. Additionally, MMTV/BLV co-infections were reported in 1.9% of the BC cases. However, the analysis did not reveal any statistically significant associations between the presence of these retroviruses and various clinicopathological variables, such as age, molecular subtypes of BC, stage, grade, lymph node involvement, tumor size, smoking status, or family history. Despite these findings, it is crucial to acknowledge that further investigation with a larger cohort is necessary to establish a clearer association and elucidate the underlying mechanisms that may explain the exact role of retroviruses in breast carcinogenesis. This study provides insights into the potential infection by MMTV and BLV of BC and lays the groundwork for future research in this area. Full article
14 pages, 2790 KiB  
Article
Closing the Diagnostic Gap in Encephalitis and Acute Disseminated Encephalomyelitis through Digital Case Classification and Viral Metagenomics
by Patrick E. Obermeier, Xiaolin Ma, Albert Heim and Barbara A. Rath
Microbiol. Res. 2024, 15(2), 900-913; https://doi.org/10.3390/microbiolres15020059 - 23 May 2024
Viewed by 867
Abstract
Encephalitis and acute disseminated encephalomyelitis (ADEM) are often caused or triggered by viruses—but the specific pathogen commonly remains unidentified in routine care. We explored the use of viral metagenomic next-generation sequencing (mNGS) in addition to PCR testing of non-invasive stool samples to see [...] Read more.
Encephalitis and acute disseminated encephalomyelitis (ADEM) are often caused or triggered by viruses—but the specific pathogen commonly remains unidentified in routine care. We explored the use of viral metagenomic next-generation sequencing (mNGS) in addition to PCR testing of non-invasive stool samples to see if unbiased testing could potentially increase diagnostic yield. To identify specific clinical cases at the point of care, we took advantage of a previously published digital app allowing instant clinical case classification based on consensus case criteria, the VACC-Tool. This hospital-based prospective digital surveillance program assessed 100 pediatric patients (mean age: 11 years, range: 0.15–17.85; 49% male) with case-confirmed encephalitis and/or ADEM. Analysis of case classification at the point of care revealed that in routine care, 96% of confirmed encephalitis/ADEM cases had been missed. Overall agreement of routine care diagnoses with digital encephalitis/ADEM case classification was <50%. Also in routine care, only 13% of cases held a virus-related diagnosis, i.e., herpesvirus (n = 8) and enterovirus infection (n = 5). Use of mNGS increased the yield of virus detection by 77% (n = 23 virus hits). Specifically, mNGS identified 10 additional virus species beyond herpes- and enteroviruses. Of the additional 23 virus hits detected with mNGS, PCR confirmation was possible post hoc in 14 cases (61%). Linking digital case classification, mNGS, and PCR testing may not be feasible in routine care at this point but may help to provide hints to the pathogenesis of encephalitis/ADEM in childhood, warranting further research and exploration. Full article
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11 pages, 1113 KiB  
Article
Antagonistic Activity of Bacteriocin-like Inhibitory Substances from Enterococcus lactis Isolated from the Surface of Jalapeno Pepper against Foodborne Pathogens
by Ezequiel Hernandez-Mendoza, Etna Aida Peña-Ramos, Vijay K. Juneja, Miguel Ángel Martínez-Téllez, Humberto González-Ríos, María de la Cruz Paredes-Aguilar, Martin Valenzuela-Melendres and Emmanuel Aispuro-Hernández
Microbiol. Res. 2024, 15(2), 889-899; https://doi.org/10.3390/microbiolres15020058 - 22 May 2024
Viewed by 698
Abstract
Lactic acid bacteria (LAB) can produce peptides known as bacteriocins with antagonistic activity against foodborne pathogens. The potential of LAB isolated from the surface of jalapeno peppers to produce bacteriocins with antagonistic activity against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, [...] Read more.
Lactic acid bacteria (LAB) can produce peptides known as bacteriocins with antagonistic activity against foodborne pathogens. The potential of LAB isolated from the surface of jalapeno peppers to produce bacteriocins with antagonistic activity against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella Typhimurium was evaluated. Previously isolated LAB strains were reactivated, and their cell-free supernatants (CFSs) were evaluated. Out of 390 reactivated strains, 60 produced bacteriocin-like inhibitory substances (BLIS) since their antagonistic activity was lost after proteases addition. Subsequently, 16 BLIS showed heat resistance (HR-BLIS), retaining their bioactivity after heat treatment (121 °C for 15 min). By 16S rRNA gene sequencing and antibiotic susceptibility tests, LAB strains producing HR-BLIS were identified as Enterococcus lactis. Four HR-BLIS exhibited a minimum inhibitory concentration (MIC) of 80 mg/mL against L. monocytogenes. MIC and minimum bactericidal concentration (MBC) of HR-BLIS-67 for S. aureus (MIC = 80 mg/mL; MBC = 320 mg/mL), S. Typhimurium (MIC = 150 mg/mL; MBC = 250 mg/mL), and E. coli O157:H7 (MIC = 250 mg/mL; MBC = 400 mg/mL) were determined. LAB isolated from the surface of jalapeno pepper produced HR-BLIS (possibly enterocin) that exhibited broad-spectrum antagonistic activity against foodborne pathogens; therefore, they are a promising source of natural antimicrobials to ensure food safety. Full article
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9 pages, 891 KiB  
Communication
Antagonistic Interactions in Onychomycosis: Antifungal Activity of Extracts from Pure and Mixed Cultures of Candida parapsilosis and Trichophyton spp.
by Thiago Henrique Lemes, Julyanna Andrade Silva Nascentes, Luis Octávio Regasini, João Paulo Zen Siqueira, Glaucia Rigotto, Ludmilla Tonani, Marcia Regina von Zeska Kress and Margarete Teresa Gottardo de Almeida
Microbiol. Res. 2024, 15(2), 880-888; https://doi.org/10.3390/microbiolres15020057 - 22 May 2024
Viewed by 620
Abstract
Onychomycoses are nail infections that require prolonged therapy and have high recurrence rates. Dermatophytes are the main etiological agents of these infections, followed by yeasts and non-dermatophyte filamentous fungi. The limited antifungal arsenal used to treat onychomycosis and the change in the susceptibility [...] Read more.
