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Microorganisms, Volume 12, Issue 7 (July 2024) – 174 articles

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13 pages, 4274 KiB  
Article
The Impact of High-Temperature Stress on Gut Microbiota and Reproduction in Siberian Hamsters (Phodopus sungorus)
by Wenjing Shen, Peng Gao, Kunying Zhou, Jin Li, Tingbei Bo and Deli Xu
Microorganisms 2024, 12(7), 1426; https://doi.org/10.3390/microorganisms12071426 (registering DOI) - 13 Jul 2024
Abstract
Global warming has induced alterations in the grassland ecosystem, such as elevated temperatures and decreased precipitation, which disturb the equilibrium of these ecosystems and impact various physiological processes of grassland rodents, encompassing growth, development, and reproduction. As global warming intensifies, the repercussions of [...] Read more.
Global warming has induced alterations in the grassland ecosystem, such as elevated temperatures and decreased precipitation, which disturb the equilibrium of these ecosystems and impact various physiological processes of grassland rodents, encompassing growth, development, and reproduction. As global warming intensifies, the repercussions of high-temperature stress on small mammals are garnering increased attention. Recently, research has highlighted that the composition and ratio of gut microbiota are not only shaped by environmental factors and the host itself but also reciprocally influence an array of physiological functions and energy metabolism in animals. In this research, we combined 16S rRNA high-throughput sequencing with conventional physiological assessments, to elucidate the consequences of high-temperature stress on the gut microbiota structure and reproductive capacity of Siberian hamsters (Phodopus sungorus). The results were as follows: 1. The growth and development of male and female hamsters in the high-temperature group were delayed, with lower body weight and reduced food intake. 2. High temperature inhibits the development of reproductive organs in both female and male hamsters. 3. High temperature changes the composition and proportion of gut microbiota, reducing bacteria that promote reproduction, such as Pseudobutyricoccus, Ruminiclostridium-E, Sporofaciens, UMGS1071, and CAG_353. Consequently, our study elucidates the specific impacts of high-temperature stress on the gut microbiota dynamics and reproductive health of Siberian hamsters, thereby furnishing insights for managing rodent populations amidst global climatic shifts. It also offers a valuable framework for understanding seasonal variations in mammalian reproductive strategies, contributing to the broader discourse on conservation and adaptation under changing environmental conditions. Full article
(This article belongs to the Section Gut Microbiota)
20 pages, 813 KiB  
Review
Drinking Water Microbiota, Entero-Mammary Pathways, and Breast Cancer: Focus on Nontuberculous Mycobacteria
by Ana Maranha, Susana Alarico, Daniela Nunes-Costa, Inês Melo-Marques, Inês Roxo, Pedro Castanheira, Olga Caramelo and Nuno Empadinhas
Microorganisms 2024, 12(7), 1425; https://doi.org/10.3390/microorganisms12071425 (registering DOI) - 13 Jul 2024
Viewed by 153
Abstract
The prospect of drinking water serving as a conduit for gut bacteria, artificially selected by disinfection strategies and a lack of monitoring at the point of use, is concerning. Certain opportunistic pathogens, notably some nontuberculous mycobacteria (NTM), often exceed coliform bacteria levels in [...] Read more.
The prospect of drinking water serving as a conduit for gut bacteria, artificially selected by disinfection strategies and a lack of monitoring at the point of use, is concerning. Certain opportunistic pathogens, notably some nontuberculous mycobacteria (NTM), often exceed coliform bacteria levels in drinking water, posing safety risks. NTM and other microbiota resist chlorination and thrive in plumbing systems. When inhaled, opportunistic NTM can infect the lungs of immunocompromised or chronically ill patients and the elderly, primarily postmenopausal women. When ingested with drinking water, NTM often survive stomach acidity, reach the intestines, and migrate to other organs using immune cells as vehicles, potentially colonizing tumor tissue, including in breast cancer. The link between the microbiome and cancer is not new, yet the recognition of intratumoral microbiomes is a recent development. Breast cancer risk rises with age, and NTM infections have emerged as a concern among breast cancer patients. In addition to studies hinting at a potential association between chronic NTM infections and lung cancer, NTM have also been detected in breast tumors at levels higher than normal adjacent tissue. Evaluating the risks of continued ingestion of contaminated drinking water is paramount, especially given the ability of various bacteria to migrate from the gut to breast tissue via entero-mammary pathways. This underscores a pressing need to revise water safety monitoring guidelines and delve into hormonal factors, including addressing the disproportionate impact of NTM infections and breast cancer on women and examining the potential health risks posed by the cryptic and unchecked microbiota from drinking water. Full article
(This article belongs to the Special Issue Advances in Waterborne Pathogens)
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12 pages, 1770 KiB  
Article
Brain Abscesses in Domestic Ruminants: Clinicopathological and Bacteriological Approaches
by Lucas Vinícius de Oliveira Ferreira, Thaís Gomes Rocha, Regina Kiomi Takahira, Renée Laufer-Amorim, Vânia Maria de Vasconcelos Machado, Márcio Garcia Ribeiro, Wanderson Adriano Biscola Pereira, José Paes Oliveira-Filho, Alexandre Secorun Borges and Rogério Martins Amorim
Microorganisms 2024, 12(7), 1424; https://doi.org/10.3390/microorganisms12071424 (registering DOI) - 13 Jul 2024
Viewed by 130
Abstract
Brain abscesses in ruminants often arise from primary infection foci, leading to an unfavorable prognosis for affected animals. This highlights the need for comprehensive studies on brain abscesses across different ruminant species. We retrospectively investigated medical records of epidemiological, clinical, neuroimaging, anatomopathological, and [...] Read more.
Brain abscesses in ruminants often arise from primary infection foci, leading to an unfavorable prognosis for affected animals. This highlights the need for comprehensive studies on brain abscesses across different ruminant species. We retrospectively investigated medical records of epidemiological, clinical, neuroimaging, anatomopathological, and bacteriological findings in six ruminants (three goats, two cows, and one sheep) diagnosed with brain abscesses. All animals studied were female. Apathy (50%), compulsive walking (33%), decreased facial sensitivity (33%), head pressing (33%), seizures (33%), semicomatous mental status (33%), strabismus (33%), unilateral blindness (33%), and circling (33%) represented the most common neurologic signs. Leukocytosis and neutrophilia were the main findings in the hematological evaluation. Cerebrospinal fluid (CSF) analysis revealed predominant hyperproteinorrachia and pleocytosis. In three cases, computed tomography or magnetic resonance imaging were used, enabling the identification of typical abscess lesions, which were subsequently confirmed during postmortem examination. Microbiological culture of the abscess samples and/or CSF revealed bacterial coinfections in most cases. Advanced imaging examinations, combined with CSF analysis, can aid in diagnosis, although confirmation typically relies on postmortem evaluation and isolation of the causative agent. This study contributes to clinicopathological aspects, neuroimages, and bacteriological diagnosis of brain abscesses in domestic ruminants. Full article
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21 pages, 3836 KiB  
Article
A Comprehensive Approach Combining Short-Chain Polyphosphate and Bacterial Biostimulants for Effective Nutrient Solubilization and Enhanced Wheat Growth
by Kaoutar Bourak, Fatima Ezzahra Oulkhir, Fatima Zahra Maghnia, Sebastien Massart, Latefa Biskri, M. Haissam Jijakli and Abdelmounaaim Allaoui
Microorganisms 2024, 12(7), 1423; https://doi.org/10.3390/microorganisms12071423 (registering DOI) - 13 Jul 2024
Viewed by 110
Abstract
Phosphorus constitutes a crucial macronutrient for crop growth, yet its availability often limits food production. Efficient phosphorus management is crucial for enhancing crop yields and ensuring food security. This study aimed to enhance the efficiency of a short-chain polyphosphate (PolyP) fertilizer by integrating [...] Read more.
