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Microorganisms, Volume 12, Issue 6 (June 2024) – 196 articles

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15 pages, 4713 KiB  
Article
A Genomics-Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in the Potential Novel Strain Streptomyces sp. 21So2-11 Isolated from Antarctic Soil
by Yu Du, Wei Han, Puyu Hao, Yongqiang Hu, Ting Hu and Yinxin Zeng
Microorganisms 2024, 12(6), 1228; https://doi.org/10.3390/microorganisms12061228 (registering DOI) - 19 Jun 2024
Abstract
Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed [...] Read more.
Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed that this strain is most closely related to Streptomyces drozdowiczii NBRC 101007T, with a similarity of 98.02%. Genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) showed that strain 21So2-11 represents a novel species of the genus Streptomyces. In addition to a large number of genes related to environmental adaptation and ecological function, a total of 28 putative biosynthetic gene clusters (BGCs) responsible for the biosynthesis of known and/or novel secondary metabolites, including terpenes, lantipeptides, polyketides, nonribosomal peptides, RiPPs and siderophores, were detected in the genome of strain 21So2-11. In addition, a total of 1456 BGCs were predicted to contribute to the biosynthesis of more than 300 secondary metabolites based on the genomes of 47 Streptomyces strains originating from polar regions. The results indicate the potential of Streptomyces sp. 21So2-11 for bioactive secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold terrestrial environments. Full article
(This article belongs to the Section Microbial Biotechnology)
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11 pages, 2333 KiB  
Article
The Description and Analysis of the Complete Genome of Dermacoccus barathri FBCC-B549 Strain
by Yeha Kim, Hyaekang Kim, Jina Kim, Ji-Hye Han, Eu Jin Chung, Seung Won Nam, Miyoung Shin and Woori Kwak
Microorganisms 2024, 12(6), 1227; https://doi.org/10.3390/microorganisms12061227 - 18 Jun 2024
Viewed by 105
Abstract
Dermacoccus barathri is the first reported pathogen within the Dermacoccus genus to cause a catheter-related bloodstream infection, which occurred in 2015. In this study, the complete genome assembly of Dermacoccus barathri was constructed, and the complete genome of Dermacoccus barathri FBCC-B549 consists of [...] Read more.
Dermacoccus barathri is the first reported pathogen within the Dermacoccus genus to cause a catheter-related bloodstream infection, which occurred in 2015. In this study, the complete genome assembly of Dermacoccus barathri was constructed, and the complete genome of Dermacoccus barathri FBCC-B549 consists of a single chromosome (3,137,745 bp) without plasmids. The constructed genome of D. barathri was compared with those of two closely related species within the Dermacoccus genus. D. barathri exhibited a pattern similar to Dermacoccus abyssi in terms of gene clusters and synteny analysis. Contrary to previous studies, biosynthetic gene cluster (BGC) analysis for predicting secondary metabolites revealed the presence of the LAP biosynthesis pathway in the complete genome of D. barathri, predicting the potential synthesis of the secondary metabolite plantazolicin. Furthermore, an analysis to investigate the potential pathogenicity of D. barathri did not reveal any antibiotic resistance genes; however, nine virulence factors were identified in the Virulence Factor Database (VFDB). According to these matching results in the VFDB, despite identifying a few factors involved in biofilm formation, further research is required to determine the actual impact of D. barathri on pathogenicity. The complete genome of D. barathri is expected to serve as a valuable resource for future studies on D. barathri, which currently lack sufficient genomic sequence information. Full article
(This article belongs to the Section Microbial Biotechnology)
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13 pages, 2627 KiB  
Article
The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties
by Yuval Dorfan, Avichay Nahami, Yael Morris, Benny Shohat and Ilana Kolodkin-Gal
Microorganisms 2024, 12(6), 1226; https://doi.org/10.3390/microorganisms12061226 - 18 Jun 2024
Viewed by 94
Abstract
The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into [...] Read more.
The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. “Mold” refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment. Full article
(This article belongs to the Special Issue An Update on Bacillus)
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15 pages, 2185 KiB  
Article
Periodontal Inflammation and Dysbiosis Relate to Microbial Changes in the Gut
by Angela R. Kamer, Smruti Pushalkar, Babak Hamidi, Malvin N. Janal, Vera Tang, Kumar Raghava Chowdary Annam, Leena Palomo, Deepthi Gulivindala, Lidia Glodzik and Deepak Saxena
Microorganisms 2024, 12(6), 1225; https://doi.org/10.3390/microorganisms12061225 - 18 Jun 2024
Viewed by 86
Abstract
Periodontal disease (PerioD) is a chronic inflammatory disease of dysbiotic etiology. Animal models and few human data showed a relationship between oral bacteria and gut dysbiosis. However, the effect of periodontal inflammation and subgingival dysbiosis on the gut is unknown. We hypothesized that [...] Read more.
Periodontal disease (PerioD) is a chronic inflammatory disease of dysbiotic etiology. Animal models and few human data showed a relationship between oral bacteria and gut dysbiosis. However, the effect of periodontal inflammation and subgingival dysbiosis on the gut is unknown. We hypothesized that periodontal inflammation and its associated subgingival dysbiosis contribute to gut dysbiosis even in subjects free of known gut disorders. We evaluated and compared elderly subjects with Low and High periodontal inflammation (assessed by Periodontal Inflamed Surface Area (PISA)) for stool and subgingival derived bacteria (assayed by 16S rRNA sequencing). The associations between PISA/subgingival dysbiosis and gut dysbiosis and bacteria known to produce short-chain fatty acid (SCFA) were assessed. LEfSe analysis showed that, in Low PISA, species belonging to Lactobacillus, Roseburia, and Ruminococcus taxa and Lactobacillus zeae were enriched, while species belonging to Coprococcus, Clostridiales, and Atopobium were enriched in High PISA. Regression analyses showed that PISA associated with indicators of dysbiosis in the gut mainly reduced abundance of SCFA producing bacteria (Radj = −0.38, p = 0.03). Subgingival bacterial dysbiosis also associated with reduced levels of gut SCFA producing bacteria (Radj = −0.58, p = 0.002). These results suggest that periodontal inflammation and subgingival microbiota contribute to gut bacterial changes. Full article
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8 pages, 600 KiB  
Communication
Impact of COVID-19 Restrictions on Incidence of Enteropathogenic Bacteria, Virus, and Parasites in Denmark: A National, Register-Based Study
by Kumanan Rune Nanthan, Eva Plantener, John Coia, Jørgen Engberg, Leif Percival Andersen, Ea Marmolin, Gitte Nyvang Hartmeyer, Hans Linde Nielsen, Christen Rune Stensvold, Anne Line Engsbro, Bente Olesen, Lars Lemming and Ming Chen
Microorganisms 2024, 12(6), 1224; https://doi.org/10.3390/microorganisms12061224 - 18 Jun 2024
Viewed by 126
Abstract
Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of [...] Read more.