Onychomycoses are nail infections that require prolonged therapy and have high recurrence rates. Dermatophytes are the main etiological agents of these infections, followed by yeasts and non-dermatophyte filamentous fungi. The limited antifungal arsenal used to treat onychomycosis and the change in the susceptibility profile of these agents contribute to the chronicity and recalcitrant profile of infections. The present study aimed to determine the antifungal activity of extracts obtained from pure and mixed cultures of Candida parapsilosis, Trichophyton mentagrophytes, and Trichophyton rubrum. Additionally, in vivo toxicity tests with Galleria mellonella and time-kill assays were carried out. The susceptibility profiles of dermatophytes were determined using a microdilution technique with minimum inhibitory concentrations (MICs) between 250 and 8000 µg/mL. The time-kill assay, compared to growth control, resulted in the death of dermatophytes within 48 h. No toxicity of the extracts was detected in experiments with Galleria mellonella larvae under the test conditions. The extracts of pure and mixed cultures of Candida parapsilosis and dermatophytes present antifungal activity against T. mentagrophytes and T. rubrum. Isolating and identifying compounds in the extracts may allow the development of new therapeutic approaches to control fungal infections. Full article
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16 pages, 7206 KiB  
Article
Diversity of Bacterial Communities in Sediment in Inland Water Bodies in Relation to Environmental Factors and Human Impacts: A Case Study on Typical Regions in Vietnam
by Hoa Thi Bui, Thuy Thi Thu Nguyen, Ha Thu Le, Dau Thi Pham, Huy Quang Nguyen, Nam Thanh Nguyen, Tam Duc Nguyen, Tam Thi Nguyen, Hoang Phuc Trinh, Cuong Van Duong and Hai The Pham
Microbiol. Res. 2024, 15(2), 864-879; https://doi.org/10.3390/microbiolres15020056 - 19 May 2024
Viewed by 589
Abstract
Environmental changes and human impact can alter biodiversity in negative manners that affect mankind’s sustainable development. Particularly, such effects on inland waters are even more concerning, as those ecosystems play essential roles in sustaining human life as well as relevant wildlife. Thus, in [...] Read more.
Environmental changes and human impact can alter biodiversity in negative manners that affect mankind’s sustainable development. Particularly, such effects on inland waters are even more concerning, as those ecosystems play essential roles in sustaining human life as well as relevant wildlife. Thus, in this study, we investigated such effects on microbial diversity in inland waters in Vietnam using bacterial communities in sediment as indicators. To do this, we collected sediment samples from various locations in three respective regions (Red river in the north, Ba river in the central area, and Mekong delta flood zone in the south) using standard methods, extracted their total DNA, sequenced their V3-V4 16S rRNA gene fragments using an Illumina Miseq platform and analyzed the sequences to infer the diversity of the bacterial communities in the samples. These communities were compared in terms of richness (alpha diversity) and composition (beta diversity), and the correlations between their diversity levels and environmental factors, as well as human activities, were analyzed by using standard statistical tools. Our results showed that the communities were different from each other solely by region, in richness and critically in composition, although there were some communities distinctively different from all the others. Among environmental factors, only water salinity (and conductivity) had negative correlations with alpha-diversity indices of the bacterial communities, and phosphate concentration and turbidity had positive correlations, while the other factors had almost no correlations, which partially explains the region-specific diversity. These results also suggest that climate change incidences, especially sea intrusion, can have significant effects on microbial diversity in inland waters. The impact of human activities did not appear severe, solely affecting bacterial community richness, but not significantly affecting bacterial community composition. However, apparently reduced bacterial diversity in several sites with intense human impacts and distinct environmental conditions should be noted and deserve further investigation. Full article
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14 pages, 1045 KiB  
Article
Urinary Tract Infections in a Single Hospital in Central Portugal, a 5-Year Analysis
by Miguel Castelo Branco, Patrícia Coelho and Francisco Rodrigues
Microbiol. Res. 2024, 15(2), 850-863; https://doi.org/10.3390/microbiolres15020055 - 17 May 2024
Viewed by 566
Abstract
Urinary tract infections are defined as the presence of microorganisms in any part of the urinary system, with the exception of the distal urethra. A majority of them are uncomplicated infections that are resolved on an outpatient basis, with empirical therapy. The objectives [...] Read more.
Urinary tract infections are defined as the presence of microorganisms in any part of the urinary system, with the exception of the distal urethra. A majority of them are uncomplicated infections that are resolved on an outpatient basis, with empirical therapy. The objectives of this work were to study the sociodemographic characteristics of patients, analyze associated strains and examine the response of the main microorganisms to antibiotics. A retrospective observational study of all positive urine cultures between 2018 and 2022 was carried out at an institution (8340 samples). Sociodemographic data were also collected. In total, 61.3% were women, with an average age of 63.4 years, and 43.2% were from the Emergency Department. A total of 13.5% were fitted, 56% of whom were women. Also, 95.9% were not taking any antibiotics, and among the individuals who were taking antibiotics, 50% were injected. Escherichia coli (53.5%) and Klebsiella pneumoniae (13.8%) are identified as the most prevalent strains. In the time periods analyzed, Escherichia coli decreased its resistance to 11 antibiotics and increased to 5 antibiotics, while Klebsiella pneumoniae decreased to 7 and increased to 7, with emphasis on the presence of 3 antibiotics with a resistance rate of 100% to all Klebsiella pneumoniae strains identified in 2022. Full article
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9 pages, 691 KiB  
Communication
Molecular Analysis of the Microbial Guild Fixing Nitrogen in Ricefield Soils in Missouri
by Prithi R. Sawli, Mark A. Buchheim and Mark A. Schneegurt
Microbiol. Res. 2024, 15(2), 841-849; https://doi.org/10.3390/microbiolres15020054 - 17 May 2024
Viewed by 465
Abstract
Non-symbiotic diazotrophic microbes are important contributors to global N budgets in cereal crops. Knowledge of the biogeography of the organisms in this functional guild increases our understanding of biological N fixation in diverse locations and climates. Here, we describe the diazotrophic community in [...] Read more.
