Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with the Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q2 (Microbiology)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.1 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about the Microorganisms.
- Companion journal: Applied Microbiology.
Impact Factor:
4.5 (2022);
5-Year Impact Factor:
4.8 (2022)
Latest Articles
The Description and Analysis of the Complete Genome of Dermacoccus barathri FBCC-B549 Strain
Microorganisms 2024, 12(6), 1227; https://doi.org/10.3390/microorganisms12061227 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Section Microbial Biotechnology)
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The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties
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Yuval Dorfan, Avichay Nahami, Yael Morris, Benny Shohat and Ilana Kolodkin-Gal
Microorganisms 2024, 12(6), 1226; https://doi.org/10.3390/microorganisms12061226 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Special Issue An Update on Bacillus)
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Periodontal Inflammation and Dysbiosis Relate to Microbial Changes in the Gut
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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 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Special Issue Intestine as a Hub for Host-Microbe Interactions and Its Impact on Local and Systemic Health)
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Open AccessCommunication
Impact of COVID-19 Restrictions on Incidence of Enteropathogenic Bacteria, Virus, and Parasites in Denmark: A National, Register-Based Study
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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 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Section Public Health Microbiology)
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Open AccessArticle
Development of Multiplex RT qPCR Assays for Simultaneous Detection and Quantification of Faecal Indicator Bacteria in Bathing Recreational Waters
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Marina Carrasco-Acosta and Pilar Garcia-Jimenez
Microorganisms 2024, 12(6), 1223; https://doi.org/10.3390/microorganisms12061223 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Collection Advances in Public Health Microbiology)
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Bioconversion of Furanic Compounds by Chlorella vulgaris—Unveiling Biotechnological Potentials
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Ricarda Kriechbaum, Oliver Spadiut and Julian Kopp
Microorganisms 2024, 12(6), 1222; https://doi.org/10.3390/microorganisms12061222 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Special Issue The Application Potential of Microalgae in Green Biotechnology)
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Role of MalQ Enzyme in a Reconstructed Maltose/Maltodextrin Pathway in Actinoplanes sp. SE50/110
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Camilla März, Sophia Nölting, Lars Wollenschläger, Alfred Pühler and Jörn Kalinowski
Microorganisms 2024, 12(6), 1221; https://doi.org/10.3390/microorganisms12061221 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Special Issue Specialized Metabolites from Microorganisms)
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Macrogenomics-Based Analysis of the Effects of Intercropped Soybean Photosynthetic Characteristics and Nitrogen-Assimilating Enzyme Activities on Yield at Different Nitrogen Levels
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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 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)
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Open AccessArticle
Ciliated Epibionts Modify the Cardiac Stress Reaction to Perceived Predation in Daphnia
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Andrew K. Davis and Helen Gloege
Microorganisms 2024, 12(6), 1219; https://doi.org/10.3390/microorganisms12061219 (registering DOI) - 18 Jun 2024
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
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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.
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(This article belongs to the Special Issue Pathobiology, Infection Biology and Control of Protozoan Parasites—the ONE HEALTH Approach)
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Effects of Weak Electric Fields on the Denitrification Performance of Pseudomonas stutzeri: Insights into Enzymes and Metabolic Pathways
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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
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
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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.
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(This article belongs to the Section Environmental Microbiology)
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Symbiodiniaceae and Ruegeria sp. Co-Cultivation to Enhance Nutrient Exchanges in Coral Holobiont
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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
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
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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.
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(This article belongs to the Special Issue Photosynthetic Microorganisms: Culturing and Biotechnological Applications)
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Open AccessCase Report
Tuberculosis in a Migrant Population: Integrated Management of a Case through the Prevention Department and Hospital Services
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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
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
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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.
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(This article belongs to the Special Issue Advances in Microbial Pathogenesis and Host Responses)
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Microbial Assessment in A Rare Norwegian Book Collection: A One Health Approach to Cultural Heritage
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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 (registering DOI) - 17 Jun 2024
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
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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.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle
Assessing PCR-Positive Acanthamoeba Keratitis—A Retrospective Chart Review
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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
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
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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.
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(This article belongs to the Special Issue Ocular Infections and Microbiota in Health and Disease 2.0)
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Open AccessArticle
FibroScan® versus Biochemical Scores: A Study of Liver Fibrosis in HIV with HBV Co-Infection
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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
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,
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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.
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(This article belongs to the Special Issue Control and Elimination of Viral Hepatitis)
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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
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
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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.
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(This article belongs to the Special Issue Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective)
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Open AccessCommunication
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
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
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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.
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(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
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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
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.
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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.
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(This article belongs to the Special Issue Gut Microbiota and Foreign Substances: Drugs, Mycotoxins and Heavy Metals in Foods)
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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
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
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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.
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(This article belongs to the Section Molecular Microbiology and Immunology)
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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
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
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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)
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