Diarrheal diseases caused by enteric pathogens are a significant public health concern. It is widely considered that close contact between persons, poor hygiene, and consumption of contaminated food are the primary causes of gastroenteritis. Clinical microbiology laboratory observations indicate that the incidence of enteropathogenic microorganisms may have been reduced in Denmark during the COVID-19 pandemic. All Departments of Clinical Microbiology in Denmark provided data on the monthly incidence of Salmonella spp., Escherichia coli, Campylobacter spp., Clostridioides difficile, Norovirus GI+GII, Giardia duodenalis, and Cryptosporidium from March 2018 to February 2021. The data were divided into three periods as follows: Control Period 1 (March 2018 to February 2019); Control Period 2 (March 2019 to February 2020); and the Restriction (pandemic) Period (March 2020 to February 2021). The incidences of pathogenic Salmonella spp.-, Escherichia coli-, and Campylobacter spp.-positive samples decreased by 57.3%, 48.1%, and 32.9%, respectively, during the restriction period. No decrease in C. difficile was observed. Norovirus GI+GII-positive samples decreased by 85.6%. Giardia duodenalis-positive samples decreased by 66.2%. Cryptosporidium species decreased by 59.6%. This study demonstrates a clear decrease in the incidence of enteropathogenic bacteria (except for C. difficile), viruses, and parasites during the SARS-CoV-2 restriction period in Denmark. Full article
(This article belongs to the Section Public Health Microbiology)
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17 pages, 3726 KiB  
Article
Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters
by Marina Carrasco-Acosta and Pilar Garcia-Jimenez
Microorganisms 2024, 12(6), 1223; https://doi.org/10.3390/microorganisms12061223 - 18 Jun 2024
Viewed by 165
Abstract
In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal [...] Read more.
In this study, we designed and validated in silico and experimentally a rapid, sensitive, and specific multiplex RT qPCR for the detection and quantification of faecal indicator bacteria (FIB) used as microbiological references in marine bathing water regulations (Escherichia coli and intestinal enterococci). The 16S rRNA gene was used to quantify group-specific enterococci and Escherichia/Shigella and species-specific such as Enterococcus faecalis and E. faecium. Additionally, a ybbW gene encoding allantoin transporter protein was used to detect E. coli. An assessment of marine coastal systems (i.e., marine water and sediment) revealed that intestinal enterococci were the predominant group compared to Escherichia/Shigella. The low contribution of E. faecalis to the intestinal enterococci group was reported. As E. faecalis and E. faecium were reported at low concentrations, it is assumed that other enterococci of faecal origin are contributing to the high gene copy number of this group-specific enterococci. Moreover, low 16S rRNA gene copy numbers with respect to E. faecalis and E. faecium were reported in seawater compared to marine sediment. We conclude that marine sediments can affect the quantification of FIBs included in bathing water regulations. Valuing the quality of the marine coastal system through sediment monitoring is recommended. Full article
(This article belongs to the Collection Advances in Public Health Microbiology)
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15 pages, 1360 KiB  
Article
Bioconversion of Furanic Compounds by Chlorella vulgaris—Unveiling Biotechnological Potentials
by Ricarda Kriechbaum, Oliver Spadiut and Julian Kopp
Microorganisms 2024, 12(6), 1222; https://doi.org/10.3390/microorganisms12061222 - 18 Jun 2024
Viewed by 192
Abstract
Lignocellulosic biomass is abundant on Earth, and there are multiple acidic pretreatment options to separate the cellulose, hemicellulose, and lignin fraction. By doing so, the fermentation inhibitors 5-Hydroxymethylfurfural (HMF) and furfural (FF) are produced in varying concentrations depending on the hydrolyzed substrate. In [...] Read more.
Lignocellulosic biomass is abundant on Earth, and there are multiple acidic pretreatment options to separate the cellulose, hemicellulose, and lignin fraction. By doing so, the fermentation inhibitors 5-Hydroxymethylfurfural (HMF) and furfural (FF) are produced in varying concentrations depending on the hydrolyzed substrate. In this study, the impact of these furanic compounds on Chlorella vulgaris growth and photosynthetic activity was analyzed. Both compounds led to a prolonged lag phase in Chlorella vulgaris growth. While the photosynthetic yield Y(II) was not significantly influenced in cultivations containing HMF, FF significantly reduced Y(II). The conversion of 5-Hydroxymethylfurfural and furfural to 5-Hydroxymethyl-2-Furoic Acid and 2-Furoic Acid was observed. In total, 100% of HMF and FF was converted in photoautotrophic and mixotrophic Chlorella vulgaris cultivations. The results demonstrate that Chlorella vulgaris is, as of now, the first known microalgal species converting furanic compounds. Full article
(This article belongs to the Special Issue The Application Potential of Microalgae in Green Biotechnology)
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16 pages, 2175 KiB  
Article
Role of MalQ Enzyme in a Reconstructed Maltose/Maltodextrin Pathway in Actinoplanes sp. SE50/110
by Camilla März, Sophia Nölting, Lars Wollenschläger, Alfred Pühler and Jörn Kalinowski
Microorganisms 2024, 12(6), 1221; https://doi.org/10.3390/microorganisms12061221 - 18 Jun 2024
Viewed by 183
Abstract
The pseudotetrasaccharide acarbose, produced by Actinoplanes sp. SE50/110, is a relevant secondary metabolite used in diabetes type II medication. Although maltose plays a crucial role in acarbose biosynthesis, the understanding of the maltose/maltodextrin metabolism and its involvement in acarbose production is at an [...] Read more.
The pseudotetrasaccharide acarbose, produced by Actinoplanes sp. SE50/110, is a relevant secondary metabolite used in diabetes type II medication. Although maltose plays a crucial role in acarbose biosynthesis, the understanding of the maltose/maltodextrin metabolism and its involvement in acarbose production is at an early stage. Here, we reconstructed the predicted maltose–maltodextrin pathway that involves four enzymes AmlE, MalZ, MalP, and MalQ. An investigation of enzyme activities was conducted through in vitro assays, leading to an expansion of previously postulated substrate spectra. The maltose-induced α-glucosidase AmlE is noteworthy for its high hydrolysis rate of linear α-1,4-glucans, and its capability to hydrolyze various glycosidic bonds. The predicted maltodextrin glucosidase MalZ showed slow hydrolysis activity on linear α-glucans, but it was resistant to acarbose and capable of releasing glucose from acarbose. AmlE compensates for the low activity of MalZ to ensure glucose supply. We determined the enzyme activity of MalP and its dual function as maltodextrin and glycogen phosphorylase. The 4-α-glucanotransferase MalQ plays a central role in the maltose/maltodextrin metabolism, alongside MalP. This study confirmed the simultaneous degradation and synthesis of long-chain α-glucans. The product distribution showed that with an increasing number of glycosidic bonds, less glucose is formed. We found that MalQ, like its sequence homolog AcbQ from the acarbose biosynthetic gene cluster, is involved in the formation of elongated acarviosyl metabolites. However, MalQ does not participate in the elongation of acarbose 7-phosphate, which is likely the more readily available acceptor molecule in vivo. Accordingly, MalQ is not involved in the formation of acarviosyl impurities in Actinoplanes sp. SE50/110. Full article
(This article belongs to the Special Issue Specialized Metabolites from Microorganisms)
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22 pages, 5345 KiB  
Article
Macrogenomics-Based Analysis of the Effects of Intercropped Soybean Photosynthetic Characteristics and Nitrogen-Assimilating Enzyme Activities on Yield at Different Nitrogen Levels
by Liqiang Zhang, Yudi Feng, Zehang Zhao, Bate Baoyin, Zhengguo Cui, Hongyu Wang, Qiuzhu Li and Jinhu Cui
Microorganisms 2024, 12(6), 1220; https://doi.org/10.3390/microorganisms12061220 - 18 Jun 2024
Viewed by 205
Abstract
Currently, China’s soybean self-sufficiency rate is only 15%, highlighting the soybean crisis and the supply chain risks that pose a major threat to China’s food security. Thus, it has become imperative to step up efforts to boost soybean production capacity while promoting the [...] Read more.