Non-symbiotic diazotrophic microbes are important contributors to global N budgets in cereal crops. Knowledge of the biogeography of the organisms in this functional guild increases our understanding of biological N fixation in diverse locations and climates. Here, we describe the diazotrophic community in the previously unstudied, extensive ricefields of southeast Missouri, using restriction fragment length polymorphism (RFLP) analysis and sequencing of nifH gene clones. While nine RFLP patterns were observed in random nifH clones, these groups were not all supported by gene sequencing, suggesting that the RFLP of nifH genes alone is not suitable for describing diazotrophic guilds. Dozens of nifH clones from Missouri ricefield soils were sequenced and analyzed phylogenetically. The nifH genes detected were predominantly from Geobacteraceae, most closely related to Geobacter and Geomonas species. There were substantial clusters of nifH clones most closely related to Desulfovibrionales and other Proteobacteria. Many of the clones did not closely cluster with nifH sequences from known isolates or clades. No cyanobacterial or archaeal sequences were detected in the Missouri ricefield soils. The microbial guild fixing N appeared to be rich in anaerobes and lithotrophs. Organisms in Geobacter and Geomonas seem to be cosmopolitan, but endemism was evident, since nifH clones were recovered that formed clusters not previously reported from ricefields in other locations. Full article
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18 pages, 3289 KiB  
Article
Endophytic Fungal Diversity in Hardwickia binata: Bridging the Gap between Traditional and Modern Techniques
by Michael Joe Xavier Sneha, Myithili Thangavel, Israel Mani, Pandy Rajapriya, Nagendraprabhu Ponnuraj and Mohan Pandi
Microbiol. Res. 2024, 15(2), 823-840; https://doi.org/10.3390/microbiolres15020053 - 16 May 2024
Viewed by 613
Abstract
Endophytic fungus is crucial for maintaining plant health and defense mechanisms, acting as protective barriers against pathogens, and producing medicinally beneficial bioactive compounds. Genome sequencing and metagenomics have significantly enhanced the understanding of fungal diversity and metabolic capabilities, enabling the identification of new [...] Read more.
Endophytic fungus is crucial for maintaining plant health and defense mechanisms, acting as protective barriers against pathogens, and producing medicinally beneficial bioactive compounds. Genome sequencing and metagenomics have significantly enhanced the understanding of fungal diversity and metabolic capabilities, enabling the identification of new genes and substances. Traditional culture-dependent methods have been complemented by culture-independent techniques, offering a more comprehensive view of fungal diversity. Using both culture-dependent and culture-independent techniques, the present research investigation explored the diversity of endophytic fungi encountered in the foliage of Hardwickia binata. The study examined the topographical characteristics and nutritional content of soil samples collected from the locality of the selected plant sample, H. binata, to better comprehend the effects on the plant’s growth. The balanced nutrient constituted approximately a pH of 7.2, which suggested an alkaline nature and promoted plant development. The ratio of nitrogen, phosphorous, and potassium remained 3:1:1. A total of 25 fungal isolates, categorized into 17 morphotypes, were obtained using the culture-dependent approach; Curvularia and Nigrospora emerged as the most common genera. Furthermore, the prediction of the ITS2 secondary structure supports the identification of species, highlighting a wide variety of fungal species present in H. binata. The culture-independent approach generated 69,570 high-quality sequences, identifying 269 Operational Taxonomic Units (OTUs). The dominant Ascomycota phylum, along with various genera, indicated a rich fungal community associated with H. binata. This study advances the understanding of the endophytic fungus communities that are associated with H. binata and the nature of soil ecology. The findings emphasize the significance of holistic techniques in the study of microbial dynamics within plant systems as well as their implications for ecosystem management and plant health. Full article
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17 pages, 1654 KiB  
Review
Microbial Diversity and Nitrogen Cycling in Peat and Marine Soils: A Review
by Akshatha Soratur, Balu Alagar Venmathi Maran, Ahmad Syazni Kamarudin and Kenneth Francis Rodrigues
Microbiol. Res. 2024, 15(2), 806-822; https://doi.org/10.3390/microbiolres15020052 - 14 May 2024
Viewed by 513
Abstract
Nitrogen is an essential nutrient for living organisms in peat and marine soils, and its transformation within the soil matrix is a complex process mediated by various microbes that inhabit these ecological niches. The metabolism of nitrogen is governed by microbially mediated biogeochemical [...] Read more.