Phosphorus constitutes a crucial macronutrient for crop growth, yet its availability often limits food production. Efficient phosphorus management is crucial for enhancing crop yields and ensuring food security. This study aimed to enhance the efficiency of a short-chain polyphosphate (PolyP) fertilizer by integrating it with plant growth-promoting bacteria (PGPB) to improve nutrient solubilization and wheat growth. Specifically, the study investigated the effects of various bacterial strains on wheat germination and growth when used in conjunction with PolyP. To achieve this, a greenhouse experiment was conducted in which the wheat rhizosphere was amended with a short-chain PolyP fertilizer. Based on the morphological aspect, eight bacteria, designated P1 to P8, were isolated and further characterized. Plant growth-promoting traits were observed in all bacterial strains, as they presented the ability to produce Indole Acetic Acid (IAA) in significant amounts ranging from 7.5 ± 0.3 µg/mL to 44.1 ± 2 µg/mL, expressed by B. tropicus P4 and P. soyae P1, respectively. They also produced ammonia, hydrogen cyanide (HCN), and siderophores. Their effect against the plant pathogen Fusarium culmorum was also assessed, with P. reinekei P2 demonstrating the highest biocontrol activity as it presented a total inhibitory effect. Additionally, some strains exhibited the ability to solubilize/hydrolyze phosphorus, potassium, and zinc. In vivo, the initial growth potential of wheat seeds indicated that those inoculated with the isolated strains exhibited elevated germination rates and enhanced root growth. Based on their plant growth-promoting traits and performance in the germination assay, three strains were selected for producing the best results, specifically phosphorus hydrolyzation/solubilization, zinc solubilization, IAA production, HCN, and siderophores production. Wheat seeds were inoculated by drenching in a bacterial suspension containing 1010 CFU/mL of log phase culture, and an in planta bioassay was conducted in a growth chamber using three selected strains (Pseudomonas soyae P1, Pseudomonas reinekei P2, and Bacillus tropicus P4), applied either individually or with PolyP on a P-deficient soil (28 mg/kg of P Olsen). Our findings demonstrated that the combination of Pseudomonas soyae P1 and PolyP achieved the highest shoot biomass, averaging 41.99 ± 0.87 g. Notably, applying P. soyae P1 or Bacillus tropicus P4 alone yielded similar results to the use of PolyP alone. At the heading growth stage, the combination of Bacillus tropicus P4 and PolyP significantly increased the Chlorophyll Content Index (CCI) to 37.02 µmol/m2, outperforming both PolyP alone (24.07 µmol/m2) and the control (23.06 µmol/m2). This study presents an innovative approach combining short-chain PolyP with bacterial biostimulants to enhance nutrient availability and plant growth. By identifying and characterizing effective bacterial strains, it offers a sustainable alternative to conventional fertilizers. Full article
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14 pages, 737 KiB  
Article
Risk Factors, Pathogens, and Outcomes of Ventilator-Associated Pneumonia in Non-Cardiac Surgical Patients: A Retrospective Analysis
by Po-Hsun Chang, Ting-Lung Lin, Ying-Ju Chen, Wei-Hung Lai, I-Ling Chen, Hui-Chuan Chang, Yu-Cheng Lin, Yu-Hung Lin, Wei-Feng Li, Yueh-Wei Liu, Chih-Chi Wang and Shih-Feng Liu
Microorganisms 2024, 12(7), 1422; https://doi.org/10.3390/microorganisms12071422 (registering DOI) - 13 Jul 2024
Viewed by 104
Abstract
Ventilator-associated pneumonia (VAP) is a critical hospital-acquired infection following non-cardiac surgeries, leading to poor outcomes. This study identifies VAP risk factors in non-cardiac surgical patients and determines the causative pathogens. A retrospective analysis with 1:4 propensity-score matching was conducted on patients in a [...] Read more.
Ventilator-associated pneumonia (VAP) is a critical hospital-acquired infection following non-cardiac surgeries, leading to poor outcomes. This study identifies VAP risk factors in non-cardiac surgical patients and determines the causative pathogens. A retrospective analysis with 1:4 propensity-score matching was conducted on patients in a surgical intensive care unit (ICU) from 2010 to 2020 at a private tertiary medical center. Among 99 VAP patients, the mortality rate was 64.7%. VAP risk factors included prolonged mechanical ventilation (odds ratio [OR] 6.435; p < 0.001), repeat intubation (OR 6.438; p < 0.001), lower oxygenation levels upon ICU admission (OR 0.950; p < 0.001), and undergoing gastrointestinal surgery (OR 2.257; p = 0.021). The 30-day mortality risk factors in the VAP group were late-onset VAP (OR 3.450; p = 0.022), inappropriate antibiotic treatment (OR 4.083; p = 0.041), and undergoing gastrointestinal surgeries (OR 4.776; p = 0.019). Nearly half of the Gram-negative infections were resistant strains, and a third were polymicrobial infections. Non-cardiac surgical patients with VAP face adverse hospital outcomes. Identifying high-risk patients and understanding VAP’s resistant and microbial nature are crucial for appropriate treatment and improved health outcomes. Full article
(This article belongs to the Special Issue Bacterial Antibiotic Resistance)
19 pages, 3252 KiB  
Article
Native Microalgae-Bacteria Consortia: A Sustainable Approach for Effective Urban Wastewater Bioremediation and Disinfection
by Joana F. Sousa, Helena M. Amaro, Sara Ribeirinho-Soares, Ana F. Esteves, Eva M. Salgado, Olga C. Nunes and José C. M. Pires
Microorganisms 2024, 12(7), 1421; https://doi.org/10.3390/microorganisms12071421 - 12 Jul 2024
Viewed by 320
Abstract
Urban wastewater is a significant by-product of human activities. Conventional urban wastewater treatment plants have limitations in their treatment, mainly concerning the low removal efficiency of conventional and emerging contaminants. Discharged wastewater also contains harmful microorganisms, posing risks to public health, especially by [...] Read more.
Urban wastewater is a significant by-product of human activities. Conventional urban wastewater treatment plants have limitations in their treatment, mainly concerning the low removal efficiency of conventional and emerging contaminants. Discharged wastewater also contains harmful microorganisms, posing risks to public health, especially by spreading antibiotic-resistant bacteria and genes. Therefore, this study assesses the potential of a native microalgae-bacteria system (MBS) for urban wastewater bioremediation and disinfection, targeting NH4+-N and PO43−-P removal, coliform reduction, and antibiotic resistance gene mitigation. The MBS showed promising results, including a high specific growth rate (0.651 ± 0.155 d−1) and a significant average removal rate of NH4+-N and PO43−-P (9.05 ± 1.24 mg L−1 d−1 and 0.79 ± 0.06 mg L−1 d−1, respectively). Microalgae-induced pH increase rapidly reduces coliforms (r > 0.9), including Escherichia coli, within 3 to 6 days. Notably, the prevalence of intI1 and the antibiotic resistance genes sul1 and blaTEM are significantly diminished, presenting the MBS as a sustainable approach for tertiary wastewater treatment to combat eutrophication and reduce waterborne disease risks and antibiotic resistance spread. Full article
(This article belongs to the Special Issue The Application Potential of Microalgae in Green Biotechnology)
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11 pages, 4669 KiB  
Article
Interleukins IL33/ST2 and IL1-β in Intrauterine Growth Restriction and Seropositivity of Anti-Toxoplasma gondii Antibodies
by Karen Franco-De León, Eva Elizabeth Camarena, Ana Laura Pereira-Suárez, Ernesto Barrios-Prieto, Andrea Soto-Venegas, Zamira Helena Hernández-Nazara, Ythzel Guadalupe Luna Rojas and María de la Luz Galván-Ramírez
Microorganisms 2024, 12(7), 1420; https://doi.org/10.3390/microorganisms12071420 - 12 Jul 2024
Viewed by 209
Abstract
Toxoplasma gondii (T. gondii) is the causal agent of toxoplasmosis. It may produce severe damage in immunocompromised individuals, as well as congenital infection and intrauterine growth restriction (IUGR). Previous reports have associated interleukin IL-33 with miscarriage, fetal damage, and premature delivery [...] Read more.