Currently, China’s soybean self-sufficiency rate is only 15%, highlighting the soybean crisis and the supply chain risks that pose a major threat to China’s food security. Thus, it has become imperative to step up efforts to boost soybean production capacity while promoting the green and sustainable development of regional farmland ecosystems. In this context, the present study comprehensively investigated the effects of intercropping and nitrogen application rate on soybean yield, as well as the changes in gradients generated by different levels of nitrogen application. Based on six consecutive years of maize–soybean intercropping planting patterns, the inter-root soils of soybeans were collected at the flowering stage and evaluated for soil nitrogen content, nitrogen-assimilating enzyme activities, and microbial community composition of soybean, which were correlated with yield, to clarify the main pathways and modes of intercropping effects. The N2 level (80 kg·ha−1) was favourable for higher yield. In comparison to monocropping, the intercropping reduced yield by 9.65–13.01%, photosynthetic characteristics by 1.33–7.31%, and plant nitrogen-assimilating enzyme activities by 8.08–32.01% at the same level of N application. Likewise, soil urease and catalase activities were reduced by 9.22 and 1.80%, while soil nitrogen content declined by an average of 6.38%. Gemmatimonas and Bradyrhizobium enrichment significantly increased soil nitrogen content, photosynthetic characteristics, and soybean yield, while it was reduced by Candidatus_Udaeobacter and Candidatus_Solibacte enrichment. The results of this study provide a theoretical basis for further optimising maize–soybean intercropping, which is crucial for enhancing the agricultural production structure and improving the overall soybean production capacity. Full article
(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)
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12 pages, 1984 KiB  
Article
Ciliated Epibionts Modify the Cardiac Stress Reaction to Perceived Predation in Daphnia
by Andrew K. Davis and Helen Gloege
Microorganisms 2024, 12(6), 1219; https://doi.org/10.3390/microorganisms12061219 - 18 Jun 2024
Viewed by 170
Abstract
When animals perceive an acute stressor like a predator, they typically undergo a suite of physiological changes that function to improve survival during the encounter, such as elevation in cardiac output, to supply more energy to muscles. If bodily energy is limited, such [...] Read more.
When animals perceive an acute stressor like a predator, they typically undergo a suite of physiological changes that function to improve survival during the encounter, such as elevation in cardiac output, to supply more energy to muscles. If bodily energy is limited, such as by parasites or infections, these functions could become less efficient and lessen host survival. In the aquatic world of microorganisms, individuals can become colonized by other organisms on their surface (epibionts), which could sap energy from their host from their weight, or even compete with the host for food. Here, we tested if one epibiont (a ciliated protozoan, Vorticella spp.) affects its hosts’ ability to mount a physiological stress reaction. We collected wild daphnia (Daphnia ambigua) that had varying burdens of these on their bodies and exposed them to a simulated stressor (crushed daphnia, to simulate nearby predation) under a microscope while monitoring for changes in their heart rates in real time. Out of 121 daphnia, those with no Vorticella epibionts showed no meaningful changes in their heart rate after exposure, but those with light or heavy burdens showed immediate elevations (within 5 min). Moreover, the heart rates of heavily burdened daphnia continued to rise for 1.5 h thereafter, to as much as 17% higher than at baseline. These patterns were unexpected, as they suggest that the ciliated epibionts act to elevate their hosts’ physiological reaction, rather than dampen it, perhaps by churning the water column around the host, thereby enhancing the chemical alarm cue. The procedures used in this study may be useful for future investigations into the acute stress reactions of daphnia or other microorganisms. Full article
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14 pages, 3615 KiB  
Article
Effects of Weak Electric Fields on the Denitrification Performance of Pseudomonas stutzeri: Insights into Enzymes and Metabolic Pathways
by Xuyan Zhu, Feng Lin, Ji Sun, Xin Li, Guangcan Zhu, Yongze Lu, Liwei Sun and Hongyang Wang
Microorganisms 2024, 12(6), 1218; https://doi.org/10.3390/microorganisms12061218 - 17 Jun 2024
Viewed by 216
Abstract
Enhanced denitrification has been reported under weak electric fields. However, it is difficult to investigate the mechanism of enhanced denitrification due to the complex interspecific interactions of mixed-culture systems. In this study, Pseudomonas stutzeri, capable of denitrification under anaerobic conditions, was selected [...] Read more.
Enhanced denitrification has been reported under weak electric fields. However, it is difficult to investigate the mechanism of enhanced denitrification due to the complex interspecific interactions of mixed-culture systems. In this study, Pseudomonas stutzeri, capable of denitrification under anaerobic conditions, was selected for treating low COD/N (2.0, ratio between concentration of chemical oxygen demand and NO3-N) artificial wastewater under constant external voltages of 0.2, 0.4, and 0.6 V. The results revealed that P. stutzeri exhibited the highest efficiency in nitrate reduction at 0.2 V. Moreover, the maximum nitrate removal rate was 15.96 mg/(L·h) among the closed-circuit groups, 19.39% higher than that under the open-circuit group. Additionally, a notable reduction in nitrite accumulation was observed under weak electric fields. Enzyme activity analysis showed that the nitrate reductase activities were significantly increased among the closed-circuit groups, while nitrite reductase activities were inhibited. Transcriptomic analysis indicated that amino acid metabolism, carbohydrate metabolism, and energy metabolism were increased, enhancing the resistance of P. stutzeri to environmental stress and the efficiency of carbon source utilization for denitrification. The current study examined the impacts of weak electric fields on enzyme activities and microbial metabolic pathways and offers valuable insights into the mechanism by which denitrification is enhanced by weak electric fields. Full article
(This article belongs to the Section Environmental Microbiology)
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19 pages, 2578 KiB  
Article
Symbiodiniaceae and Ruegeria sp. Co-Cultivation to Enhance Nutrient Exchanges in Coral Holobiont
by Yawen Liu, Huan Wu, Yang Shu, Yanying Hua and Pengcheng Fu
Microorganisms 2024, 12(6), 1217; https://doi.org/10.3390/microorganisms12061217 - 17 Jun 2024
Viewed by 196
Abstract
The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of [...] Read more.
The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of coral reefs. However, most studies have primarily focused on coral–Symbiodiniaceae–bacterial interactions as a whole, neglecting the interactions between Symbiodiniaceae and bacteria, which remain largely unexplored. In this study, we proposed a hypothesis that there exists an inner symbiotic loop of Symbiodiniaceae and bacteria within the coral symbiotic loop. We conducted experiments to demonstrate how metabolic exchanges between Symbiodiniaceae and bacteria facilitate the nutritional supply necessary for cellular growth. It was seen that the beneficial bacterium, Ruegeria sp., supplied a nitrogen source to the Symbiodiniaceae strain Durusdinium sp., allowing this dinoflagellate to thrive in a nitrogen-free medium. The Ruegeria sp.–Durusdinium sp. interaction was confirmed through 15N-stable isotope probing–single cell Raman spectroscopy, in which 15N infiltrated into the bacterial cells for intracellular metabolism, and eventually the labeled nitrogen source was traced within the macromolecules of Symbiodiniaceae cells. The investigation into Symbiodiniaceae loop interactions validates our hypothesis and contributes to a comprehensive understanding of the intricate coral holobiont. These findings have the potential to enhance the health of coral reefs in the face of global climate change. Full article
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10 pages, 1543 KiB  
Case Report
Tuberculosis in a Migrant Population: Integrated Management of a Case through the Prevention Department and Hospital Services
by Nahuel Fiorito, Daniela Piacentini, Serena Cian, Anna Voltolini, Jacopo Fagherazzi, Erica Bino, Marika Brancher, Giorgia De Luca, Marica Battistin, Mattia Manzi, Vincenzo Marcotrigiano, Angela Vedana, Christian Napoli and Sandro Cinquetti
Microorganisms 2024, 12(6), 1216; https://doi.org/10.3390/microorganisms12061216 - 17 Jun 2024
Viewed by 186
Abstract
Among numerous public health actions, the Prevention Departments of Local Health Authorities take charge of the migrant asylum-seeking population for health assessments, for the implementation of preventive activities, and for any consequent actions. This report describes two cases of tuberculosis in Belluno Province [...] Read more.