Nitrogen is an essential nutrient for living organisms in peat and marine soils, and its transformation within the soil matrix is a complex process mediated by various microbes that inhabit these ecological niches. The metabolism of nitrogen is governed by microbially mediated biogeochemical transformations, such as nitrification, anammox, and denitrification, which contribute to the assimilated pool of nitrogen and fixed nitrogen loss. One of the major challenges facing the field of peat and marine microbiology is the lack of understanding of the correlation between ecosystem-driven nitrogen transformation and microbial diversity. This is crucial because of growing concerns regarding the impacts of human-induced activities and global climate change on microbial nitrogen-cycling processes in peat and marine soils. Thus, this review aimed to provide a comprehensive overview of the current understanding of the microbial communities involved in peat and marine nitrification, anammox, and denitrification; the factors influencing the niche differentiation and distribution of the main functional components; the genes involved; and the main effects of human-induced activities and global climate change on the peat and marine nitrogen cycle. The implications of this review will facilitate an understanding of the complex mechanisms associated with ecosystem function in relation to nitrogen cycling, the role of peat and marine soils as carbon sinks, pollution remediation using naturally occurring populations of diverse microbes, and the development of policies to mitigate the effects of anthropogenic influences in peat and marine soils. Full article
(This article belongs to the Special Issue Microorganisms as a Tool for Restoring the Environment)
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19 pages, 3111 KiB  
Article
In Vitro Evaluation of Gastrointestinal Stability of Pediococcus pentosaceus Isolated from Fermented Maize and Pearl Millet for Possible Novel Chicken Probiotic Development
by Gifty Ziema Bumbie, Leonardo Abormegah, Peter Asiedu, Akua Durowaa Oduro-Owusu, Kwame Owusu Amoah, Frederick Danso, Bernard Bortei Bortieh, Theresah Nkrumah, Taha Mohamed Mohamed and Zhiru Tang
Microbiol. Res. 2024, 15(2), 787-805; https://doi.org/10.3390/microbiolres15020051 - 14 May 2024
Viewed by 440
Abstract
Research has identified certain bio-based products, such as probiotics, as alternatives to antibiotics for use in animal feed. They are capable of controlling, preventing or minimizing the colonization of the gastrointestinal tract by pathogenic bacteria. To isolate Pediococcus spp. and assess its technological [...] Read more.
Research has identified certain bio-based products, such as probiotics, as alternatives to antibiotics for use in animal feed. They are capable of controlling, preventing or minimizing the colonization of the gastrointestinal tract by pathogenic bacteria. To isolate Pediococcus spp. and assess its technological properties for possible probiotic development, maize and pearl millet were used. The cereals were steeped and wet milled after 48 h of fermentation. The milled cereals were kneaded into dough for 24 h, after which a 10% slurry was prepared for tenfold serial dilution to enumerate the LAB by employing pour plate techniques using MRS Agar. Based on the cell morphology of the isolated bacteria, eight isolates (four from maize and four from millet) that were selected for identification using MALDI-TOF MS showed that five were Pediococcus pentosaceus (P. pentosaceus), one was Pediococcus acidilactici, and two did not match any organism. Subsequently, the six isolates were labeled as MZ1, MZ2, MZ3, MZ4 for the maize isolate and MLT5 and MLT7 for the millet isolate. The six Pediococcus spp. were assessed in vitro for acid and bile salt tolerance, gastric juice and intestinal fluid tolerance and antibiotic resistance and antimicrobial susceptibility tests were performed, and the survivability rate of the strains was calculated. With regard to the mean count, there was a reduction in log10 CFU/mL under the lower pH conditions and their duration of exposure with regard to time. Among the isolates, no differences were noted at the various periods of exposure (0 h, 1 h, 2 h and 3 h) at pH 4 (p > 0.05). However, significant differences were noted at pH 3, 2 and 1 among the isolates (p < 0.05). The percentage survival of MZ4 and MLT7 at pH 1 was higher compared to the other isolates at 0 h. Significant differences were observed among the isolated at pH 2, 3 and 4 across the various periods. The mean count of the isolates in gastric juice was similar at 0 and 1 h, but significant differences were noted at 2 and 3 h, where MLT7 was highest (p < 0.05). A similar trend was observed for percentage survival. The mean count and the percentage survival of isolates under different concentrations of bile salt were similar. Significant differences were noted among isolates in both mean count and percentage survival when exposed to intestinal fluid (p < 0.05). All of the isolates were highly tolerant to the antibiotics tested and possessed antibacterial properties against the selected pathogens. The LABs proved to be good probiotic materials, according to the results obtained. However, the Pediococcus strain MLT7 proved to be the LAB of choice; therefore, its molecular identity was verified using the 16S rRNA sequence and was labeled as Pediococcus pentosaceus GT001 after it was discovered to have 100% similarity with some strains of Pediococcus pentosaceus. Full article
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24 pages, 3515 KiB  
Article
Exploring the Antimicrobial and Antioxidant Activities of Streptomyces sp. EIZ2 Isolated from Moroccan Agricultural Soil
by Said Rammali, Fatima Zahra Kamal, Mohamed El Aalaoui, Abdellatif Rahim, Aziz Baidani, Khadija Dari, Abdelkrim Khattabi, Alin Ciobică, Bogdan Novac, Antoneta Petroaie, Radu Lefter and Bouchaib Bencharki
Microbiol. Res. 2024, 15(2), 762-786; https://doi.org/10.3390/microbiolres15020050 - 13 May 2024
Viewed by 602
Abstract
Antibiotics play a crucial role in preserving and improving public health, saving millions of lives every year. However, their effectiveness is currently under threat due to the ability of bacteria to adapt and develop resistance to these treatments. Therefore, this study was carried [...] Read more.