Toxoplasma gondii (T. gondii) is the causal agent of toxoplasmosis. It may produce severe damage in immunocompromised individuals, as well as congenital infection and intrauterine growth restriction (IUGR). Previous reports have associated interleukin IL-33 with miscarriage, fetal damage, and premature delivery due to infections with various microorganisms. However, IL-33 has not been associated with congenital toxoplasmosis. The sST2 receptor has been reported in patients who have had recurrent miscarriages. On the other hand, IL-1β was not found in acute Toxoplasma infection. Our aim was to analyze the associations between the serum levels of IL-33 and IL-1β in IUGR and toxoplasmosis during pregnancy. Eighty-four serum samples from pregnant women who had undergone 26 weeks of gestation were grouped as follows: with anti-Toxoplasma antibodies, without anti-Toxoplasma antibodies, IUGR, and the control group. IgG and IgM anti-T. gondii antibodies, as well as IL-33, ST2, and IL-1β, were determined using an ELISA assay. Statistical analyses were performed using the Pearson and Chi-square correlation coefficients, as well as the risk factors and Odds Ratios (ORs), with a confidence interval of 95% (CI 95). The results showed that 15/84 (17.8%) of cases were positive for IgG anti-Toxoplasma antibodies and 2/84 (2.38%) of cases were positive for IgM. A statistically significant difference was found between IUGR and IL-33 (p < 0.001), as well as between ST2 and IUGR (p < 0.001). In conclusion, IUGR was significantly associated with IL-33 and ST2 positivity based on the overall IUGR grade. No significant association was found between IUGR and the presence of anti-Toxoplasma antibodies. There was no association between IL-1β and IUGR. More research is needed to strengthen the utility of IL-33 and ST2 as biomarkers of IUGR. Full article
(This article belongs to the Special Issue Advances in Toxoplasma gondii and Toxoplasmosis)
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15 pages, 4132 KiB  
Article
Comparative Analysis of Gut Microbiota between Captive and Wild Long-Tailed Gorals for Ex Situ Conservation
by Chang-Eon Park, Young-Jae Jo, Da-Ryung Jung, Hee-Cheon Park and Jae-Ho Shin
Microorganisms 2024, 12(7), 1419; https://doi.org/10.3390/microorganisms12071419 - 12 Jul 2024
Viewed by 239
Abstract
The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions [...] Read more.
The long-tailed goral is close to extinction, and ex situ conservation is essential to prevent this phenomenon. Studies on the gut microbiome of the long-tailed goral are important for understanding the ecology of this species. We amplified DNA from the 16S rRNA regions and compared the microbiomes of wild long-tailed gorals and two types of captive long-tailed gorals. Our findings revealed that the gut microbiome diversity of wild long-tailed gorals is greatly reduced when they are reared in captivity. A comparison of the two types of captive long-tailed gorals confirmed that animals with a more diverse diet exhibit greater gut microbiome diversity. Redundancy analysis confirmed that wild long-tailed gorals are distributed throughout the highlands, midlands, and lowlands. For the first time, it was revealed that the long-tailed goral are divided into three groups depending on the height of their habitat, and that the gut bacterial community changes significantly when long-tailed gorals are raised through ex situ conservation. This provides for the first time a perspective on the diversity of food plants associated with mountain height that will be available to long-tailed goral in the future. Full article
(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology)
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13 pages, 497 KiB  
Review
Liver Stiffness Evaluation in Chronic Hepatitis C Patients with Cirrhosis before and after Direct-Acting Antivirals
by Cristina Stasi and Stefano Brillanti
Microorganisms 2024, 12(7), 1418; https://doi.org/10.3390/microorganisms12071418 - 12 Jul 2024
Viewed by 224
Abstract
After the introduction of direct-acting antivirals, parallel significant clinical progress has been achieved in the assessment of liver fibrosis progression/regression before treatment and during the follow-up of the cirrhotic patients with chronic hepatitis C virus (HCV) infection. The evolution of chronic hepatitis C [...] Read more.
After the introduction of direct-acting antivirals, parallel significant clinical progress has been achieved in the assessment of liver fibrosis progression/regression before treatment and during the follow-up of the cirrhotic patients with chronic hepatitis C virus (HCV) infection. The evolution of chronic hepatitis C into liver cirrhosis is correlated with an extensive accumulation of the extracellular matrix, leading to the formation of large amounts of fibrotic tissues that, initially, are concentrated in periportal areas and, in the later stages, surround the nodules of regenerating hepatocytes. The progressive increase in the fibrotic matrix contributes to vascular disturbances (favoring the development of portal hypertension) and to microenvironmental changes. The four clinical stages of liver cirrhosis are predictors for different clinical scenarios. The wide-ranging functions of the liver require different methods for their assessment. The non-invasive evaluation using transient elastography is useful in determining the longitudinal modifications of fibrosis during and after treatment with direct-acting antivirals. The liver stiffness evaluation, known to have a wide range of values in cirrhotic patients, can offer different prognostic implications after sustained virological response. This review discusses the different time points of liver stiffness evaluation that appear to show a more well-defined propensity to identify adequate monitoring schedules for these patients. Full article
(This article belongs to the Special Issue Human Infectious Diseases)
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14 pages, 5397 KiB  
Article
Exosomal Small RNA Sequencing Profiles in Plasma from Subjects with Latent Mycobacterium tuberculosis Infection
by Xiaogang Cui, Hangting Meng, Miao Li, Xia Chen, Dan Yuan and Changxin Wu
Microorganisms 2024, 12(7), 1417; https://doi.org/10.3390/microorganisms12071417 - 12 Jul 2024
Viewed by 238
Abstract
Despite huge efforts, tuberculosis (TB) is still a major public health threat worldwide, with approximately 23% of the human population harboring a latent TB infection (LTBI). LTBI can reactivate and progress to active and transmissible TB disease, contributing to its spread within the [...] Read more.
Despite huge efforts, tuberculosis (TB) is still a major public health threat worldwide, with approximately 23% of the human population harboring a latent TB infection (LTBI). LTBI can reactivate and progress to active and transmissible TB disease, contributing to its spread within the population. The challenges in diagnosing and treating LTBI patients have been major factors contributing to this phenomenon. Exosomes offer a novel avenue for investigating the process of TB infection. In this study, we conducted small RNA sequencing to investigate the small RNA profiles of plasma exosomes derived from individuals with LTBI and healthy controls. Our findings revealed distinct miRNA profiles in the exosomes between the two groups. We identified 12 differentially expressed miRNAs through this analysis, which were further validated via qRT-PCR using the same exosomes. Notably, six miRNAs (hsa-miR-7850-5p, hsa-miR-1306-5p, hsa-miR-363-5p, hsa-miR-374a-5p, hsa-miR-4654, has-miR-6529-5p, and hsa-miR-140-5p) exhibited specifically elevated expression in individuals with LTBI. Gene ontology and KEGG pathway analyses revealed that the targets of these miRNAs were enriched in functions associated with ferroptosis and fatty acid metabolism, underscoring the critical role of these miRNAs in regulating the intracellular survival of Mycobacterium tuberculosis (Mtb). Furthermore, our results indicated that the overexpression of miR-7850-5p downregulated the expression of the SLC11A1 protein in both Mtb-infected and Mtb-uninfected THP1 cells. Additionally, we observed that miR-7850-5p promoted the intracellular survival of Mtb by suppressing the expression of the SLC11A1 protein. Overall, our findings provide valuable insights into the role of miRNAs and repetitive region-derived small RNAs in exosomes during the infectious process of Mtb and contribute to the identification of potential molecular targets for the detection and diagnosis of latent tuberculosis. Full article
(This article belongs to the Special Issue Prevention, Treatment and Diagnosis of Tuberculosis, 2nd Edition)
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11 pages, 1145 KiB  
Article
Cryptosporidium Infections in Neonatal Calves on a Dairy Farm
by Michaela Kaduková, Andrea Schreiberová, Pavol Mudroň, Csilla Tóthová, Pavel Gomulec and Gabriela Štrkolcová
Microorganisms 2024, 12(7), 1416; https://doi.org/10.3390/microorganisms12071416 - 12 Jul 2024
Viewed by 223
Abstract
This study was conducted with the aim of the molecular identification of the protozoan parasite Cryptosporidium spp. in calves in the early stage of their development on a dairy farm in Eastern Slovakia. Twenty-five Holstein and Holstein cross calves were included in the [...] Read more.