Among numerous public health actions, the Prevention Departments of Local Health Authorities take charge of the migrant asylum-seeking population for health assessments, for the implementation of preventive activities, and for any consequent actions. This report describes two cases of tuberculosis in Belluno Province managed by a multidisciplinary team made up of healthcare workers that involved numerous diagnostic, clinical, and prophylactic implications, as well as an analysis of the epidemiological aspects related to the incidence of cases along the migration route. Although the cases occurred in a northeastern Italian territory, the management methods described here may represent good practices to share on this operational line, which can promote the strengthening of cooperation between Health Authorities and Emergency Reception Centers to correctly identify cases of active tuberculosis that may not have been initially screen-detected. Full article
(This article belongs to the Special Issue Advances in Microbial Pathogenesis and Host Responses)
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17 pages, 5657 KiB  
Article
Microbial Assessment in A Rare Norwegian Book Collection: A One Health Approach to Cultural Heritage
by Sílvia O. Sequeira, Ekaterina Pasnak, Carla Viegas, Bianca Gomes, Marta Dias, Renata Cervantes, Pedro Pena, Magdalena Twarużek, Robert Kosicki, Susana Viegas, Liliana Aranha Caetano, Maria João Penetra, Inês Silva, Ana Teresa Caldeira and Catarina Pinheiro
Microorganisms 2024, 12(6), 1215; https://doi.org/10.3390/microorganisms12061215 - 17 Jun 2024
Viewed by 442
Abstract
Microbial contamination poses a threat to both the preservation of library and archival collections and the health of staff and users. This study investigated the microbial communities and potential health risks associated with the UNESCO-classified Norwegian Sea Trade Archive (NST Archive) collection exhibiting [...] Read more.
Microbial contamination poses a threat to both the preservation of library and archival collections and the health of staff and users. This study investigated the microbial communities and potential health risks associated with the UNESCO-classified Norwegian Sea Trade Archive (NST Archive) collection exhibiting visible microbial colonization and staff health concerns. Dust samples from book surfaces and the storage environment were analysed using culturing methods, qPCR, Next Generation Sequencing, and mycotoxin, cytotoxicity, and azole resistance assays. Penicillium sp., Aspergillus sp., and Cladosporium sp. were the most common fungi identified, with some potentially toxic species like Stachybotrys sp., Toxicladosporium sp., and Aspergillus section Fumigati. Fungal resistance to azoles was not detected. Only one mycotoxin, sterigmatocystin, was found in a heavily contaminated book. Dust extracts from books exhibited moderate to high cytotoxicity on human lung cells, suggesting a potential respiratory risk. The collection had higher contamination levels compared to the storage environment, likely due to improved storage conditions. Even though overall low contamination levels were obtained, these might be underestimated due to the presence of salt (from cod preservation) that could have interfered with the analyses. This study underlines the importance of monitoring microbial communities and implementing proper storage measures to safeguard cultural heritage and staff well-being. Full article
(This article belongs to the Section Environmental Microbiology)
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11 pages, 3004 KiB  
Article
Assessing PCR-Positive Acanthamoeba Keratitis—A Retrospective Chart Review
by Frank Blaser, Anahita Bajka, Felix Grimm, Simone Metzler, Didier Herrmann, Daniel Barthelmes, Sandrine Anne Zweifel and Sadiq Said
Microorganisms 2024, 12(6), 1214; https://doi.org/10.3390/microorganisms12061214 - 17 Jun 2024
Viewed by 254
Abstract
Ophthalmologists’ diagnostic and treatment competence in Acanthamoeba keratitis varies widely. This investigator-initiated, retrospective, single-center chart review examined the electronic patient files regarding PCR-positive Acanthamoeba keratitis. We included corneal and contact lens assessments. We further reviewed the patient’s medical history, corneal scraping results regarding [...] Read more.
Ophthalmologists’ diagnostic and treatment competence in Acanthamoeba keratitis varies widely. This investigator-initiated, retrospective, single-center chart review examined the electronic patient files regarding PCR-positive Acanthamoeba keratitis. We included corneal and contact lens assessments. We further reviewed the patient’s medical history, corneal scraping results regarding viral or fungal co-infections, and the duration from symptom onset to final diagnosis. We identified 59 eyes of 52 patients from February 2010 to February 2023, with 31 of 52 (59.6%) being female patients. The median (IQR, range) patient age was 33 (25.3 to 45.5 [13 to 90]) years, and the mean (SD, range) time to diagnosis after symptom onset was 18 (10.5 to 35 [3 to 70]) days. Overall, 7 of 52 (7.7%) patients displayed a bilateral Acanthamoeba infection, and 48 (92.3%) used contact lenses at symptom onset. Regarding other microbiological co-infections, we found virologic PCR testing in 45 of 52 (86.5%) patients, with 3 (6.7%) positive corneal scrapings. Fungal cultures were performed in 49 of 52 (94.2%) patients, with 5 (10.2%) positive corneal scrapings. The medical treatment success rate was 45/46 (97.8%). This study raises awareness of patient education in contact lens handling and screens for further microbial co-infections in suspected Acanthamoeba cases. Full article
(This article belongs to the Special Issue Ocular Infections and Microbiota in Health and Disease 2.0)
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22 pages, 3642 KiB  
Article
FibroScan® versus Biochemical Scores: A Study of Liver Fibrosis in HIV with HBV Co-Infection
by Giorgiana Nicoleta Lungu, Gheorghe Iulian Diaconescu, Florentina Dumitrescu, Anca Oana Docea, Radu Mitrut, Lucian Giubelan, Ovidiu Zlatian and Paul Mitrut
Microorganisms 2024, 12(6), 1213; https://doi.org/10.3390/microorganisms12061213 - 16 Jun 2024
Viewed by 319
Abstract
The study aimed to determine liver fibrosis in human immunodeficiency virus (HIV) positive individuals using transient elastography (FibroScan®), Fibrosis-4 (FIB-4) score, and aspartate aminotransferase (AST) to Platelet Ratio Index (APRI) in the HIV Department from Infectious Diseases Hospital “Victor Babeș” Craiova, [...] Read more.
The study aimed to determine liver fibrosis in human immunodeficiency virus (HIV) positive individuals using transient elastography (FibroScan®), Fibrosis-4 (FIB-4) score, and aspartate aminotransferase (AST) to Platelet Ratio Index (APRI) in the HIV Department from Infectious Diseases Hospital “Victor Babeș” Craiova, Romania. Of the analyzed HIV-positive subjects (n = 161), 93 (57.76%) had HIV mono-infection, and 68 (42.24%) had Hepatitis B Virus (HBV) co-infection. The prevalence of advanced liver fibrosis was higher (F2: 11.76% and F3: 13.24%, F4: 4.41%) in the HIV-HBV co-infected group compared to the HIV mono-infected group. The univariate and multivariate analysis identified HBV co-infection (OR = 5.73) male sex (OR = 5.34), serum aspartate amino-transferase levels (Pearson’s rho = 0.273), low platelet count (Pearson’s rho = −0.149) and erythrocyte sedimentation rate (OR = 1.030) as risk factors for the presence of liver fibrosis. Body mass index (OR = 1.08), serum lipid levels (OR = 0.96), viral load at diagnosis (OR = 1.00005), and low CD4+ cell count (OR = 0.977) were also correlated with liver fibrosis. The FIB-4 and APRI scores were strongly correlated with each other. In conclusion, HBV co-infection seems to be a determinant factor for liver fibrosis development in people living with HIV, together with other risk factors. Full article
(This article belongs to the Special Issue Control and Elimination of Viral Hepatitis)
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17 pages, 2146 KiB  
Article
Effect of Bacterial Extracellular Polymeric Substances from Enterobacter spp. on Rice Growth under Abiotic Stress and Transcriptomic Analysis
by Yosra Aoudi, Shin-ichiro Agake, Safiullah Habibi, Gary Stacey, Michiko Yasuda and Naoko Ohkama-Ohtsu
Microorganisms 2024, 12(6), 1212; https://doi.org/10.3390/microorganisms12061212 - 16 Jun 2024
Viewed by 375
Abstract
Plant biostimulants have received attention as sustainable alternatives to chemical fertilizers. Extracellular polymeric substances (EPSs), among the compounds secreted by plant growth-promoting rhizobacteria (PGPRs), are assumed to alleviate abiotic stress. This study aims to investigate the effect of purified EPSs on rice under [...] Read more.