Antibiotics play a crucial role in preserving and improving public health, saving millions of lives every year. However, their effectiveness is currently under threat due to the ability of bacteria to adapt and develop resistance to these treatments. Therefore, this study was carried out on two soil samples collected in two areas of Arba Aounate, Sidi Bennour province, Morocco, to identify natural antibiotic-producing Actinobacteria capable of combating multi-drug-resistant (MDR) bacteria. A primary screening revealed that of the 50 isolates, 16 exhibited antimicrobial activity against Pseudomonas aeruginosa ATCC 27,853, Staphylococcus aureus ATCC 25,923, Escherichia coli ATCC 25,922, and Candida albicans ATTC 60193. A secondary screening showed that of the 16 isolates, only EIZ1 and EIZ2 isolates displayed outstanding antimicrobial and antifungal activity against 6 MDR bacteria, including Escherichia coli 19L2418, Listeria monocytogenes, Proteus sp. 19K1313, Klebsiella pneumoniae 19K 929, Proteus vulgaris 16C1737, and Klebsiella pneumoniae 20B1572. These two isolates were also characterized culturally, morphologically, physiologically, and biochemically. Afterward, the amplification of 16S rRNA revealed that isolate EIZ2 was 99.06% strongly related to the genus Streptomyces. Furthermore, this extract exhibits strong antioxidant activity against DPPH and ABTS free radicals and elevated ferric-reducing antioxidant power. A significant (p < 0.0001) positive correlation was observed between antioxidant activities and total phenolic and flavonoid contents. A GC–MS analysis of the ethyl acetate extract revealed the presence of 10 compounds, mainly diethyl phthalate (97%) and benzeneacetic acid (94%). This research demonstrates that Streptomyces sp. strain EIZ2 represents a potential source of antimicrobial and antioxidant compounds. These compounds could offer considerable potential as therapeutic agents, paving the way for future developments in medical applications. Full article
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16 pages, 4806 KiB  
Article
A Quadruplex Reverse Transcription Quantitative Polymerase Chain Reaction for Detecting Canine Coronavirus, Canine Rotavirus, Canine Parvovirus, and Canine Distemper Virus
by Yandi Shi, Feng Long, Kaichuang Shi, Mengyi He, Yuwen Shi, Shuping Feng, Yanwen Yin, Xiankai Wei and Zongqiang Li
Microbiol. Res. 2024, 15(2), 746-761; https://doi.org/10.3390/microbiolres15020049 - 10 May 2024
Viewed by 608
Abstract
Background: Canine coronavirus (CCoV), canine rotavirus (CRV), canine parvovirus (CPV), and canine distemper virus (CDV) cause gastroenteritis in dogs, and co-infections of these pathogens are common in China. In particular, CCoV and CRV are confirmed to have important zoonotic potential and cause public [...] Read more.
Background: Canine coronavirus (CCoV), canine rotavirus (CRV), canine parvovirus (CPV), and canine distemper virus (CDV) cause gastroenteritis in dogs, and co-infections of these pathogens are common in China. In particular, CCoV and CRV are confirmed to have important zoonotic potential and cause public health issues. It is difficult to diagnose these diseases based only on clinical manifestations and pathological damage. Methods: In this study, four pairs of specific primers and probes targeting the CCoV M, CRV VP7, CPV VP2, and CDV N genes were designed. The reaction conditions, including the primer and probe concentrations, annealing temperatures, and reaction cycles, were optimized for the development of a quadruplex RT-qPCR for the detection of CCoV, CRV, CPV, and CDV. The assay was used to test 1028 clinical samples to validate its application. Results: A quadruplex RT-qPCR was successfully established for the differential detection of CCoV, CRV, CPV, and CDV, with good specificity, high sensitivity, and excellent repeatability. The assay could specifically detect CCoV, CRV, CPV, and CDV without cross-reactivity with the other canine viruses tested. It showed high sensitivity with limits of detection (LOD) of 1.1 × 102 copies/reaction for all four plasmid constructs. It showed excellent repeatability, with 0.05–0.90% intra-assay variation and 0.02–0.94% inter-assay variation. The 1028 clinical samples were tested using the quadruplex RT-qPCR and a reported reference RT-qPCR. The positivity rates of CCoV, CRV, CPV, and CDV were 9.53%, 0.97%, 25.68%, and 5.06% using the developed assay, and 9.05%, 0.88%, 25.68%, and 4.86% using the reference assay, with agreements higher than 99.32%. Conclusion: The results indicated that a rapid and accurate quadruplex RT-qPCR was developed for the detection and differentiation of CCoV, CRV, CPV, and CDV. Full article
(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)
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12 pages, 1646 KiB  
Article
In Saccharomyces cerevisiae ρ0 Cells, UME6 Contributes to the Activation of ABC Transporter Genes and Pleiotropic Drug Resistance via RPD3 and PDR3
by Mai Funasaka, Mahiro Ota and Yoichi Yamada
Microbiol. Res. 2024, 15(2), 734-745; https://doi.org/10.3390/microbiolres15020048 - 9 May 2024
Viewed by 574
Abstract
In Saccharomyces cerevisiae, the Rpd3L complex includes the histone deacetylase Rpd3 and the DNA binding proteins Ume6 and Ash1 and serves as a transcriptional silencer or enhancer. In S. cerevisiae, the transcription of PDR5, which encodes a major drug efflux [...] Read more.
In Saccharomyces cerevisiae, the Rpd3L complex includes the histone deacetylase Rpd3 and the DNA binding proteins Ume6 and Ash1 and serves as a transcriptional silencer or enhancer. In S. cerevisiae, the transcription of PDR5, which encodes a major drug efflux pump, and pleiotropic drug resistance (PDR) are hyperactivated by the transcription factor Pdr3 in ρ0/− cells, which lack mitochondrial DNA. We previously showed that RPD3 and UME6 are required for the activation of PDR5 transcription and PDR in S. cerevisiae ρ0 cells. Here, using real-time PCR analysis, we revealed that RPD3 and UME6 are responsible for the activated basal expression of the ABC transporter-encoding genes SNQ2, PDR15, and PDR5 in S. cerevisiae ρ0 cells. Furthermore, using real-time PCR analysis and a spot dilution assay, we found that Ume6 increases the basal expression of PDR5 and PDR15 and induces PDR in a manner dependent on RPD3 and PDR3 in ρ0 cells. This finding may contribute to the elucidation of the relationships between the molecules required for the activation of ABC transporter genes in S. cerevisiae ρ0/− cells and in pathogenic Candida species. Full article
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13 pages, 2476 KiB  
Article
Weissella koreensis KJ, Which Increases Gut Tight Junction Protein Expression, Alleviates TNBS-Induced Colitis by Suppressing Inflammatory Cytokines
by Kyung-Joo Kim, Hyoleem Lee, Yoon Sin Oh and Se-Eun Jang
Microbiol. Res. 2024, 15(2), 721-733; https://doi.org/10.3390/microbiolres15020047 - 8 May 2024
Cited by 1 | Viewed by 770
Abstract
Inflammatory bowel disease (IBD), a chronic inflammatory disease, results from dysregulation of the immune responses. The IBD prevalence rate was 321.2 per 100,000 people in 2021 and, compared with that in 2006 (200 per 100,000 people), had increased at a rate of +46%. [...] Read more.