This study was conducted with the aim of the molecular identification of the protozoan parasite Cryptosporidium spp. in calves in the early stage of their development on a dairy farm in Eastern Slovakia. Twenty-five Holstein and Holstein cross calves were included in the study and monitored from their birth to the fifth week of life (1–5 weeks). Fresh fecal samples were collected from the same group of calves each week, except during the fourth week, and with the exception of Sample 8. All samples were analyzed using the Ziehl–Neelsen staining method and coproantigen was tested using the ELISA test as the screening method. Using the ELISA method, the highest incidence of cryptosporidiosis was observed in the second week of life of the calves, while the antigen was detected in 21 (91.6%) calves. Using the Ziehl–Neelsen staining method, the highest incidence was also observed in the second week, with an incidence rate of 62.5%. Positive isolates confirmed by the ELISA test were molecularly characterized. The species and subtypes of Cryptosporidium in the positive isolates were identified using PCR and the sequence analysis of the small subunit of the ribosomal 18S RNA (ssu rRNA) and the 60 kDa glycoprotein (gp60) genes of the parasite. The sequence analysis of 29 isolates at the 18S rRNA loci confirmed the presence of two species—Cryptosporidium parvum and Cryptosporidium ryanae. Out of 29 isolates, 25 were assigned to the species C. parvum, with the gp60 locus identified as genotype IIaA17G1R1. Among the individual animal groups, calves are the most common reservoirs of the C. parvum zoonotic species. This disease has significant public health implications as contact with livestock and their feces and working with barn manure are major sources of infection, not only for other animals but also for humans. Full article
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19 pages, 7972 KiB  
Article
Rapid Classification and Differentiation of Sepsis-Related Pathogens Using FT-IR Spectroscopy
by Shwan Ahmed, Jawaher Albahri, Sahand Shams, Silvana Sosa-Portugal, Cassio Lima, Yun Xu, Rachel McGalliard, Trevor Jones, Christopher M. Parry, Dorina Timofte, Enitan D. Carrol, Howbeer Muhamadali and Royston Goodacre
Microorganisms 2024, 12(7), 1415; https://doi.org/10.3390/microorganisms12071415 - 12 Jul 2024
Viewed by 314
Abstract
Sepsis is a life-threatening condition arising from a dysregulated host immune response to infection, leading to a substantial global health burden. The accurate identification of bacterial pathogens in sepsis is essential for guiding effective antimicrobial therapy and optimising patient outcomes. Traditional culture-based bacterial [...] Read more.
Sepsis is a life-threatening condition arising from a dysregulated host immune response to infection, leading to a substantial global health burden. The accurate identification of bacterial pathogens in sepsis is essential for guiding effective antimicrobial therapy and optimising patient outcomes. Traditional culture-based bacterial typing methods present inherent limitations, necessitating the exploration of alternative diagnostic approaches. This study reports the successful application of Fourier-transform infrared (FT-IR) spectroscopy in combination with chemometrics as a potent tool for the classification and discrimination of microbial species and strains, primarily sourced from individuals with invasive infections. These samples were obtained from various children with suspected sepsis infections with bacteria and fungi originating at different sites. We conducted a comprehensive analysis utilising 212 isolates from 14 distinct genera, comprising 202 bacterial and 10 fungal isolates. With the spectral analysis taking several weeks, we present the incorporation of quality control samples to mitigate potential variations that may arise between different sample plates, especially when dealing with a large sample size. The results demonstrated a remarkable consistency in clustering patterns among 14 genera when subjected to principal component analysis (PCA). Particularly, Candida, a fungal genus, was distinctly recovered away from bacterial samples. Principal component discriminant function analysis (PC-DFA) allowed for distinct discrimination between different bacterial groups, particularly Gram-negative and Gram-positive bacteria. Clear differentiation was also observed between coagulase-negative staphylococci (CNS) and Staphylococcus aureus isolates, while methicillin-resistant S. aureus (MRSA) was also separated from methicillin-susceptible S. aureus (MSSA) isolates. Furthermore, highly accurate discrimination was achieved between Enterococcus and vancomycin-resistant enterococci isolates with 98.4% accuracy using partial least squares-discriminant analysis. The study also demonstrates the specificity of FT-IR, as it effectively discriminates between individual isolates of Streptococcus and Candida at their respective species levels. The findings of this study establish a strong groundwork for the broader implementation of FT-IR and chemometrics in clinical and microbiological applications. The potential of these techniques for enhanced microbial classification holds significant promise in the diagnosis and management of invasive bacterial infections, thereby contributing to improved patient outcomes. Full article
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21 pages, 3723 KiB  
Article
Fecal Microbiota Characteristics in Constipation-Predominant and Mixed-Type Irritable Bowel Syndrome
by Mariya Gryaznova, Yuliya Smirnova, Inna Burakova, Polina Morozova, Svetlana Lagutina, Pavel Chizhkov, Olga Korneeva and Mikhail Syromyatnikov
Microorganisms 2024, 12(7), 1414; https://doi.org/10.3390/microorganisms12071414 - 12 Jul 2024
Viewed by 227
Abstract
Background: Irritable bowel syndrome (IBS) is a common condition that affects the lifestyle of patients. It is associated with significant changes in the composition of the gut microbiome, but the underlying microbial mechanisms remain to be fully understood. We study the fecal microbiome [...] Read more.
Background: Irritable bowel syndrome (IBS) is a common condition that affects the lifestyle of patients. It is associated with significant changes in the composition of the gut microbiome, but the underlying microbial mechanisms remain to be fully understood. We study the fecal microbiome of patients with constipation-predominant IBS (IBS-C) and mixed-type IBS (IBS-M). Methods: We sequenced the V3 region of the 16S rRNA on the Ion Torrent PGM sequencing platform to study the microbiome. Results: In the patients with IBS-C and IBS-M, an increase in alpha diversity was found, compared to the healthy group, and differences in beta diversity were also noted. At the phylum level, both IBS subtypes showed an increase in the Firmicutes/Bacteroidetes ratio, as well as an increase in the abundance of Actinobacteria and Verrucomicrobiota. Changes in some types of bacteria were characteristic of only one of the IBS subtypes, while no statistically significant differences in the composition of the microbiome were detected between IBS-C and IBS-M. Conclusions: This study was the first to demonstrate the association of Turicibacter sanguinis, Mitsuokella jalaludinii, Erysipelotrichaceae UCG-003, Senegalimassilia anaerobia, Corynebacterium jeikeium, Bacteroides faecichinchillae, Leuconostoc carnosum, and Parabacteroides merdae with IBS subtypes. Full article
(This article belongs to the Section Gut Microbiota)
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17 pages, 5684 KiB  
Article
Description and Whole-Genome Sequencing of Mariniflexile litorale sp. nov., Isolated from the Shallow Sediments of the Sea of Japan
by Lyudmila Romanenko, Evgeniya Bystritskaya, Yuliya Savicheva, Viacheslav Eremeev, Nadezhda Otstavnykh, Valeriya Kurilenko, Peter Velansky and Marina Isaeva
Microorganisms 2024, 12(7), 1413; https://doi.org/10.3390/microorganisms12071413 - 12 Jul 2024
Viewed by 195
Abstract
A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the [...] Read more.