Plant biostimulants have received attention as sustainable alternatives to chemical fertilizers. Extracellular polymeric substances (EPSs), among the compounds secreted by plant growth-promoting rhizobacteria (PGPRs), are assumed to alleviate abiotic stress. This study aims to investigate the effect of purified EPSs on rice under abiotic stress and analyze their mechanisms. A pot experiment was conducted to elucidate the effects of inoculating EPSs purified from PGPRs that increase biofilm production in the presence of sugar on rice growth in heat-stress conditions. Since all EPSs showed improvement in SPAD after the stress, Enterobacter ludwigii, which was not characterized as showing higher PGP bioactivities such as phytohormone production, nitrogen fixation, and phosphorus solubilization, was selected for further analysis. RNA extracted from the embryos of germinating seeds at 24 h post-treatment with EPSs or water was used for transcriptome analysis. The RNA-seq analysis revealed 215 differentially expressed genes (DEGs) identified in rice seeds, including 139 up-regulated and 76 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the ROS scavenging processes, detoxification pathways, and response to oxidative stress. For example, the expression of the gene encoding OsAAO5, which is known to function in detoxifying oxidative stress, was two times increased by EPS treatment. Moreover, EPS application improved SPAD and dry weights of shoot and root by 90%, 14%, and 27%, respectively, under drought stress and increased SPAD by 59% under salt stress. It indicates that bacterial EPSs improved plant growth under abiotic stresses. Based on our results, we consider that EPSs purified from Enterobacter ludwigii can be used to develop biostimulants for rice. Full article
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8 pages, 1990 KiB  
Communication
Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Typing Ochrobactrum anthropi
by Yihan Wu, Liping Wang, Xiachun Hui and Guozhong Tian
Microorganisms 2024, 12(6), 1211; https://doi.org/10.3390/microorganisms12061211 - 16 Jun 2024
Viewed by 208
Abstract
Ochrobactrum anthropi (O. anthropi) is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of O. anthropi mainly [...] Read more.
Ochrobactrum anthropi (O. anthropi) is found in water, soil, plants and animals. Even though it has low virulence, it has increasingly been found to cause a number of infectious diseases in people with low immunity. The identification of O. anthropi mainly uses biochemical methods, such as the API 20NE or Vitek-2. The typing studies of O. anthropi have mainly utilized PFGE, rep-PCR, AFLP, 16s rDNA sequencing, RecA-PCR RFLP, and MALDI-TOF MS. This study aims to evaluate the polymorphisms of variable-number tandem-repeats (VNTRs) within genomic DNA of O. anthropi strains. The tandem repeats (TRs) in genomic DNA are discovered using Tandem Repeat Finder software (version 4.09). Twelve different VNTRs are designated and assigned to the nomenclature. The primers for PCR of 12 loci are designed. The PCR product size is converted to the number of tandem repeats in every locus. The relatedness of 65 O. anthropi strains from geographically different countries are analyzed by means of 12-variable-number tandem-repeat analysis(MLVA-12). A total of 51 different genotypes are found in 65 O. anthropi strains. These strains, which were collected from the same environmental samples, hospitals, and countries, are clustered within the same or closely genotypes. The MLVA-12 assay has a good discriminatory power for species determination, typing of O. anthropi, and inferring the origin of bacteria. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
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11 pages, 2482 KiB  
Article
Fried Soybean Oil Causes Systemic Low-Grade Inflammation by Disrupting the Balance of Gut Microbiota in Mice
by Lianhua Hu, Ling Huang, Zhijia Fang, Chen Wang, Jinjin Luo, Qi Deng, Defeng Xu, Lijun Sun and Ravi Gooneratne
Microorganisms 2024, 12(6), 1210; https://doi.org/10.3390/microorganisms12061210 - 16 Jun 2024
Viewed by 204
Abstract
Previous reports have mainly investigated the long-term effects (>30 d), such as gut microbiota dysbiosis and systemic low-grade inflammation, in mice fed fried oil. However, short-term intake of deep-fried oil is more likely to occur in daily life, and such studies are lacking. [...] Read more.
Previous reports have mainly investigated the long-term effects (>30 d), such as gut microbiota dysbiosis and systemic low-grade inflammation, in mice fed fried oil. However, short-term intake of deep-fried oil is more likely to occur in daily life, and such studies are lacking. This study aimed to investigate the short-term effects of fried oil intake on systemic low-grade inflammation. Male Kunming mice were fed non-fried soybean oil or low (25%), medium (50%), or high (100%)—fried oil at 4.4 g/kg for 6 d. Serum and fecal samples were collected on day 7. In all groups fed fried oil, the serum levels of tumor necrosis factor (TNF-α) were significantly elevated 2-4-fold. Among the gut microbiota, the abundance of Alloprevotella significantly decreased by up to 76%, while Lactobacilli significantly increased by up to 385%. The fecal valeric acid content was significantly increased and positively correlated with TNF-α levels. Both valeric acid and TNF-α levels were positively correlated with the abundance of Lactobacilli and negatively correlated with that of Alloprevotella. In summary, a short-term ingestion of even low doses of fried oil alters the gut microbiota Alloprevotella and Lactobacilli and increases fecal valeric acid content, which correlates with increased serum TNF-α levels. Full article
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12 pages, 2629 KiB  
Article
The Mucus-Binding Factor Mediates Lacticaseibacillus rhamnosus CRL1505 Adhesion but Not Immunomodulation in the Respiratory Tract
by Binghui Zhou, Mariano Elean, Lorena Arce, Kohtaro Fukuyama, Kae Tomotsune, Stefania Dentice Maidana, Sudeb Saha, Fu Namai, Keita Nishiyama, María Guadalupe Vizoso-Pinto, Julio Villena and Haruki Kitazawa
Microorganisms 2024, 12(6), 1209; https://doi.org/10.3390/microorganisms12061209 - 16 Jun 2024
Viewed by 260
Abstract
Lacticaseibacillus rhamnosus CRL1505 possesses immunomodulatory activities in the gastrointestinal and respiratory tracts when administered orally. Its adhesion to the intestinal mucosa does not condition its beneficial effects. The intranasal administration of L. rhamnosus CRL1505 is more effective than the oral route at modulating [...] Read more.