Inflammatory bowel disease (IBD), a chronic inflammatory disease, results from dysregulation of the immune responses. The IBD prevalence rate was 321.2 per 100,000 people in 2021 and, compared with that in 2006 (200 per 100,000 people), had increased at a rate of +46%. Therefore, the development of a safe and new treatment for IBD is urgently needed. Weissella koreensis, a strain of lactic acid bacteria (LABs), was isolated from kimchi and shown to inhibit a pro-inflammatory cytokine, tumor necrosis factor-alpha (TNF-α). Its anti-inflammatory effect was further assessed using a mouse model of colitis induced by 2,4,6-trinitrobenzenesulfonic acid (TNBS). The administration of TNBS significantly increased myeloperoxidase (MPO) expression, macroscopic score, and colonic shortening. Oral administration of W. koreensis KJ suppressed the TNBS-induced response and significantly inhibited the expression of the pro-inflammatory cytokines TNF-α, interleukin (IL)-1β, and IL-6 in the intestinal tissues. In particular, W. koreensis KJ reversed the TNBS-induced decrease in the expression of these tight junction proteins. Therefore, since W. koreensis KJ isolated from kimchi, which increases gut tight junction proteins, attenuating colitis by suppressing inflammatory cytokines, it can be used as a therapeutic candidate for treating colitis such as IBD. Full article
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13 pages, 1246 KiB  
Review
Ice-Nucleating Gut Microbes in Insects: A Scoping Review
by Matan Shelomi
Microbiol. Res. 2024, 15(2), 708-720; https://doi.org/10.3390/microbiolres15020046 - 30 Apr 2024
Viewed by 502
Abstract
(1) Background. At subzero temperatures, water crystallizes on ice nucleation agents. Researchers have identified ice-nucleating microbes (INMs) in insect digestive tracts that can raise the insect’s supercooling point, causing freezing at higher temperatures but slower rates. For freeze-tolerant insects, such gut microbes should [...] Read more.
(1) Background. At subzero temperatures, water crystallizes on ice nucleation agents. Researchers have identified ice-nucleating microbes (INMs) in insect digestive tracts that can raise the insect’s supercooling point, causing freezing at higher temperatures but slower rates. For freeze-tolerant insects, such gut microbes should allow for slower freezing away from tissues and higher survival rates. For freeze-susceptible insects, however, such microbes could cause a fatal freeze at higher temperatures, and could possibly be used as biocontrol. (2) Methods. A first-ever scoping review was carried out of research on insect-associated INMs, from observational studies attempting to isolate these microbes, to experimental studies applying them and checking for increased mortality. (3) Results. Relatively few research groups have studied insect-associated INMs in any capacity. (4) Conclusions. Several authors hypothesized that such microbes are probably abundant, and their contribution to ice nucleation activity in insects is under-reported. Biocontrol assays using ice-nucleating microbes showed promise, but a risk to non-target organisms has been experimentally confirmed. Future surveys of insect–microbe interactions using molecular tools are likely to reveal new examples, if not new microbe species capable of ice nucleation. Full article
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15 pages, 1621 KiB  
Article
Genetic Diversity of Plasmodium vivax Surface Ookinete Protein Pvs25 and Host Genes in Individuals Living along the Thai–Myanmar Border and Their Relationships with Parasite Density
by Abdifatah Abdullahi Jalei, Wanna Chaijaroenkul and Kesara Na-Bangchang
Microbiol. Res. 2024, 15(2), 693-707; https://doi.org/10.3390/microbiolres15020045 - 30 Apr 2024
Viewed by 894
Abstract
Plasmodium vivax (Pv) accounts for over 50% of malaria cases in Latin America and Asia. Despite a significant reduction in Pv transmission in Thailand, the parasite remains endemic to the border areas. This study aimed to investigate the genetic diversity of [...] Read more.
Plasmodium vivax (Pv) accounts for over 50% of malaria cases in Latin America and Asia. Despite a significant reduction in Pv transmission in Thailand, the parasite remains endemic to the border areas. This study aimed to investigate the genetic diversity of the parasites and the host factors, as well as their relation to parasite density in Pvisolates, along the Thai–Myanmar border. Genetic variations in Pv markers, specifically the ookinete surface protein Pvs25, and host genes, including Toll-like receptor 6 (TLR6), TLR9, TIR Domain-containing adaptor protein (TIRAP), Toll-interacting protein (TOLLIP), Duffy antigen receptor for chemokines (DARC), and intercellular adhesion molecule 1 (ICAM-1), were investigated using polymerase chain reaction (PCR) with restriction fragment length polymorphism (RFLP). A total of 548 PCR-positive Pv samples collected from Tak and Kanchanaburi provinces during two periods (2006–2007 and 2014–2016) were included in the study. Pvs25 exhibited four haplotypes, with H1 (EGTKV) being the most prevalent in both provinces. Kanchanaburi isolates exhibited greater genetic diversity than Tak isolates. No significant deviations from neutrality were observed for Pvs25 in either area. ICAM-1 and TOLLIP s3750920 heterozygous carriers had greater median parasite densities than homozygous mutants. The TLR9 rs187084 T genotype had a significantly higher parasite density than the non-T genotype. The findings underscore the significant association between the rs3750920 C/T, rs5498 A/G, and rs187084 T genotypes and high parasite density in patients infected with Pv, highlighting their potentially critical role in malaria susceptibility. Full article
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26 pages, 2150 KiB  
Review
An Update on Zika Virus Vaccine Development and New Research Approaches
by Angie Lizeth Buitrago-Pabón, Salvador Ruiz-Sáenz, Alicia Jiménez-Alberto, Gerardo Aparicio-Ozores, Juan Arturo Castelán-Vega and Rosa María Ribas-Aparicio
Microbiol. Res. 2024, 15(2), 667-692; https://doi.org/10.3390/microbiolres15020044 - 29 Apr 2024
Viewed by 1184
Abstract
Zika virus (ZIKV) is an emerging flavivirus that represents significant public health challenges, particularly in the Americas, and is a substantial risk to other parts of the world due to its rapid expansion and its established association with neurological disorders, including Guillain–Barré syndrome [...] Read more.