A Gram-negative, aerobic, rod-shaped, non-motile, yellow-pigmented bacterium, KMM 9835T, was isolated from the sediment sample obtained from the Amur Bay of the Sea of Japan seashore, Russia. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences positioned the novel strain KMM 9835T in the genus Mariniflexile as a separate line sharing the highest 16S rRNA gene sequence similarities of 96.6% and 96.2% with Mariniflexile soesokkakense RSSK-9T and Mariniflexile fucanivorans SW5T, respectively, and similarity values of <96% to other recognized Mariniflexile species. The average nucleotide identity and digital DNA–DNA hybridization values between strain KMM 9835T and M. soesokkakense KCTC 32427T, Mariniflexile gromovii KCTC 12570T, M. fucanivorans DSM 18792T, and M. maritimum M5A1MT were 83.0%, 82.5%, 83.4%, and 78.3% and 30.7%, 29.6%, 29.5%, and 24.4%, respectively. The genomic DNA GC content of strain KMM 9835T was 32.5 mol%. The dominant menaquinone was MK-6, and the major fatty acids were iso-C15:0, iso-C15:1ω10c, and C15:0. The polar lipids of strain KMM 9835T consisted of phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, and six unidentified lipids. A pan-genome analysis showed that the KMM 9835T genome encoded 753 singletons. The annotated singletons were more often related to transport protein systems (SusC), transcriptional regulators (AraC, LytTR, LacI), and enzymes (glycosylases). The KMM 9835T genome was highly enriched in CAZyme-encoding genes, the proportion of which reached 7.3%. Moreover, the KMM 9835T genome was characterized by a high abundance of CAZyme gene families (GH43, GH28, PL1, PL10, CE8, and CE12), indicating its potential to catabolize pectin. This may represent part of an adaptation strategy facilitating microbial consumption of plant polymeric substrates in aquatic environments near shorelines and freshwater sources. Based on the combination of phylogenetic and phenotypic characterization, the marine sediment strain KMM 9835T (=KCTC 92792T) represents a novel species of the genus Mariniflexile, for which the name Mariniflexile litorale sp. nov. is proposed. Full article
(This article belongs to the Special Issue Marine Microorganisms and Ecology)
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12 pages, 3141 KiB  
Article
Analysis of the Fungal Community Composition in Endemic Orchids with Terrestrial Habitat in Subtropical Regions
by Xinyue Hu, Xiujin Qi, María Daniela Artigas Ramírez, Qi Wu, Shiyong Liu, Zhenhai Deng, Xiuzhong Li, Nan Zhang, Hongfeng Zhang, Heran Dai, Rongshi Xin, Xiaofeng Wu and Jin Cheng
Microorganisms 2024, 12(7), 1412; https://doi.org/10.3390/microorganisms12071412 - 12 Jul 2024
Viewed by 182
Abstract
Habenaria and Liparis are well-known orchid genera that grow in terrestrial habitats in the tropics, subtropics or temperate zones. Three species have been found in subtropical regions of China, inhabiting terrestrial to epiphytic habitats. This study focuses on three species, H. dentata (distributed [...] Read more.
Habenaria and Liparis are well-known orchid genera that grow in terrestrial habitats in the tropics, subtropics or temperate zones. Three species have been found in subtropical regions of China, inhabiting terrestrial to epiphytic habitats. This study focuses on three species, H. dentata (distributed in Asia), H. yachangensis, and L. gigantea. For H. yachangensis and L. gigantea, there is no information about the mycorrhizal community in these species. This study aims to conduct the fungal community screening of Chinese ground orchids from subtropical regions. We performed a comparative analysis of the fungal community among H. dentata, H. yachangensis, and L. gigantea, determining their ITS regions using NGS paired-end sequences. The results clarified the diversity and the predominance of fungal genera. Ascomycota was abundant compared to Basidiomycota or other fungi groups in all communities, with a high dominance in all populations, especially for L. gigantea. At different root spatial locations, the fungal community diversity and richness were higher in the soil than in the rhizosphere or inner root. However, the results suggest that L. gigantea has a different fungal community compared to Habenaria species. In this order, the subtropical terrestrial orchids have a different fungal network compared to the northern terrestrial orchids. Also, there is a high probability of co-existence and co-evolution of endophytic fungi in these terrestrial orchids, indicating the potential role of host plants in selecting an endophytic fungal community. Furthermore, our results highlight the need to elucidate the microbe interactions of these unique orchids for long-term purposes, such as isolating indigenous fungi for suitable inoculants for further orchid propagation, restoration, and conservation. Full article
(This article belongs to the Section Plant Microbe Interactions)
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10 pages, 711 KiB  
Article
A Scoring System to Predict Severe Acute Lower Respiratory Infection in Children Caused by Respiratory Syncytial Virus
by Ri De, Mingli Jiang, Yu Sun, Siyuan Huang, Runan Zhu, Qi Guo, Yutong Zhou, Dong Qu, Ling Cao, Fengmin Lu and Linqing Zhao
Microorganisms 2024, 12(7), 1411; https://doi.org/10.3390/microorganisms12071411 - 12 Jul 2024
Viewed by 249
Abstract
There were several factors associated with respiratory syncytial virus (RSV) severe acute lower respiratory infection (RSV-sALRI) in infants and young children. It is vital to develop a convenient scoring system to predict RSV-sALRI in children. Pediatric patients with RSV-ALRI from January 2009 to [...] Read more.
There were several factors associated with respiratory syncytial virus (RSV) severe acute lower respiratory infection (RSV-sALRI) in infants and young children. It is vital to develop a convenient scoring system to predict RSV-sALRI in children. Pediatric patients with RSV-ALRI from January 2009 to December 2021 were recruited retrospectively. Two-third of them were randomly grouped into the development set and one-third to the validation set. In the development set, risk factors for RSV-sALRI were transferred into the logistic regression analysis, then their receiver operating characteristic (ROC) curves were built to obtain the area under the ROC curve (AUC), and regression coefficients for each predictor were converted to points. Finally, the value of the scoring system was evaluated in the validation set. A total of 1 066 children with RSV-ALRI were recruited, including 710 in the development set and 356 in the validation set. By logistic regression analysis, six factors (younger than 2 years, gestational age <37 weeks, have siblings, birth weight ≤2500 g, artificial/mix feeding, CHD) showed statistical difference and then were scored with points according to the coefficient value (OR) in the development set. In the validation set, the sensitivity of the scoring system was 70.25%, the specificity 85.53%, the positive predictive value 71.43%, the negative predictive value 84.81%, and coincidence rate 0.80. The Kolmogorov–Smirnov test showed the distribution of AUC 0.765 (SE = 0.027; 95% CI = 0.713–0.818; p < 0.001). A simplified scoring system was developed in the study with high prediction value for RSV-sALRI in children. Full article
(This article belongs to the Special Issue Human Respiratory Syncytial Virus—Biology, Diagnosis and Prevention)
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15 pages, 5588 KiB  
Article
Multi-Omics Analysis Reveals the Regulatory Mechanism of Different Probiotics on Growth Performance and Intestinal Health of Salmo trutta (S. trutta)
by Mengjuan Chen, Zhitong Wang, Hui He, Wenjia He, Zihao Zhang, Shuaijie Sun and Wanliang Wang
Microorganisms 2024, 12(7), 1410; https://doi.org/10.3390/microorganisms12071410 - 12 Jul 2024
Viewed by 234
Abstract
Probiotics play an important role in animal production, providing health benefits to the host by improving intestinal microbial balance. In this study, we added three different probiotics, Saccharomyces cerevisiae (SC), Bacillus licheniformis (BL), and lactic acid bacteria (LAB), and compared them with the [...] Read more.