Lacticaseibacillus rhamnosus CRL1505 possesses immunomodulatory activities in the gastrointestinal and respiratory tracts when administered orally. Its adhesion to the intestinal mucosa does not condition its beneficial effects. The intranasal administration of L. rhamnosus CRL1505 is more effective than the oral route at modulating immunity in the respiratory tract. Nonetheless, it has not yet been established whether the adherence of the CRL1505 strain to the respiratory mucosa is needed to provide the immune benefits to the host. In this study, we evaluated the role of adhesion to the respiratory mucosa of the mucus-binding factor (mbf) knock-out L. rhamnosus CRL1505 mutant (Δmbf CRL1505) in the context of a Toll-like receptor 3 (TLR3)-triggered innate immunity response. In vitro adhesion studies in porcine bronchial epitheliocytes (PBE cells) indicated that L. rhamnosus Δmbf CRL1505 adhered weakly compared to the wild-type strain. However, in vivo studies in mice demonstrated that the Δmbf CRL1505 also reduced lung damage and modulated cytokine production in the respiratory tract after the activation of TLR3 to a similar extent as the wild-type strain. In addition, the mutant and the wild-type strains modulated the production of cytokines and antiviral factors by alveolar macrophages in the same way. These results suggest that the Mbf protein is partially involved in the ability of L. rhamnosus CRL1505 to adhere to the respiratory epithelium, but the protein is not necessary for the CRL1505 strain to exert its immunomodulatory beneficial effects. These findings are a step forward in the understanding of molecular interactions that mediate the beneficial effects of nasally administered probiotics. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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12 pages, 1888 KiB  
Article
The Pathogenic Mechanism of Enterocytozoon hepatopenaei in Litopenaeus vannamei
by Rongrong Ma, Bo Zhu, Jinbo Xiong and Jiong Chen
Microorganisms 2024, 12(6), 1208; https://doi.org/10.3390/microorganisms12061208 - 15 Jun 2024
Viewed by 311
Abstract
Enterocytozoon hepatopenaei (EHP) is a parasite in shrimp farming. EHP mainly parasitizes the hepatopancreas of shrimp, causing slow growth, which severely restricts the economic income of shrimp farmers. To explore the pathogenic mechanism of EHP, the host subcellular construction, molecular biological characteristics, and [...] Read more.
Enterocytozoon hepatopenaei (EHP) is a parasite in shrimp farming. EHP mainly parasitizes the hepatopancreas of shrimp, causing slow growth, which severely restricts the economic income of shrimp farmers. To explore the pathogenic mechanism of EHP, the host subcellular construction, molecular biological characteristics, and mitochondrial condition of Litopenaeus vannamei were identified using transmission electron microscopy (TEM), real-time qPCR, an enzyme assay, and flow cytometry. The results showed that EHP spores, approximately 1 μm in size, were located on the cytoplasm of the hepatopancreas. The number of mitochondria increased significantly, and mitochondria morphology showed a condensed state in the high-concentration EHP-infected shrimp by TEM observation. In addition, there were some changes in mitochondrial potential, but apoptosis was not significantly different in the infected shrimp. The qPCR results showed that the gene expression levels of hexokinase and pyruvate kinase related to energy metabolism were both upregulated in the diseased L. vannamei. Enzymatic activity showed hexokinase and lactate dehydrogenase were significantly increased in the shrimp infected with EHP, indicating EHP infection can increase the glycolysis process and decrease the oxidative phosphorylation process of L. vannamei. Previous transcriptomic data analysis results also support this conclusion. Full article
(This article belongs to the Special Issue Current Insights into Host–Parasite Interactions)
18 pages, 2340 KiB  
Article
Hepatitis B Virus Prevalence among HIV-Uninfected People Living in Rural and Peri-Urban Areas in Botswana
by Motswedi Anderson, Thabo Mangogola, Bonolo B. Phinius, Gorata Mpebe, Christopher O. Aimakhu, Wonderful T. Choga, Basetsana Phakedi, Lynnette N. Bhebhe, Doreen Ditshwanelo, Kabo Baruti, Linda Mpofu-Dobo, Lebogang Othusitse, Tsholofelo Ratsoma, Tendani Gaolathe, Joseph Makhema, Roger Shapiro, Shahin Lockman, Sikhulile Moyo and Simani Gaseitsiwe
Microorganisms 2024, 12(6), 1207; https://doi.org/10.3390/microorganisms12061207 - 15 Jun 2024
Viewed by 418
Abstract
(1) Background: we determined the prevalence of the hepatitis B virus (HBV) amongst people without human immunodeficiency virus (HIV) in rural and peri-urban areas in Botswana. (2) Methods: We screened for the hepatitis B surface antigen (HBsAg) from archived plasma samples of people [...] Read more.
(1) Background: we determined the prevalence of the hepatitis B virus (HBV) amongst people without human immunodeficiency virus (HIV) in rural and peri-urban areas in Botswana. (2) Methods: We screened for the hepatitis B surface antigen (HBsAg) from archived plasma samples of people without HIV (n = 2135) randomly selected from the Botswana Combination Prevention Program (BCPP) (2013–2018). We sequenced 415 bp of the surface region using BigDye sequencing chemistry. (3) Results: The median age of participants was 31 (IQR: 24–46) and 64% (1360/2135) were female. HBV prevalence was 4.0% (86/2135) [95% CI: 3.3–4.9]) and ranged between 0–9.2%. Older participants (>35 years) had increased odds of HBV positivity (OR: 1.94; 95% CI: [1.32–2.86]; p = 0.001). Thirteen samples were sequenced and seven (53.8%) were genotype A, three (23.1%) were genotype D and genotype E each. Clinically significant mutations were identified in the surface region, but no classic drug resistance mutations were identified. (4) Conclusions: We report an HBV prevalence of 4.0% (95% CI 3.3–4.9) among people without HIV in rural and peri-urban communities in Botswana with varying rates in different communities. A comprehensive national HBV program is required in Botswana to guide HBV prevention, testing and management. Full article
(This article belongs to the Special Issue Control and Elimination of Viral Hepatitis)
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23 pages, 1487 KiB  
Review
Current and Ongoing Developments in Targeting Clostridioides difficile Infection and Recurrence
by Wendy Y. Cun, Paul A. Keller and Stephen G. Pyne
Microorganisms 2024, 12(6), 1206; https://doi.org/10.3390/microorganisms12061206 - 15 Jun 2024
Viewed by 207
Abstract
Clostridioides difficile is a Gram-positive, spore-forming anaerobic bacterial pathogen that causes severe gastrointestinal infection in humans. This review provides background information on C. difficile infection and the pathogenesis and toxigenicity of C. difficile. The risk factors, causes, and the problem of recurrence [...] Read more.
Clostridioides difficile is a Gram-positive, spore-forming anaerobic bacterial pathogen that causes severe gastrointestinal infection in humans. This review provides background information on C. difficile infection and the pathogenesis and toxigenicity of C. difficile. The risk factors, causes, and the problem of recurrence of disease and current therapeutic treatments are also discussed. Recent therapeutic developments are reviewed including small molecules that inhibit toxin formation, disrupt the cell membrane, inhibit the sporulation process, and activate the host immune system in cells. Other treatments discussed include faecal microbiota treatment, antibody-based immunotherapies, probiotics, vaccines, and violet-blue light disinfection. Full article
(This article belongs to the Special Issue Latest Review Papers in Antimicrobial Agents and Resistance 2024)
13 pages, 1039 KiB  
Article
Quantification of HPV16 E7 Oncoproteins in Urine Specimens from Women with Cervical Intraepithelial Neoplasia
by Daiki Makioka, Mikio Inada, Masayuki Awano, Ema Saito, Takuya Shinoda, Satoko Abe, Teruki Yoshimura, Martin Müller, Toshiyuki Sasagawa and Etsuro Ito
Microorganisms 2024, 12(6), 1205; https://doi.org/10.3390/microorganisms12061205 - 14 Jun 2024
Viewed by 237
Abstract
We present the validity of using an ultrasensitive enzyme-linked immunosorbent assay (ELISA) for quantifying high-risk human papillomavirus (HPV) 16 E7 oncoproteins in urine specimens as a noninvasive method of analyzing the oncogenic activity of HPV. Some reports claim that the oncogenic activity of [...] Read more.