Zika virus (ZIKV) is an emerging flavivirus that represents significant public health challenges, particularly in the Americas, and is a substantial risk to other parts of the world due to its rapid expansion and its established association with neurological disorders, including Guillain–Barré syndrome and an intrauterine fetal infection that can cause microcephaly, blindness, and other congenital neurological complications. To date, no vaccine to prevent ZIKV infections has been approved. Therefore, developing a safe and effective vaccine against this virus is a global health priority. This review analyzes the ZIKV outbreaks, as well as associated neurological complications, its genome, and immunological responses. The current vaccines in development have reported results from preclinical and clinical trials about novel approaches to obtain safer and more effective vaccines and the challenges faced by ZIKV vaccine development. Full article
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12 pages, 4200 KiB  
Article
Exposure of Dairy Cows to Coxiella burnetii in Greece: Surveillance Results and Association of Bacterial Presence with Environmental Variables
by George Valiakos, Ioannis Gouvias, Marios Lysitsas, Ilias Bouzalas, Stefania Tampach, Eleni Malissiova, Alexis Giannakopoulos, Constantina N. Tsokana, Dimitrios Vourvidis, Anna Kyrma and Charalambos Billinis
Microbiol. Res. 2024, 15(2), 655-666; https://doi.org/10.3390/microbiolres15020043 - 25 Apr 2024
Viewed by 702
Abstract
The exposure of dairy cows to Coxiella burnetii using molecular and serological techniques was investigated in this study. Bulk tank milk and serum samples were collected from various farms in Greece (mainly northern Greece). DNA extraction was performed on milk samples, and qPCR [...] Read more.
The exposure of dairy cows to Coxiella burnetii using molecular and serological techniques was investigated in this study. Bulk tank milk and serum samples were collected from various farms in Greece (mainly northern Greece). DNA extraction was performed on milk samples, and qPCR targeting the IS1111 insertion sequence was performed to detect bacterial pathogens. An ELISA was used to detect specific antibodies in bulk milk and individual serum samples. Data on farms were collected in the field using handheld Global Positioning System Garmin units. The collected data were analyzed using an Ecological Niche Model within the framework of a geographic information system. The results indicated that in more than half of the dairy farms (35/60, 58.3%), C. burnetii is present in milk. Specific antibodies were also detected in almost all milk samples (57/60, 95.0%). At least one seropositive animal was identified using ELISA in the majority of the examined farms (25/28, 89.3%). C. burnetii PCR-positive farms were located in the low-altitude zone with a mean value of 97 m above sea level (range: 2–681). The environmental variable with the highest gain when used in isolation is precipitation in the wettest quarter (28.3% contribution), which therefore appears to have the most useful information by itself. The environmental variable that decreases the gain the most when omitted is the minimal temperature of the coldest month (6.9% contribution). The analysis demonstrated that a mild climate with low precipitation favors a positive status. The exposure of dairy cattle farms to C. burnetii is massive, raising significant concerns regarding livestock production and public health implications. Full article
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21 pages, 3741 KiB  
Review
Methanotrophy: A Biological Method to Mitigate Global Methane Emission
by Anju Rani, Aarushi Pundir, Medhashree Verma, Samiksha Joshi, Geeta Verma, Snežana Andjelković, Snežana Babić, Jasmina Milenković and Debasis Mitra
Microbiol. Res. 2024, 15(2), 634-654; https://doi.org/10.3390/microbiolres15020042 - 25 Apr 2024
Viewed by 1211
Abstract
Methanotrophy is a biological process that effectively reduces global methane emissions by utilizing microorganisms that can utilize methane as a source of energy under both oxic and anoxic conditions, using a variety of different electron acceptors. Methanotrophic microbes, which utilize methane as their [...] Read more.
Methanotrophy is a biological process that effectively reduces global methane emissions by utilizing microorganisms that can utilize methane as a source of energy under both oxic and anoxic conditions, using a variety of different electron acceptors. Methanotrophic microbes, which utilize methane as their primary source of carbon and energy, are microorganisms found in various environments, such as soil, sediments, freshwater, and marine ecosystems. These microbes play a significant role in the global carbon cycle by consuming methane, a potent greenhouse gas, and converting it into carbon dioxide, which is less harmful. However, methane is known to be the primary contributor to ozone formation and is considered a major greenhouse gas. Methane alone contributes to 30% of global warming; its emissions increased by over 32% over the last three decades and thus affect humans, animals, and vegetation adversely. There are different sources of methane emissions, like agricultural activities, wastewater management, landfills, coal mining, wetlands, and certain industrial processes. In view of the adverse effects of methane, urgent measures are required to reduce emissions. Methanotrophs have attracted attention as multifunctional bacteria with potential applications in biological methane mitigation and environmental bioremediation. Methanotrophs utilize methane as a carbon and energy source and play significant roles in biogeochemical cycles by oxidizing methane, which is coupled to the reduction of various electron acceptors. Methanotrophy, a natural process that converts methane into carbon dioxide, presents a promising solution to mitigate global methane emissions and reduce their impact on climate change. Nonetheless, additional research is necessary to enhance and expand these approaches for extensive use. In this review, we summarize the key sources of methane, mitigation strategies, microbial aspects, and the application of methanotrophs in global methane sinks with increasing anthropogenic methane emissions. Full article
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8 pages, 2857 KiB  
Case Report
First Molecular Detection and Characterization of Fowl Aviadenovirus Serotype 11 from Broiler Chickens in Chile
by Leandro Cádiz, Miguel Guzmán, Fernando Navarrete, Paulina Torres and Hector Hidalgo
Microbiol. Res. 2024, 15(2), 626-633; https://doi.org/10.3390/microbiolres15020041 - 23 Apr 2024
Viewed by 856
Abstract
Fowl aviadenovirus (FAdV) is a member of the Aviadenovirus genus within the Adenoviridae family. FAdVs are divided into five species based on genomic differences: Fowl aviadenovirus A to Fowl aviadenovirus E (FAdV-A to FAdV-E). They are classified into twelve serotypes (FAdV-1 to FAdV-8a [...] Read more.