Probiotics play an important role in animal production, providing health benefits to the host by improving intestinal microbial balance. In this study, we added three different probiotics, Saccharomyces cerevisiae (SC), Bacillus licheniformis (BL), and lactic acid bacteria (LAB), and compared them with the control group (CON), to investigate the effects of probiotic supplementation on growth performance, gut microbiology, and gut flora of S. trutta. Our results showed that feeding probiotics improved the survival, growth, development, and fattening of S. trutta. Additionally, probiotic treatment causes changes in the gut probiotic community, and the gut flora microorganisms that cause significant changes vary among the probiotic treatments. However, in all three groups, the abundance of Pseudomonas, Acinetobacter, and Rhizophagus bacterial genera was similar to that in the top three comparative controls. Furthermore, differences in the composition of intestinal microbiota among feed types were directly associated with significant changes in the metabolomic landscape, including lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. The probiotic treatment altered the gut microbiome, gut metabolome, and growth performance of S. trutta. Using a multi-omics approach, we discovered that the addition of probiotics altered the composition of gut microbiota, potentially leading to modifications in gut function and host phenotype. Overall, our results highlight the importance of probiotics as a key factor in animal health and productivity, enabling us to better evaluate the functional potential of probiotics. Full article
(This article belongs to the Section Veterinary Microbiology)
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13 pages, 281 KiB  
Review
Integrated Benefits to Agriculture with Trichoderma and Other Endophytic or Root-Associated Microbes
by Gary E. Harman
Microorganisms 2024, 12(7), 1409; https://doi.org/10.3390/microorganisms12071409 - 12 Jul 2024
Viewed by 236
Abstract
The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte–plant relationship and the fungi and bacteria [...] Read more.
The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte–plant relationship and the fungi and bacteria involved. Their abilities to alleviate biotic (diseases and pests) and abiotic stresses (drought, salt, and flooding) to remediate pollution and increase photosynthetic capabilities will be described. Their mechanisms of action will be elucidated. These frequently result in increased plant yields. Finally, methods and practices for formulation and commercial use will be described. Full article
10 pages, 1352 KiB  
Article
Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil
by Amanda Yaeko Yamada, Andreia Rodrigues de Souza, Amanda Maria de Jesus Bertani, Karoline Rodrigues Campos, Claudio Tavares Sacchi, Denise Brandão de Assis, Enéas de Carvalho, Elizabeth Harummyy Takagi, Marcos Paulo Vieira Cunha, Monique Ribeiro Tiba-Casas and Carlos Henrique Camargo
Microorganisms 2024, 12(7), 1408; https://doi.org/10.3390/microorganisms12071408 - 12 Jul 2024
Viewed by 308
Abstract
Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, [...] Read more.
Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes. Full article
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14 pages, 1945 KiB  
Article
Whole-Genome Deep Sequencing of the Healthy Adult Nasal Microbiome
by Mark Cannon, Gustavo Ferrer, Mari Tesch and Matthew Schipma
Microorganisms 2024, 12(7), 1407; https://doi.org/10.3390/microorganisms12071407 - 12 Jul 2024
Viewed by 399
Abstract
This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential [...] Read more.
This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the “gateway microbiomes”. Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness. Full article
(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)
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18 pages, 2624 KiB  
Article
Adsorption of Cd2+ by Lactobacillus plantarum Immobilized on Distiller’s Grains Biochar: Mechanism and Action
by Guangxu Zhu, Xingfeng Wang, Ronghui Du, Shuangxi Wen, Lifen Du and Qiang Tu
Microorganisms 2024, 12(7), 1406; https://doi.org/10.3390/microorganisms12071406 - 11 Jul 2024
Viewed by 261
Abstract
Immobilized microbial technology has recently emerged as a prominent research focus for the remediation of heavy metal pollution because of its superior treatment efficiency, ease of operation, environmental friendliness, and cost-effectiveness. This study investigated the adsorption characteristics and mechanisms of Cd2+ solutions [...] Read more.
Immobilized microbial technology has recently emerged as a prominent research focus for the remediation of heavy metal pollution because of its superior treatment efficiency, ease of operation, environmental friendliness, and cost-effectiveness. This study investigated the adsorption characteristics and mechanisms of Cd2+ solutions by Lactobacillus plantarum adsorbed immobilized on distiller’s grains biochar (XIM) and Lactobacillus plantarum–encapsulated immobilized on distiller’s grains biochar (BIM). The findings reveal that the maximum adsorption capacity and efficiency were achieved at a pH solution of 6.0. Specifically, at an adsorption equilibrium concentration of cadmium at 60 mg/L, XIM and BIM had adsorption capacities of 8.40 ± 0.30 mg/g and 12.23 ± 0.05 mg/g, respectively. BIM demonstrated noticeably greater adsorption capacities than XIM at various cadmium solution concentrations. A combination of isothermal adsorption modeling, kinetic modeling, scanning electron microscopy–energy dispersive X-ray spectroscopy, X-ray diffractometer (XRD), and Fourier-transform infrared spectroscopy (FTIR) analyses showed that cadmium adsorption by XIM primarily involved physical adsorption and pore retention. In contrast, the adsorption mechanism of BIM was mainly attributed to the formation of Cd(CN)2 crystals. Full article
(This article belongs to the Special Issue Application of Microbes in Environmental Remediation)
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11 pages, 1564 KiB  
Review
Multiple Functions of Hepatitis E Virus ORF3
by Fengyuan Jiao, Yu Zhao, Gengxu Zhou, Chi Meng, Lingjie Wang, Shengping Wu, Jixiang Li, Liting Cao, Bo Zhou, Yichen Luo and Hanwei Jiao
Microorganisms 2024, 12(7), 1405; https://doi.org/10.3390/microorganisms12071405 - 11 Jul 2024
Viewed by 233
Abstract
Hepatitis E (Hepatitis E, HE) is an acute and chronic infectious hepatitis caused by hepatitis E virus (Hepatitis E Virus, HEV) infection, which is responsible for most acute hepatitis in the world and is a significant public health problem. The pathogen, HEV, has [...] Read more.
Hepatitis E (Hepatitis E, HE) is an acute and chronic infectious hepatitis caused by hepatitis E virus (Hepatitis E Virus, HEV) infection, which is responsible for most acute hepatitis in the world and is a significant public health problem. The pathogen, HEV, has three Open Reading Frames (ORFs) ORF1, ORF2, and ORF3, each of which has a different function. Most of the current research is focused on ORF1 and ORF2, while the research on ORF3 is still relatively small. To provide more ideas for the study of HEV pathogenesis and the prevention and treatment of HE, this paper reviews the effects of ORF3 on the ERK pathway, growth factors, immune response, and virus release. Full article
(This article belongs to the Section Virology)
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11 pages, 717 KiB  
Article
Prevalence of HPV Genotypes among Greek Women in Association with Their Potential to Cause Precancerous Lesions
by Athanasia Kafasi, Georgios Kaparos, Vassiliki C. Pitiriga, Nikolaos Spanakis, Nikolaos Vlachos, Nikolaos Thomakos, Stamatios Stournaras and Athanasios Tsakris
Microorganisms 2024, 12(7), 1404; https://doi.org/10.3390/microorganisms12071404 - 11 Jul 2024
Viewed by 418
Abstract
The escalating global rates of precancerous lesions associated with human papillomavirus (HPV) types not targeted by current vaccines underscore the need to explore the prevalence of HPV types within the Greek female population and their involvement in precancerous lesion development. In the current [...] Read more.