We present the validity of using an ultrasensitive enzyme-linked immunosorbent assay (ELISA) for quantifying high-risk human papillomavirus (HPV) 16 E7 oncoproteins in urine specimens as a noninvasive method of analyzing the oncogenic activity of HPV. Some reports claim that the oncogenic activity of HPV is a more relevant clinical indicator than the presence of HPV DNA for estimating malignant potential. In the present study, urine containing HPV16 and related types were selected by uniplex E6/E7 polymerase chain reaction and classified according to the pathologic diagnosis of cervical intraepithelial neoplasia (CIN) in cervical biopsy specimens. Our ultrasensitive ELISA was able to detect attomole levels of HPV16 E7 oncoproteins, and it detected HPV16-positive SiHa cells at >500 cells/mL without detecting HPV18-positive cells. Our ELISA results showed E7 oncoproteins in 80% (4/5) of urine specimens from women with HPV16-positive CIN1, 71% (5/7) of urine specimens from CIN2 patients, and 38% (3/8) of urine specimens from CIN3 patients. Some urine specimens with undetectable E7 oncoproteins were thought to be negative for live HPV 16-positive cells or in an inactivated state of infection. These results provide the basis for assessing oncogenic activity by quantifying E7 oncoproteins in patient urine. Full article
(This article belongs to the Special Issue Detection of Pathogenic Microorganism)
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10 pages, 594 KiB  
Article
The Spread of Southern Rice Black-Streaked Dwarf Virus Was Not Caused by Biological Changes in Vector Sogatella furcifera
by Keiichiro Matsukura and Masaya Matsumura
Microorganisms 2024, 12(6), 1204; https://doi.org/10.3390/microorganisms12061204 - 14 Jun 2024
Viewed by 238
Abstract
The pandemic of Southern rice black-streaked dwarf virus (SRBSDV) in and after the late 2000s caused serious yield losses in rice in Southeast and East Asia. This virus was first recorded in China in 2001, but its exclusive vector insect, Sogatella furcifera, [...] Read more.
The pandemic of Southern rice black-streaked dwarf virus (SRBSDV) in and after the late 2000s caused serious yield losses in rice in Southeast and East Asia. This virus was first recorded in China in 2001, but its exclusive vector insect, Sogatella furcifera, occurred there before then. To clarify the evolutionary origin of SRBSDV as the first plant virus transmitted by S. furcifera, we tested virus transmission using three chronological strains of S. furcifera, two of which were established before the first report of SRBSDV. When the strains fed on SRBSDV-infected rice plants were transferred to healthy rice plants, those established in 1989 and 1999 transmitted the virus to rice similarly to the strain established in 2010. SRBSDV quantification by RT-qPCR confirmed virus accumulation in the salivary glands of all three strains. Therefore, SRBSDV transmission by S. furcifera was not caused by biological changes in the vector, but probably by the genetic change of the virus from a closely related Fijivirus, Rice black-streaked dwarf virus, as suggested by ecological and molecular biological comparisons between the two viruses. This result will help us to better understand the evolutionary relationship between plant viruses and their vector insects and to better manage viral disease in rice cropping in Asia. Full article
(This article belongs to the Special Issue Interactions between Plant Pathogens and Insect Vectors)
15 pages, 3423 KiB  
Article
Inhibitory Potential of Bifidobacterium longum FB1-1 Cell-Free Supernatant against Carbapenem-Resistant Klebsiella pneumoniae Drug Resistance Spread
by Jing Wang, Dan-Cai Fan, Rui-Shan Wang, Yu Chang, Xue-Meng Ji, Xin-Yang Li, Yan Zhang, Jing-Min Liu, Shuo Wang and Jin Wang
Microorganisms 2024, 12(6), 1203; https://doi.org/10.3390/microorganisms12061203 - 14 Jun 2024
Viewed by 262
Abstract
The widespread dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) and its drug resistance transfer poses a global public health threat. While previous studies outlined CRKP’s drug resistance mechanism, there is limited research on strategies inhibiting CRKP drug resistance spread. This study investigates the potential [...] Read more.
The widespread dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) and its drug resistance transfer poses a global public health threat. While previous studies outlined CRKP’s drug resistance mechanism, there is limited research on strategies inhibiting CRKP drug resistance spread. This study investigates the potential of Bifidobacterium longum (B. longum) FB1-1, a probiotic, in curbing the spread of drug resistance among CRKP by evaluating its cell-free supernatant (CFS) for antibacterial activity. Evaluating the inhibitory effect of FB1-1 CFS on CRKP drug resistance spread involved analyzing its impact on drug resistance and virulence gene expression; drug resistance plasmid transfer FB1-1 CFS exhibited an MIC range of 125 μL/mL against CRKP. After eight hours of co-culture, CFS achieved a 96% and 100% sterilization rate at two and four times the MIC, respectively. At sub-inhibitory concentrations (1/2× MIC), FB1-1 CFS reduced the expression of the bla_KPC gene, which is pivotal for carbapenem resistance, by up to 62.13% across different CRKP strains. Additionally, it markedly suppressed the expression of the uge gene, a key virulence factor, by up to 91%, and the fim_H gene, essential for bacterial adhesion, by up to 53.4%. Our study primarily focuses on determining the inhibitory effect of FB1-1 CFS on CRKP strains harboring the bla_KPC gene, which is a critical resistance determinant in CRKP. Furthermore, FB1-1 CFS demonstrated the ability to inhibit the transfer of drug resistance plasmids among CRKP strains, thus limiting the horizontal spread of resistance genes. This study highlights FB1-1 CFS's inhibitory effect on CRKP drug resistance spread, particularly in strains carrying the bla_KPC gene, thus offering a novel idea and theoretical foundation for developing antibacterial drugs targeting CRKP resistance. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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16 pages, 4647 KiB  
Article
Biological Traits and Comprehensive Genomic Analysis of Novel Enterococcus faecalis Bacteriophage EFP6
by Sajjad Ahmad, Qingwen Leng, Gongmingzhu Hou, Yan Liang, Yanfang Li and Yonggong Qu
Microorganisms 2024, 12(6), 1202; https://doi.org/10.3390/microorganisms12061202 - 14 Jun 2024
Viewed by 208
Abstract
Enterococcus faecalis is a prevalent opportunistic pathogen associated with chicken embryonic and neonatal chick mortality, posing a significant challenge in poultry farming. In the current study, E. faecalis strain EF6, isolated from a recent hatchery outbreak, served as the host bacterium for the [...] Read more.