Fowl aviadenovirus (FAdV) is a member of the Aviadenovirus genus within the Adenoviridae family. FAdVs are divided into five species based on genomic differences: Fowl aviadenovirus A to Fowl aviadenovirus E (FAdV-A to FAdV-E). They are classified into twelve serotypes (FAdV-1 to FAdV-8a and FAdV-8b to FAdV-11) through cross-neutralization tests. FAdVs are mainly associated with hepatitis hydropericardium syndrome (HHS), adenoviral gizzard erosion (AGE), and inclusion body hepatitis (IBH). The serotypes commonly involved in IBH are FAdV-2, FAdV-11, FAdV-8a, and FAdV-8b. IBH causes significant economic losses in the poultry industry, mainly due to high mortality, reduced productivity, and immunosuppression. This is the first case report on IBH in Chile caused—according to post-mortem findings, molecular analysis, sequencing, and phylogenetic analysis—by FAdV-11. Since the serotype had not previously been reported in Chile, continued monitoring of IBH cases is required to determine the serotype of the circulating FAdVs and adapt preventative vaccination programs. Full article
(This article belongs to the Special Issue Evolution of Viral Virulence)
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12 pages, 1951 KiB  
Article
Ingested Microplastics Can Act as Microbial Vectors of Ichthyofauna
by Abdulhusein Jawdhari, György Deák, Dan Florin Mihăilescu, Nicolai Crăciun, Andrea Cristina Staicu, Ioana Stanca, Derniza Cozorici, Sergiu Fendrihan, Cristian-Emilian Pop and Maria Mernea
Microbiol. Res. 2024, 15(2), 614-625; https://doi.org/10.3390/microbiolres15020040 - 23 Apr 2024
Viewed by 882
Abstract
Microplastics (plastic particles < 5 mm) are ubiquitous pollutants that have the ability to carry microbiota, including pathogens. Microbial adhesion is usually a sign of pathogenicity; thus, we investigated the adherent microbiota found on 4 mm nylon strips, which were ingested and excreted [...] Read more.
Microplastics (plastic particles < 5 mm) are ubiquitous pollutants that have the ability to carry microbiota, including pathogens. Microbial adhesion is usually a sign of pathogenicity; thus, we investigated the adherent microbiota found on 4 mm nylon strips, which were ingested and excreted by wild fish specimens. Retention times were recorded and the polymer analysis of the excreted samples was performed, which showed no signs of degradation, nor did their controls, represented by the nylon strips submerged in the same water tanks. Both the ingested samples and controls presented pathogens in large quantities. Following Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight identification, the dominant genus was represented by Aeromonas, revealing the fact that nylon microplastics can serve as undegradable physical carriers for this pathogen, among others, in the aquatic environment. Full article
(This article belongs to the Special Issue Zoonotic Bacteria: Infection, Pathogenesis and Drugs)
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16 pages, 3512 KiB  
Article
Correlation between Aerosol Particulates, Carcass Dirtiness, and Hygiene Indicators of Bovine Carcasses in the Abattoir Environment: Results of a Study in Italy
by Beniamino T. Cenci-Goga, Emma Tedeschini, Egidia Costanzi, Margherita Maranesi, Musafiri Karama, Saeed El-Ashram, Cristina Saraiva, Juan García-Díez, Massimo Zerani, Ebtesam M. Al-Olayan and Luca Grispoldi
Microbiol. Res. 2024, 15(2), 598-613; https://doi.org/10.3390/microbiolres15020039 - 22 Apr 2024
Viewed by 894
Abstract
The objective of this study was to demonstrate the possible correlation of visible carcass contamination and abattoir aerosol quality with microbial hygiene criteria. A total of 279 bovine carcasses were analyzed on 23 different working days. The aerobic colony count and total coliforms [...] Read more.
The objective of this study was to demonstrate the possible correlation of visible carcass contamination and abattoir aerosol quality with microbial hygiene criteria. A total of 279 bovine carcasses were analyzed on 23 different working days. The aerobic colony count and total coliforms on the carcasses were calculated together with the presence of Escherichia coli. To determine the visible contamination of carcasses, we used a 100 cm2 sheet of transparent, adhesive plastic material, applied to the side of the carcass, to collect all the particles, which were then counted against both black and white backgrounds. The daily particulate index in the abattoir aerosol was determined using an air sampler device. The results showed that aerobic colony counts, which ranged from 1.41 to 2.40 log cfu cm−2, total coliforms (from 0.00 to 0.73 log cfu cm−2), and E. coli presence (from 0.00% to 60% of the sampled carcasses per day) are not correlated with the carcasses’ visual dirtiness or the aerosol quality. The factor analysis showed a correlation between the three groups of variables investigated: group 1, representing “aerosol quality”, group 2, representing the “microbiology of the carcass”, and group 3, the “visual dirtiness of the carcass”. Thus, even though microbiology analysis is useful in diagnosing the microorganisms which the official veterinarian is unable to detect during the post-mortem inspection, it is ineffective in evaluating slaughtering procedures. Aerosol monitoring and the visual classification of carcass dirtiness, instead, could provide good indications of the slaughtering process and the quality of the abattoir environment, and guarantee control of manufacturing practices, protecting both animals’ and operators’ health. Full article
(This article belongs to the Special Issue Molecular Microbiology Underlying Foodborne Viruses)
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