The escalating global rates of precancerous lesions associated with human papillomavirus (HPV) types not targeted by current vaccines underscore the need to explore the prevalence of HPV types within the Greek female population and their involvement in precancerous lesion development. In the current study, we enrolled a cohort of 253 women aged 18 to 65 years, residing in Greece, who underwent routine screening in three tertiary care referral hospitals. Each participant completed a demographic questionnaire. An HPV DNA test was administered using the VisionArray® HPV kit (ZytoVision GmbH) to qualitatively detect and genotype 41 clinically relevant HPV genotypes. Of all 253 women examined, 114 (45.1%) tested positive for HPV DNA. The primary type detected was HPV51 (high-risk), present in 21 women (8.3% of the total), followed by HPV54 (low-risk) in 17 women (6.7%); HPV16 (high-risk) ranked third, identified in 14 women (5.5%). Among the HPV-positive women, 65 were positive for high-risk HPV types (57% of HPV-positive women) and were referred for colposcopy and cervical biopsy. These procedures identified 24 women with cervical intraepithelial neoplasia 1 (CIN1) lesions and 2 with cervical intraepithelial neoplasia 2 (CIN2) lesions. The most prevalent HPV type among women with CIN1 lesions was HPV16, found in nine (37.5%) women, while HPV51 ranked second, identified in six (25%) women. Both women with CIN2 lesions tested positive for HPV16, whereas one of them was also tested positive for HPV45. Our study is the first to report the prevalence of HPV51 among HPV-positive women in the Greek female population. This highlights the need for further research to fully understand the potential of HPV types not covered by current vaccines, such as HPV51, to cause high-grade lesions or cervical cancer. Full article
(This article belongs to the Special Issue Overviews of Clinical Microbial Infection)
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15 pages, 5926 KiB  
Article
Fermented Purslane (Portulaca oleracea L.) Supplementation Enhances Growth and Immune Function Parallel to the Regulation of Gut Microbial Butyrate Production in Weaned Piglets
by Lei Xu, Ge Gao, Zian Zhou, Zixi Wei, Wenjuan Sun, Yanpin Li, Xianren Jiang, Jingang Gu, Xilong Li and Yu Pi
Microorganisms 2024, 12(7), 1403; https://doi.org/10.3390/microorganisms12071403 - 11 Jul 2024
Viewed by 224
Abstract
Weaning is a challenging period for piglets, characterized by stress-related growth checks, compromised immunity, and gut dysbiosis. Purslane (Portulaca oleracea L.), known for its rich content of antioxidants, has potential as a functional feed ingredient. This study investigates the effects of feeding [...] Read more.
Weaning is a challenging period for piglets, characterized by stress-related growth checks, compromised immunity, and gut dysbiosis. Purslane (Portulaca oleracea L.), known for its rich content of antioxidants, has potential as a functional feed ingredient. This study investigates the effects of feeding fermented purslane (FP) on the growth performance, immune function, intestinal microbiota, and metabolic profiles of weaned piglets. Forty-eight weaned piglets were randomly divided into two groups, with eight pens in each group and three pigs in each pen: a control diet (CON group) and a diet supplemented with 0.20% FP (FP group). The experiment lasted 28 days. The results show that FP supplementation did not affect the average daily feed intake (ADFI) but significantly increased the average daily gain (ADG) during the initial 14 days post-weaning. FP supplementation decreased diarrhea occurrence, with a pronounced reduction from days 10 to 13 (p < 0.05). Immunologically, the FP group had a trend towards reduced serum IgA levels on day 14 (p < 0.10). Importantly, the serum concentrations of the pro-inflammatory cytokine IL-6 were significantly reduced on both days 14 and 28 post-weaning. The antioxidative analysis showed increased serum superoxide dismutase (SOD) and decreased catalase (CAT) activities on day 14 (p < 0.05). In addition, FP supplementation significantly decreased serum diamine oxidase (DAO) activity and D-lactate levels by day 28, indicating a potential improvement in gut integrity. Fecal microbiota assessment demonstrated a distinctive clustering of microbial communities between the FP and CON groups, with an increase in the abundance of Clostridium_sensu_stricto_1, Tyzzerella, and Prevotellaceae_NK3B31_group and a decrease in Lactobacillus, Bacillus, and Subdoligranulum in the FP group (p < 0.05). Functional predictions suggested that the relative abundance of microbial butyrate synthesis enzymes (EC 2.7.2.7 and EC 2.3.1.19) was significantly enhanced by FP treatment. This modulation was further corroborated by elevated fecal butyrate levels (p < 0.05). In summary, dietary supplementation with FP promotes early-growth performance and has beneficial effects on immune function and intestinal health in weaned piglets. The enhancements may be attributed to distinct microbiota compositional changes and targeted modulation of microbial butyrate metabolism, which are crucial for piglet post-weaning adaptation and overall health. Full article
(This article belongs to the Special Issue Nutritional Regulation on Gut Microbiota, 2nd Edition)
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11 pages, 1179 KiB  
Article
The Challenge of a Recall Program from a Community-Based Hepatitis C Screening Campaign: The Effectiveness in HCV Microelimination
by Cheng-Hung Chien, Tien-Shin Chou, Li-Wei Chen, Chih-Lang Lin, Jia-Jang Chang, Ching-Jung Liu, Shuo-Wei Chen, Ching-Chih Hu and Rong-Nan Chien
Microorganisms 2024, 12(7), 1402; https://doi.org/10.3390/microorganisms12071402 - 11 Jul 2024
Viewed by 222
Abstract
The optimal strategy for the microelimination of HCV within community settings remains ambiguous. We evaluated the percentage of participants who achieved linkage to care (LTC) following the conclusion of a screening campaign and examined the diverse factors influencing LTC among these individuals. The [...] Read more.
The optimal strategy for the microelimination of HCV within community settings remains ambiguous. We evaluated the percentage of participants who achieved linkage to care (LTC) following the conclusion of a screening campaign and examined the diverse factors influencing LTC among these individuals. The effectiveness of recall intervention for the non-LTC population and its barriers were analyzed. We initiated an HCV patient recall program to identify HCV participants who might not be treated after the HCV screening campaign. The program staff recalled HCV participants who were lost to follow-up via telephone from March 2019 to June 2019. They were informed of HCV treatment’s importance, efficacy, availability, and safety. Among 185 participants infected with HCV, 109 (58.9%) obtained LTC. Compared with those who had LTC, those without LTC were older, had lower education levels, were less aware of their HCV infection, less frequently lived in urban areas, and had less health insurance. At the end of the recall program, 125 (67.6%) persons had linkage to care. The proportion of LTC increased by 8.7%. In total, 119 persons had an HCV RNA test, and 82 (68.9%) had viremia. Of the 82 patients with viremia, 78 (95.1%) received antiviral therapy, and 76 (97.4%) achieved a sustained virological response. After a community screening campaign, 59% of participants with anti-HCV-positive tests had LTC. The recall program increased this by 9%. However, 32% of HCV participants still could not be linked to care. Outreach care for non-LTC patients is a method worth trying in order to achieve the microelimination of HCV in rural communities. Full article
(This article belongs to the Section Virology)
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8 pages, 1317 KiB  
Communication
Intermediate Disturbances Enhance Microbial Enzyme Activities in Soil Ecosystems
by Hojeong Kang, Sunghyun Kim, Keunyea Song, Min-Jung Kwon and Jaehyun Lee
Microorganisms 2024, 12(7), 1401; https://doi.org/10.3390/microorganisms12071401 - 11 Jul 2024
Viewed by 205
Abstract
The Intermediate Disturbance Hypothesis (IDH) posits that maximal plant biodiversity is attained in environments characterized by moderate ecological disturbances. Although the applicability of the IDH to microbial diversity has been explored in a limited number of studies, there is a notable absence of [...] Read more.
The Intermediate Disturbance Hypothesis (IDH) posits that maximal plant biodiversity is attained in environments characterized by moderate ecological disturbances. Although the applicability of the IDH to microbial diversity has been explored in a limited number of studies, there is a notable absence of experimental reports on whether soil microbial ‘activity’ demonstrates a similar response to the frequency or intensity of environmental disturbances. In this investigation, we conducted five distinct experiments employing soils or wetland sediments exposed to varying intensities or frequencies of disturbances, with a specific emphasis on disturbances associated with human activity, such as chemical contamination, hydrologic changes, and forest thinning. Specifically, we examined the effects of bactericide and heavy metal contamination, long-term drainage, tidal flow, and thinning management on microbial enzyme activities in soils. Our findings revealed that microbial enzyme activities were highest at intermediate disturbance levels. Despite the diversity in experiment conditions, each trial consistently demonstrated analogous patterns, suggesting the robustness of the IDH in elucidating microbial activities alongside diversity in soils. These outcomes bear significant implications for ecological restoration and management, as intermediate disturbance may expedite organic matter decomposition and nutrient cycles, crucial for sustaining ecosystem services in soils. Full article
(This article belongs to the Special Issue Soil Microbiome and Ecological Biogeochemical Cycles)
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13 pages, 2134 KiB  
Article
Establishment of a Protocol for Viability qPCR in Dental Hard Tissues
by Torsten Sterzenbach, Vanessa Neumann, Evelyn Trips, Sabine Basche, Christian Hannig and Marie-Theres Kühne
Microorganisms 2024, 12(7), 1400; https://doi.org/10.3390/microorganisms12071400 - 11 Jul 2024
Viewed by 207
Abstract
The aim of the study was to establish a live/dead qPCR with propidium monoazide (PMA) that can quantitatively differentiate between viable/non-viable microorganisms in dental hard tissues. Human premolars (n = 88) were prepared with nickel–titanium instruments and incubated with E. faecalis (21 d). [...] Read more.