Enterococcus faecalis is a prevalent opportunistic pathogen associated with chicken embryonic and neonatal chick mortality, posing a significant challenge in poultry farming. In the current study, E. faecalis strain EF6, isolated from a recent hatchery outbreak, served as the host bacterium for the isolation of a novel phage EFP6, capable of lysing E. faecalis. Transmission electron microscopy revealed a hexagonal head and a short tail, classifying EFP6 as a member of the Autographiviridae family. EFP6 showed sensitivity to ultraviolet radiation and resistance to chloroform. The lytic cycle duration of EFP6 was determined to be 50 min, highlighting its efficacy in host eradication. With an optimal multiplicity of infection of 0.001, EFP6 exhibited a narrow lysis spectrum and strong specificity towards host strains. Additionally, EFP6 demonstrated optimal growth conditions at 40 °C and pH 8.0. Whole genome sequencing unveiled a genome length of 18,147 bp, characterized by a GC concentration of 33.21% and comprising 25 open reading frames. Comparative genomic assessment underscored its collinearity with related phages, notably devoid of lysogenic genes, thus ensuring genetic stability. This in-depth characterization forms the basis for understanding the biological attributes of EFP6 and its potential utilization in phage therapy, offering promising prospects for mitigating E. faecalis-associated poultry infections. Full article
(This article belongs to the Section Veterinary Microbiology)
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11 pages, 1335 KiB  
Article
Validation of a Pseudovirus Neutralization Assay for Severe Acute Respiratory Syndrome Coronavirus 2: A High-Throughput Method for the Evaluation of Vaccine Immunogenicity
by Zhaohui Cai, Raj Kalkeri, Mi Wang, Benjamin Haner, Dominic Dent, Bahar Osman, Paul Skonieczny, Jeremy Ross, Sheau-Line Feng, Rongman Cai, Mingzhu Zhu, Shane Cloney-Clark and Joyce S. Plested
Microorganisms 2024, 12(6), 1201; https://doi.org/10.3390/microorganisms12061201 - 14 Jun 2024
Viewed by 288
Abstract
The evaluation of coronavirus disease 2019 (COVID-19) vaccine immunogenicity remains essential as the severe acute respiratory syncytial virus 2 (SARS-CoV-2) pandemic continues to evolve and as additional variants emerge. Neutralizing antibodies are a known correlate of protection for SARS-CoV-2 vaccines. A pseudovirus neutralization [...] Read more.
The evaluation of coronavirus disease 2019 (COVID-19) vaccine immunogenicity remains essential as the severe acute respiratory syncytial virus 2 (SARS-CoV-2) pandemic continues to evolve and as additional variants emerge. Neutralizing antibodies are a known correlate of protection for SARS-CoV-2 vaccines. A pseudovirus neutralization (PNT) assay was developed and validated at Novavax Clinical Immunology Laboratories to allow for the detection of neutralizing antibodies in vaccine clinical trial sera. The PNT assay was precise, accurate, linear, and specific in measuring SARS-CoV-2 neutralization titers in human serum for ancestral strain and the Omicron subvariants BA.5 and XBB.1.5, with an overall geometric coefficient of variation of ≤43.4%, a percent relative bias within the expected range of −60% to 150%, and a linearity value of R2 > 0.98 for all three strains. This pseudovirus assay will be useful for the analysis of vaccine clinical trial samples to assess vaccine immunogenicity. Future work will focus on modifying the assay for emerging variants, including XBB.1.16, EG.5.1, BA.2.86, and any other variants that emerge in the ongoing pandemic. Full article
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10 pages, 216 KiB  
Article
Determinants of COVID-19 Vaccine Hesitancy: A Cross-Sectional Study in Three Communities in the United States and Lebanon
by Mohamad Yasmin, Mohamad Ali Tfaily, Rayyan Wazzi Mkahal, Rita Obeid, Rebecca P. Emery, Habiba Hassouna, Mudita Bhugra, Robert A. Bonomo and Zeina A. Kanafani
Microorganisms 2024, 12(6), 1200; https://doi.org/10.3390/microorganisms12061200 - 14 Jun 2024
Viewed by 238
Abstract
The COVID-19 pandemic underscores the significance of vaccine hesitancy in shaping vaccination outcomes. Understanding the factors underpinning COVID-19 vaccination hesitancy is crucial for tailoring effective vaccination strategies. This cross-sectional study, conducted in three communities across the United States and Lebanon, employed surveys to [...] Read more.
The COVID-19 pandemic underscores the significance of vaccine hesitancy in shaping vaccination outcomes. Understanding the factors underpinning COVID-19 vaccination hesitancy is crucial for tailoring effective vaccination strategies. This cross-sectional study, conducted in three communities across the United States and Lebanon, employed surveys to assess respondents’ knowledge, attitudes, and perceptions regarding COVID-19 infection and vaccination. Among the 7196 participants, comprising 6775 from the US and 422 from Lebanon, vaccine hesitancy rates were comparable at 12.2% and 12.8%, respectively. Notably, a substantial proportion of respondents harbored misconceptions, such as attributing the potential to alter DNA (86.4%) or track individuals (92.8%) to COVID-19 vaccines and believing in the virus’s artificial origins (81%). US participants had more misconceptions about the COVID-19 vaccine, such as altering DNA or causing infertility. Lebanese participants were more likely to question the origins of the virus and the speed of vaccine development. Additionally, US respondents were less worried about infection, while Lebanese respondents were more indecisive but less likely to outright reject the vaccine. Primary determinants of hesitancy included perceptions that the vaccine poses a greater risk than the infection itself (aOR = 8.7 and 9.4, respectively) and negative recommendations from healthcare providers (aOR = 6.5 and 5.4, respectively). Conversely, positive endorsements from healthcare providers were associated with reduced hesitancy (aOR = 0.02 and 0.4, respectively). Targeting healthcare providers to dispel misinformation and elucidate COVID-19 vaccine risks holds promise for enhancing vaccination uptake. Full article
16 pages, 504 KiB  
Article
Exploring the Effects of Freeze-Dried Sourdoughs with Lactiplantibacillus pentosus 129 and Limosilactobacillus fermentum 139 on the Quality of Long-Fermentation Bread
by Joanderson Gama Santos, Evandro Leite de Souza, Marcus Vinícius de Souza Couto, Tatiana Zanella Rodrigues, Ana Regina Simplício de Medeiros, Angela Maria Tribuzy de Magalhães Cordeiro, Marcos dos Santos Lima, Maria Elieidy Gomes de Oliveira, Maiara da Costa Lima, Noádia Priscilla Rodrigues de Araújo, Ingrid Conceição Dantas Gonçalves and Estefânia Fernandes Garcia
Microorganisms 2024, 12(6), 1199; https://doi.org/10.3390/microorganisms12061199 - 14 Jun 2024
Viewed by 250
Abstract
Sourdough production is a complex fermentation process. Natural sourdough fermentation without standardization causes great variability in microbial communities and derived products. Starter cultures have emerged as alternatives to natural fermentation processes, which could improve bakery quality and produce bioactive compounds. This study aimed [...] Read more.
Sourdough production is a complex fermentation process. Natural sourdough fermentation without standardization causes great variability in microbial communities and derived products. Starter cultures have emerged as alternatives to natural fermentation processes, which could improve bakery quality and produce bioactive compounds. This study aimed to evaluate the impacts of freeze-drying on the production and viability of sourdoughs with Lactiplantibacillus pentosus 129 (Lp) and Limosilactobacillus fermentum 139 (Lf), as well as their effects on the quality of long-fermentation bread. These strains were selected based on their better performance considering acidification and exopolysaccharide production capacity. Sourdough with Lp and Lf were propagated until the 10th day, when physicochemical and microbiological parameters were determined. The produced sourdoughs were freeze-dried, and bread samples were produced. The freeze-drying process resulted in high survival rates and few impacts on the metabolic activity of Lp and Lf until 60 days of storage. Incorporating Lp and Lf improved the microbiological and physicochemical properties of sourdough and long-fermentation breads. Tested freeze-dried sourdoughs led to reduced bread aging (higher specific volume and decreased starch retrogradation) and increased digestibility. The results show the potential of the freeze-dried sourdoughs produced with Lp and Lf as innovative strategies for standardizing production protocols for the bakery industry, especially for producing long-term fermentation bread. Full article
(This article belongs to the Section Food Microbiology)
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