The aim of the study was to establish a live/dead qPCR with propidium monoazide (PMA) that can quantitatively differentiate between viable/non-viable microorganisms in dental hard tissues. Human premolars (n = 88) were prepared with nickel–titanium instruments and incubated with E. faecalis (21 d). Subsequently, the bacteria in half of the teeth were devitalized by heat inactivation (100 °C, 2 h). The following parameters were tested: PMA concentrations at 0 µmol (control), 50 µmol, 100 µmol, and 200 µmol; PMA incubation times of 30 min and 60 min, and blue light treatment for 30 min and 60 min. The teeth were ground using a cryomill and the bacterial DNA was quantified using qPCR, ANOVA, and p = 0.05. The qPCR of the control group detected a similar number of avital 9.94 × 106 and vital 1.61 × 107 bacterial cells. The use of PMA inhibited the amplification of DNA from non-viable cells during qPCR. As a result, the best detection of avital bacteria was achieved with the following PMA parameters: (concentration, incubation time, blue light treatment) 200-30-30; 5.53 × 104 (avital) and 1.21 × 100.7 (vital). The live/dead qPCR method using PMA treatment is suitable for the differentiation and quantification of viable/non-viable microorganisms in dentin, as well as to evaluate the effectiveness of different preparation procedures and antimicrobial irrigants in other biological hard substances. Full article
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14 pages, 1699 KiB  
Article
Antibacterial, Antibiofilm, and Antioxidant Activities of Aqueous Crude Gymnema inodorum Leaf Extract against Vancomycin-Resistant Enterococcus faecium
by Sakaewan Ounjaijean, Voravuth Somsak, Morteza Saki, Watcharapong Mitsuwan and Chonticha Romyasamit
Microorganisms 2024, 12(7), 1399; https://doi.org/10.3390/microorganisms12071399 - 11 Jul 2024
Viewed by 289
Abstract
Vancomycin-resistant Enterococcus faecium (VREF) causes nosocomial infections with high mortality and morbidity rates. This study aimed to evaluate the antibacterial and antibiofilm activities of aqueous crude Gymnema inodorum leaf extract (GIE) against the VREF ATCC 700221 strain. The antimicrobial activity of GIE against [...] Read more.
Vancomycin-resistant Enterococcus faecium (VREF) causes nosocomial infections with high mortality and morbidity rates. This study aimed to evaluate the antibacterial and antibiofilm activities of aqueous crude Gymnema inodorum leaf extract (GIE) against the VREF ATCC 700221 strain. The antimicrobial activity of GIE against VREF was performed using disk diffusion and broth microdilution. The antibiofilm activities were evaluated using the crystal violet staining assay. The antioxidant potential was evaluated. Preliminary screening of the antimicrobial activity of 50 and 100 µg/disk of GIE against VREF revealed inhibition zones of 8.33 ± 0.58 mm and 8.67 ± 0.29 mm, respectively. Additionally, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values against VREF were 125 and ≥ 250 mg/mL, respectively. SEM analysis showed that treatment with GIE caused morphological changes, including incomplete cell division, damaged cell walls, and cell content leakage, suggesting a disruption of bacterial cells. GIE also inhibited and eradicated biofilms formed by VREF. The extract exhibited antioxidant activities in the DPPH and ABTS assays. While GIE shows potential as an antibacterial and antibiofilm agent, further studies are necessary to fully understand the underlying mechanisms and optimize its use for therapeutic applications. Full article
(This article belongs to the Special Issue Antimicrobial Compounds from Alternative Sources 2.0)
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8 pages, 208 KiB  
Communication
Factors Influencing the Degree of Gastric Atrophy in Helicobacter pylori Eradication Patients with Drinking Habits
by Kayoko Ozeki, Kazuhiro Hada and Yoshifumi Wakiya
Microorganisms 2024, 12(7), 1398; https://doi.org/10.3390/microorganisms12071398 - 10 Jul 2024
Viewed by 281
Abstract
Chronic gastritis caused by Helicobacter pylori (H. pylori) infection can lead to gastric atrophy. This study aimed to identify the factors associated with gastric atrophy in H. pylori eradication patients with drinking habits. Of the 250 patients who visited Hamamatsu University [...] Read more.
Chronic gastritis caused by Helicobacter pylori (H. pylori) infection can lead to gastric atrophy. This study aimed to identify the factors associated with gastric atrophy in H. pylori eradication patients with drinking habits. Of the 250 patients who visited Hamamatsu University Hospital for H. pylori eradication and underwent eradication treatment between April 2017 and December 2020, 127 patients with drinking habits were included in this study. The degree of gastric atrophy of the patients was classified based on endoscopy. The relationship between patient attributes (sex, age, alcohol consumption, frequency of drinking, smoking status, and medication use) and a highly atrophic stomach was statistically analyzed. The results showed that gastric atrophy was significantly higher in males and in those aged 60 years or older and that gastric atrophy tended to be higher in those who drank 20 g or more per day and 5 days or more a week. There was also a trend toward higher atrophy in sake drinkers and lower atrophy in wine drinkers. This study provides useful knowledge for patient management and guidance after H. pylori eradication treatment and indicates the importance of comprehensive measures, including alcohol consumption control and lifestyle modification, especially for men and older people. Full article
(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)
14 pages, 2808 KiB  
Article
Serological Screening and Risk Factors Associated with Leishmania infantum Positivity in Newly Diagnosed HIV Patients in Greece
by Chrysa Voyiatzaki, Apollon Dareios Zare Chormizi, Maria E. Tsoumani, Antonia Efstathiou, Konstantinos Konstantinidis, Georgios Chrysos, Aikaterini Argyraki, Vasileios Papastamopoulos, Effie G. Papageorgiou and Marika Kotsianopoulou
Microorganisms 2024, 12(7), 1397; https://doi.org/10.3390/microorganisms12071397 - 10 Jul 2024
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Abstract
A serological screening was conducted to detect IgG antibodies against Leishmania infantum (L. infantum) in newly diagnosed human immunodeficiency virus (HIV) patients in Greece. The study also examined potential risk factors and the agreement of commercially available serological methods. IgG antibodies [...] Read more.
A serological screening was conducted to detect IgG antibodies against Leishmania infantum (L. infantum) in newly diagnosed human immunodeficiency virus (HIV) patients in Greece. The study also examined potential risk factors and the agreement of commercially available serological methods. IgG antibodies against L. infantum were detected using enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence antibody test (IFAT), and Western blot (WB). Out of 155 samples, 14 (9.0%) tested positive for IgG antibodies against L. infantum using at least two methods. Statistical analysis showed substantial agreement between WB and IFAT methods (Cohen’s kappa = 0.75) but moderate overall agreement among the three methods (Fleiss’ kappa = 0.42). Additionally, HIV+ intravenous drug users faced 3.55 times (p = 0.025) higher risk of testing positive for L. infantum IgG, positing that anthroponotic transmission between these patients is a plausible hypothesis based on existing literature. Non-invasive and cost-effective techniques are preferred to detect asymptomatic infections, and leishmaniasis screening should be conducted immediately after HIV diagnosis in endemic regions to enable prophylactic treatment for leishmaniasis in addition to antiretroviral therapy. To maximize sensitivity, performing at least two different serological methods for each patient is recommended. Full article
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